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A conda-smithy repository for r-base.

License: BSD 3-Clause "New" or "Revised" License

Shell 79.61% Batchfile 3.59% C 16.43% R 0.37%

r-base-feedstock's Introduction

About r-base-feedstock

Feedstock license: BSD-3-Clause

Home: http://www.r-project.org/

Package license: GPL-2.0-or-later

Summary: R is a free software environment for statistical computing and graphics.

Current build status

Travis linux
Azure
VariantStatus
linux_64 variant
linux_aarch64 variant
linux_ppc64le variant
osx_64 variant
osx_arm64 variant

Current release info

Name Downloads Version Platforms
Conda Recipe Conda Downloads Conda Version Conda Platforms
Conda Recipe Conda Downloads Conda Version Conda Platforms

Installing r-base

Installing r-base from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, cross-r-base, r-base can be installed with conda:

conda install cross-r-base r-base

or with mamba:

mamba install cross-r-base r-base

It is possible to list all of the versions of cross-r-base available on your platform with conda:

conda search cross-r-base --channel conda-forge

or with mamba:

mamba search cross-r-base --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search cross-r-base --channel conda-forge

# List packages depending on `cross-r-base`:
mamba repoquery whoneeds cross-r-base --channel conda-forge

# List dependencies of `cross-r-base`:
mamba repoquery depends cross-r-base --channel conda-forge

About conda-forge

Powered by NumFOCUS

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating r-base-feedstock

If you would like to improve the r-base recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/r-base-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

  • If the version of a package is not being increased, please add or increase the build/number.
  • If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

r-base-feedstock's People

Contributors

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Stargazers

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Watchers

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r-base-feedstock's Issues

Packages require rebuilding with conda-build > 2.0

I've run into an issues with a couple of packages (from the r channel) which give me the error:

PaddingError: Placeholder of length '80' too short in package [channel]::[package]
The package must be rebuilt with conda-build > 2.0.

While these are coming from the r channel, I believe this is the new home for these packages? Or at least could be?

The packages are:

  • r::r-base-3.2.1-0
  • r::r-base-3.2.2-0

Windows 32-bit builds missing

Seems we only have 64-bit builds on Windows, but are missing 32-bit builds. Is that intentional or is this a bug?

screen shot 2017-02-12 at 15 59 05

Cannot install Bioconductor package ShortRead

Issue:
Installing the Bioconductor package ShortRead from inside R (not from conda) fails with the error:

> setRepositories(g=FALSE)
--- Please select repositories for use in this session ---


1: + CRAN
2:   BioC software
3:   BioC annotation
4:   BioC experiment
5:   CRAN (extras)
6:   Omegahat
7:   R-Forge
8:   rforge.net

Enter one or more numbers separated by spaces, or an empty line to cancel
1: 1 2 3 4
> install.packages("ShortRead")
...lots of dependencies are installed, until finally...
checking for gzeof in -lz... no
configure: error: zlib not found
ERROR: configuration failed for package ‘ShortRead’

This has been previously reported here, here and here, without any truly satisfactory resolution, except for the observation that the difference was introduced with zlib 1.2.11.

I tried this:

$ conda create -n test1 zlib=1.2.11
$ conda create -n test2 zlib=1.2.8
$ diff -r $CONDA_PREFIX/test1 $CONDA_PREFIX/test2

but none of the results seemed to explain any possible difference.

I then tried

$ conda install -n test1 r-base=3.4.1
$ conda install -n test2 r-base=3.4.1
$ diff -r $CONDA_PREFIX/test1 $CONDA_PREFIX/test2

This yielded, unsurprisingly, a LOT of results. Using GUI diff tools and grep guesswork, I finally found this:

diff -r $CONDA_PREFIX/envs/test1/lib/R/bin /libtool $CONDA_PREFIX/envs/test2/lib/R/bin/libtool
3c3
< # Libtool was configured on host c84bcb0f5cfa:
---
> # Libtool was configured on host bf6a7e593731:
168c168
< LTCFLAGS="-I/home/brendan/miniconda3/envs/test1/include"
---
> LTCFLAGS="-I/home/brendan/miniconda3/envs/test2/include"
285c285
< sys_lib_search_path_spec="/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2 /opt/rh/devtoolset-2/root/usr/lib64 /lib64 /usr/lib64 /opt/rh/devtoolset-2/root/usr/lib /lib /usr/lib "
---
> sys_lib_search_path_spec="/home/brendan/miniconda3/envs/test2/lib/gcc/x86_64-unknown-linux-gnu/4.8.5 /home/brendan/miniconda3/envs/test2/lib/gcc /home/brendan/miniconda3/envs/test2/lib /lib /usr/lib "
308c308
< LD="/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld -m elf_x86_64"
---
> LD="/opt/rh/devtoolset-2/root/usr/bin/ld -m elf_x86_64"
11664c11664
< LD="/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld -m elf_x86_64"
---
> LD="/opt/rh/devtoolset-2/root/usr/bin/ld -m elf_x86_64"
11795c11795
< compiler_lib_search_dirs="/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2 /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/../../../../lib64 /lib/../lib64 /usr/lib/../lib64 /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/../../.."
---
> compiler_lib_search_dirs="/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5 /home/brendan/miniconda3/envs/test2/bin/../lib/gcc /home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../../../lib /lib/../lib /usr/lib/../lib /home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../.."
11799,11800c11799,11800
< predep_objects="/usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/crtbeginS.o"
< postdep_objects="/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o"
---
> predep_objects="/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crti.o /home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crtbeginS.o"
> postdep_objects="/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crtendS.o /home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crtn.o"
11806c11806
< compiler_lib_search_path="-L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/../../.."
---
> compiler_lib_search_path="-L/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5 -L/home/brendan/miniconda3/envs/test2/bin/../lib/gcc -L/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../.."
11813c11813
< LD="/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld -m elf_x86_64"
---
> LD="/opt/rh/devtoolset-2/root/usr/bin/ld -m elf_x86_64"
11965c11965
< LD="/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld -m elf_x86_64"
---
> LD="/opt/rh/devtoolset-2/root/usr/bin/ld -m elf_x86_64"
12099c12099
< compiler_lib_search_dirs="/home/brendan/miniconda3/envs/test1/lib"
---
> compiler_lib_search_dirs="/home/brendan/miniconda3/envs/test2/lib"
12104c12104
< postdep_objects="/usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/crtbeginS.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o"
---
> postdep_objects="/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crti.o /home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crtbeginS.o /home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crtendS.o /home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crtn.o"
12106c12106
< postdeps="-l -l -L/home/brendan/miniconda3/envs/test1/lib -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux/4.8.2/../../.. -lgfortran -lm -lgcc_s -lquadmath -lm -lgcc_s -lc -lgcc_s"
---
> postdeps="-l -l -L/home/brendan/miniconda3/envs/test2/lib -L/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5 -L/home/brendan/miniconda3/envs/test2/bin/../lib/gcc -L/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/home/brendan/miniconda3/envs/test2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../.. -lgfortran -lm -lgcc_s -lquadmath -lm -lgcc_s -lc -lgcc_s"
12110c12110
< compiler_lib_search_path="-L/home/brendan/miniconda3/envs/test1/lib"
---
> compiler_lib_search_path="-L/home/brendan/miniconda3/envs/test2/lib"

I am a bit out of my depth here, and maybe I'm on the wrong track entirely, but I can see that the version of r-base installed with zlib=1.2.11 references directories which are not in my conda installation, and don't exist on my machine.

Here are the environments:

Test1 with zlib=1.2.11 (not working)

$ conda list
# packages in environment at /home/brendan/miniconda3/envs/test1:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1  
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.14.12           h80bd089_1005    conda-forge
curl                      7.61.0               h93b3f91_2    conda-forge
fontconfig                2.13.1            h2176d3f_1000    conda-forge
freetype                  2.9.1             h94bbf69_1005    conda-forge
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
glib                      2.56.2            had28632_1001    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gsl                       2.2.1                h0c605f7_3  
harfbuzz                  1.9.0             he243708_1001    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.14.6                        0    conda-forge
libffi                    3.2.1             hf484d3e_1005    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgfortran               3.0.0                         1    conda-forge
libiconv                  1.15              h14c3975_1004    conda-forge
libpng                    1.6.36            h84994c4_1000    conda-forge
libssh2                   1.8.0             h1ad7b7a_1003    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtiff                   4.0.10            h648cc4a_1001    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openssl                   1.0.2r               h14c3975_0    conda-forge
pango                     1.40.14           hf0c64fd_1003    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
pixman                    0.34.0            h14c3975_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
r-base                    3.4.1                h4fe35fd_8    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
tk                        8.6.9             h84994c4_1000    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h14c3975_1004    conda-forge
xorg-libsm                1.2.3             h4937e3b_1000    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.2             h14c3975_1007    conda-forge
xorg-libxext              1.3.3             h14c3975_1004    conda-forge
xorg-libxrender           0.9.10            h14c3975_1002    conda-forge
xorg-libxt                1.1.5             h14c3975_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge

test2 with zlib=1.2.8 (working)

$ conda list
# packages in environment at /home/brendan/miniconda3/envs/test2:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1  
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.14.6                        4    conda-forge
curl                      7.54.1                        0    conda-forge
fontconfig                2.12.1                        6    conda-forge
freetype                  2.7                           1    conda-forge
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
glib                      2.51.4                        0    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gsl                       2.1                           2    conda-forge
harfbuzz                  1.4.3                         0    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.14.6                        0    conda-forge
libffi                    3.2.1             hf484d3e_1005    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libiconv                  1.15              h14c3975_1004    conda-forge
libpng                    1.6.28                        1    conda-forge
libssh2                   1.8.0                         1    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtiff                   4.0.7                         0    conda-forge
libxml2                   2.9.5                         0    conda-forge
ncurses                   5.9                          10    conda-forge
openssl                   1.0.2r               h14c3975_0    conda-forge
pango                     1.40.4                        0    conda-forge
pcre                      8.39                          0    conda-forge
pixman                    0.34.0            h14c3975_1003    conda-forge
r-base                    3.4.1                         0    conda-forge
readline                  6.2                           0    conda-forge
tk                        8.5.19                        2    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.8                         3    conda-forge

And my conda info:

$ conda info

     active environment : test2
    active env location : /home/brendan/miniconda3/envs/test2
            shell level : 3
       user config file : /home/brendan/.condarc
 populated config files : /home/brendan/.condarc
          conda version : 4.6.7
    conda-build version : not installed
         python version : 3.7.1.final.0
       base environment : /home/brendan/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/brendan/miniconda3/pkgs
                          /home/brendan/.conda/pkgs
       envs directories : /home/brendan/miniconda3/envs
                          /home/brendan/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.7 requests/2.21.0 CPython/3.7.1 Linux/3.16.0-77-generic ubuntu/16.04.5 glibc/2.23
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

(edit to fix details formatting)

Error: package ‘###’ was installed before R 4.0.0: please re-install it

Issue:
I am using university server, we are allowed to use conda enviroment. I need to install a R package R>=4.0 with github, so I need to use devtools.
I made a new conda environment, installed r-base v4 via conda-forge, installed r-devtools build for R4, then I start R, but when I got an error:

> devtools::install_github("HelenaLC/muscat", ref = "master")
Error: package ‘devtools’ was installed before R 4.0.0: please re-install it

and I am getting this error for every package I try to load:

> library(cli)
Error: package or namespace load failed for ‘cli’:
 package ‘cli’ was installed before R 4.0.0: please re-install it
> library(devtools)
Loading required package: usethis
Error: package or namespace load failed for ‘usethis’:
 package ‘usethis’ was installed before R 4.0.0: please re-install it
Error: package ‘usethis’ could not be loaded
> library(tidyverse)
Error: package or namespace load failed for ‘tidyverse’:
 package ‘tidyverse’ was installed before R 4.0.0: please re-install it

Environment (conda list):
$ conda list
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
attrs                     19.3.0                     py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
binutils_impl_linux-64    2.34                 h53a641e_0    conda-forge
binutils_linux-64         2.34                hc952b39_18    conda-forge
bleach                    3.1.5              pyh9f0ad1d_0    conda-forge
bwidget                   1.9.14                        0    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2020.4.5.1           hecc5488_0    conda-forge
cairo                     1.16.0            hcf35c78_1003    conda-forge
certifi                   2020.4.5.1       py38h32f6830_0    conda-forge
curl                      7.69.1               h33f0ec9_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
entrypoints               0.3             py38h32f6830_1001    conda-forge
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.1               he06d7ca_0    conda-forge
fribidi                   1.0.9                h516909a_0    conda-forge
gcc_impl_linux-64         7.3.0                hd420e75_5    conda-forge
gcc_linux-64              7.3.0               h553295d_18    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_5    conda-forge
gfortran_linux-64         7.3.0               h553295d_18    conda-forge
glib                      2.64.2               h6f030ca_0    conda-forge
graphite2                 1.3.13            he1b5a44_1001    conda-forge
gsl                       2.6                  h294904e_0    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_5    conda-forge
gxx_linux-64              7.3.0               h553295d_18    conda-forge
harfbuzz                  2.4.0                h9f30f68_3    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
importlib-metadata        1.6.0            py38h32f6830_0    conda-forge
importlib_metadata        1.6.0                         0    conda-forge
ipykernel                 5.2.1            py38h23f93f0_0    conda-forge
ipython                   7.14.0           py38h32f6830_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.17.0           py38h32f6830_0    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.2.0            py38h32f6830_1    conda-forge
jupyter_client            6.1.3                      py_0    conda-forge
jupyter_core              4.6.3            py38h32f6830_1    conda-forge
krb5                      1.17.1               h2fd8d38_0    conda-forge
ld_impl_linux-64          2.34                 h53a641e_0    conda-forge
libblas                   3.8.0               16_openblas    conda-forge
libcblas                  3.8.0               16_openblas    conda-forge
libcurl                   7.69.1               hf7181ac_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libiconv                  1.15              h516909a_1006    conda-forge
liblapack                 3.8.0               16_openblas    conda-forge
libopenblas               0.3.9                h5ec1e0e_0    conda-forge
libpng                    1.6.37               hed695b0_1    conda-forge
libsodium                 1.0.17               h516909a_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc7e4089_6    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp-base              1.1.0                h516909a_3    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
llvm-openmp               10.0.0               hc9558a2_0    conda-forge
lz4-c                     1.9.2                he1b5a44_1    conda-forge
make                      4.3                  h516909a_0    conda-forge
markupsafe                1.1.1            py38h1e0a361_1    conda-forge
mistune                   0.8.4           py38h1e0a361_1001    conda-forge
nbconvert                 5.6.1            py38h32f6830_1    conda-forge
nbformat                  5.0.6                      py_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
notebook                  6.0.3            py38h32f6830_0    conda-forge
openssl                   1.1.1g               h516909a_0    conda-forge
packaging                 20.1                       py_0    conda-forge
pandoc                    2.9.2.1                       0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.42.4               h7062337_4    conda-forge
parso                     0.7.0              pyh9f0ad1d_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
pcre2                     10.34                h2f06484_0    conda-forge
pexpect                   4.8.0            py38h32f6830_1    conda-forge
pickleshare               0.7.5           py38h32f6830_1001    conda-forge
pip                       20.1               pyh9f0ad1d_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt-toolkit            3.0.5                      py_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pygments                  2.6.1                      py_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyrsistent                0.16.0           py38h1e0a361_0    conda-forge
python                    3.8.2           he5300dc_7_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.8                      1_cp38    conda-forge
pyzmq                     19.0.1           py38ha71036d_0    conda-forge
r-askpass                 1.1               r40hcdcec82_2    conda-forge
r-assertthat              0.2.1             r40h6115d3f_2    conda-forge
r-backports               1.1.6             r40hcdcec82_2    conda-forge
r-base                    4.0.0                hdca8982_3    conda-forge
r-base64enc               0.1_3           r40hcdcec82_1004    conda-forge
r-boot                    1.3_25            r40h6115d3f_1    conda-forge
r-brew                    1.0_6           r40h6115d3f_1003    conda-forge
r-broom                   0.5.6             r40h6115d3f_1    conda-forge
r-callr                   3.4.3             r40h6115d3f_1    conda-forge
r-caret                   6.0_86            r40hcdcec82_2    conda-forge
r-cellranger              1.1.0           r40h6115d3f_1003    conda-forge
r-class                   7.3_17            r40hcdcec82_1    conda-forge
r-cli                     2.0.2             r40h6115d3f_1    conda-forge
r-clipr                   0.7.0             r40h6115d3f_1    conda-forge
r-cluster                 2.1.0             r40h9bbef5b_3    conda-forge
r-codetools               0.2_16          r40h6115d3f_1002    conda-forge
r-colorspace              1.4_1             r40hcdcec82_2    conda-forge
r-commonmark              1.7             r40hcdcec82_1002    conda-forge
r-covr                    3.5.0             r40h0357c0b_1    conda-forge
r-crayon                  1.3.4           r40h6115d3f_1003    conda-forge
r-crosstalk               1.1.0.1           r40h6115d3f_1    conda-forge
r-curl                    4.3               r40hcdcec82_1    conda-forge
r-data.table              1.12.8            r40hcdcec82_1    conda-forge
r-dbi                     1.1.0             r40h6115d3f_1    conda-forge
r-dbplyr                  1.4.3             r40h6115d3f_1    conda-forge
r-desc                    1.2.0           r40h6115d3f_1003    conda-forge
r-devtools                2.3.0             r40h6115d3f_1    conda-forge
r-digest                  0.6.25            r40h0357c0b_2    conda-forge
r-dplyr                   0.8.5             r40h0357c0b_1    conda-forge
r-dt                      0.13              r40h6115d3f_1    conda-forge
r-ellipsis                0.3.0             r40hcdcec82_1    conda-forge
r-essentials              4.0                    r40_2002    conda-forge
r-evaluate                0.14              r40h6115d3f_2    conda-forge
r-fansi                   0.4.1             r40hcdcec82_1    conda-forge
r-farver                  2.0.3             r40h0357c0b_1    conda-forge
r-fastmap                 1.0.1             r40h0357c0b_1    conda-forge
r-forcats                 0.5.0             r40h6115d3f_1    conda-forge
r-foreach                 1.5.0             r40h6115d3f_1    conda-forge
r-foreign                 0.8_79            r40hcdcec82_0    conda-forge
r-formatr                 1.7               r40h6115d3f_2    conda-forge
r-fs                      1.4.1             r40h0357c0b_1    conda-forge
r-generics                0.0.2           r40h6115d3f_1003    conda-forge
r-ggplot2                 3.3.0             r40h6115d3f_1    conda-forge
r-gh                      1.1.0             r40h6115d3f_1    conda-forge
r-gistr                   0.5.0             r40h6115d3f_1    conda-forge
r-git2r                   0.27.1            r40h7253d3a_0    conda-forge
r-glmnet                  3.0_2             r40h9bbef5b_1    conda-forge
r-glue                    1.4.0             r40hcdcec82_1    conda-forge
r-gower                   0.2.1             r40hcdcec82_2    conda-forge
r-gtable                  0.3.0             r40h6115d3f_3    conda-forge
r-haven                   2.2.0             r40hde08347_1    conda-forge
r-hexbin                  1.28.1            r40h9bbef5b_1    conda-forge
r-highr                   0.8               r40h6115d3f_2    conda-forge
r-hms                     0.5.3             r40h6115d3f_1    conda-forge
r-htmltools               0.4.0             r40h0357c0b_1    conda-forge
r-htmlwidgets             1.5.1             r40h6115d3f_1    conda-forge
r-httpuv                  1.5.2             r40h0357c0b_2    conda-forge
r-httr                    1.4.1             r40h6115d3f_2    conda-forge
r-ini                     0.3.1           r40h6115d3f_1003    conda-forge
r-ipred                   0.9_9             r40hcdcec82_2    conda-forge
r-irdisplay               0.7                    r40_1002    conda-forge
r-irkernel                1.1               r40h6115d3f_1    conda-forge
r-isoband                 0.2.1             r40h0357c0b_1    conda-forge
r-iterators               1.0.12            r40h6115d3f_1    conda-forge
r-jsonlite                1.6.1             r40hcdcec82_1    conda-forge
r-kernsmooth              2.23_17           r40hfa343cc_1    conda-forge
r-knitr                   1.28              r40h6115d3f_1    conda-forge
r-labeling                0.3             r40h6115d3f_1003    conda-forge
r-later                   1.0.0             r40h0357c0b_1    conda-forge
r-lattice                 0.20_41           r40hcdcec82_2    conda-forge
r-lava                    1.6.7             r40h6115d3f_1    conda-forge
r-lazyeval                0.2.2             r40hcdcec82_2    conda-forge
r-lifecycle               0.2.0             r40h6115d3f_1    conda-forge
r-lubridate               1.7.8             r40h0357c0b_1    conda-forge
r-magrittr                1.5             r40h6115d3f_1003    conda-forge
r-maps                    3.3.0           r40hcdcec82_1004    conda-forge
r-markdown                1.1               r40hcdcec82_1    conda-forge
r-mass                    7.3_51.6          r40hcdcec82_2    conda-forge
r-matrix                  1.2_18            r40h7fa42b6_3    conda-forge
r-memoise                 1.1.0           r40h6115d3f_1004    conda-forge
r-mgcv                    1.8_31            r40h7fa42b6_1    conda-forge
r-mime                    0.9               r40hcdcec82_1    conda-forge
r-modelmetrics            1.2.2.2           r40h0357c0b_1    conda-forge
r-modelr                  0.1.7             r40h6115d3f_1    conda-forge
r-munsell                 0.5.0           r40h6115d3f_1003    conda-forge
r-nlme                    3.1_147           r40h9bbef5b_1    conda-forge
r-nnet                    7.3_14            r40hcdcec82_1    conda-forge
r-numderiv                2016.8_1.1        r40h6115d3f_2    conda-forge
r-openssl                 1.4.1             r40he5c4762_1    conda-forge
r-pbdzmq                  0.3_3           r40h559a7a4_1003    conda-forge
r-pillar                  1.4.4             r40h6115d3f_0    conda-forge
r-pkgbuild                1.0.8             r40h6115d3f_0    conda-forge
r-pkgconfig               2.0.3             r40h6115d3f_1    conda-forge
r-pkgload                 1.0.2           r40h0357c0b_1002    conda-forge
r-plogr                   0.2.0           r40h6115d3f_1003    conda-forge
r-plyr                    1.8.6             r40h0357c0b_1    conda-forge
r-praise                  1.0.0           r40h6115d3f_1004    conda-forge
r-prettyunits             1.1.1             r40h6115d3f_1    conda-forge
r-proc                    1.16.2            r40h0357c0b_1    conda-forge
r-processx                3.4.2             r40hcdcec82_1    conda-forge
r-prodlim                 2019.11.13        r40h0357c0b_1    conda-forge
r-progress                1.2.2             r40h6115d3f_2    conda-forge
r-promises                1.1.0             r40h0357c0b_1    conda-forge
r-pryr                    0.1.4           r40h0357c0b_1004    conda-forge
r-ps                      1.3.3             r40hcdcec82_0    conda-forge
r-purrr                   0.3.4             r40hcdcec82_1    conda-forge
r-quantmod                0.4.17            r40h6115d3f_1    conda-forge
r-r6                      2.4.1             r40h6115d3f_1    conda-forge
r-randomforest            4.6_14          r40h9bbef5b_1003    conda-forge
r-rbokeh                  0.5.0           r40h6115d3f_1003    conda-forge
r-rcmdcheck               1.3.3             r40h6115d3f_3    conda-forge
r-rcolorbrewer            1.1_2           r40h6115d3f_1003    conda-forge
r-rcpp                    1.0.4.6           r40h0357c0b_1    conda-forge
r-readr                   1.3.1           r40h0357c0b_1004    conda-forge
r-readxl                  1.3.1             r40hde08347_4    conda-forge
r-recipes                 0.1.12            r40h6115d3f_1    conda-forge
r-recommended             4.0                    r40_1004    conda-forge
r-rematch                 1.0.1           r40h6115d3f_1003    conda-forge
r-rematch2                2.1.2             r40h6115d3f_1    conda-forge
r-remotes                 2.1.1             r40h6115d3f_1    conda-forge
r-repr                    1.1.0             r40h6115d3f_1    conda-forge
r-reprex                  0.3.0             r40h6115d3f_2    conda-forge
r-reshape2                1.4.4             r40h0357c0b_1    conda-forge
r-rex                     1.2.0             r40h6115d3f_1    conda-forge
r-rlang                   0.4.6             r40hcdcec82_0    conda-forge
r-rmarkdown               2.1               r40h6115d3f_1    conda-forge
r-roxygen2                7.1.0             r40h0357c0b_1    conda-forge
r-rpart                   4.1_15            r40hcdcec82_2    conda-forge
r-rprojroot               1.3_2           r40h6115d3f_1003    conda-forge
r-rstudioapi              0.11              r40h6115d3f_1    conda-forge
r-rversions               2.0.1             r40h6115d3f_1    conda-forge
r-rvest                   0.3.5             r40h6115d3f_1    conda-forge
r-scales                  1.1.0             r40h6115d3f_1    conda-forge
r-selectr                 0.4_2             r40h6115d3f_1    conda-forge
r-sessioninfo             1.1.1           r40h6115d3f_1002    conda-forge
r-shape                   1.4.4                  r40_1003    conda-forge
r-shiny                   1.4.0.2           r40h6115d3f_1    conda-forge
r-sourcetools             0.1.7           r40he1b5a44_1002    conda-forge
r-spatial                 7.3_12            r40hcdcec82_1    conda-forge
r-squarem                 2020.2            r40h6115d3f_1    conda-forge
r-stringi                 1.4.6             r40h0e574ca_2    conda-forge
r-stringr                 1.4.0             r40h6115d3f_2    conda-forge
r-survival                3.1_12            r40hcdcec82_1    conda-forge
r-sys                     3.3               r40hcdcec82_1    conda-forge
r-testthat                2.3.2             r40h0357c0b_1    conda-forge
r-tibble                  3.0.1             r40hcdcec82_1    conda-forge
r-tidyr                   1.0.3             r40h0357c0b_0    conda-forge
r-tidyselect              1.0.0             r40h6115d3f_1    conda-forge
r-tidyverse               1.3.0             r40h6115d3f_2    conda-forge
r-timedate                3043.102        r40h6115d3f_1002    conda-forge
r-tinytex                 0.22              r40h6115d3f_1    conda-forge
r-ttr                     0.23_6            r40hcdcec82_1    conda-forge
r-usethis                 1.6.1             r40h6115d3f_1    conda-forge
r-utf8                    1.1.4           r40hcdcec82_1003    conda-forge
r-uuid                    0.1_4             r40hcdcec82_1    conda-forge
r-vctrs                   0.2.4             r40hcdcec82_1    conda-forge
r-viridislite             0.3.0           r40h6115d3f_1003    conda-forge
r-whisker                 0.4               r40h6115d3f_1    conda-forge
r-withr                   2.2.0             r40h6115d3f_1    conda-forge
r-xfun                    0.13              r40h6115d3f_1    conda-forge
r-xml2                    1.3.2             r40h0357c0b_1    conda-forge
r-xopen                   1.0.0           r40h6115d3f_1003    conda-forge
r-xtable                  1.8_4             r40h6115d3f_3    conda-forge
r-xts                     0.12_0            r40hcdcec82_1    conda-forge
r-yaml                    2.2.1             r40hcdcec82_1    conda-forge
r-zeallot                 0.1.0           r40h6115d3f_1002    conda-forge
r-zoo                     1.8_8             r40hcdcec82_0    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
sed                       4.7               h1bed415_1000    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                46.1.3           py38h32f6830_0    conda-forge
six                       1.14.0                     py_1    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
terminado                 0.8.3            py38h32f6830_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
tktable                   2.10                 h555a92e_3    conda-forge
tornado                   6.0.4            py38h1e0a361_1    conda-forge
traitlets                 4.3.3            py38h32f6830_1    conda-forge
wcwidth                   0.1.9              pyh9f0ad1d_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.34.2                     py_1    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.9                h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_0    conda-forge
zeromq                    4.3.2                he1b5a44_2    conda-forge
zipp                      3.1.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h6597ccf_3    conda-forge

Details about conda and system ( conda info ):
$ conda info
     active environment : muscatR4_2
    active env location : /export/home2/#####/.conda/envs/muscatR4_2
            shell level : 1
       user config file : /export/home2/#####/.condarc
 populated config files : /export/home2/#####/.condarc
          conda version : 4.8.3
    conda-build version : 3.18.11
         python version : 3.7.6.final.0
       virtual packages : __glibc=2.17
       base environment : /export/home/#####/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /export/home/#####/anaconda3/pkgs
                          /export/home2/#####/.conda/pkgs
       envs directories : /export/home/#####/anaconda3/envs
                          /export/home2/#####/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.3 requests/2.22.0 CPython/3.7.6 Linux/3.10.0-957.12.2.el7.x86_64 centos/7.6.1810 glibc/2.17
                UID:GID : 65363:65363
             netrc file : None
           offline mode : False

Did I do anything wrong?
Thanks

Unable to update pins for R 3.4.1 on win-64

tl;dr We haven't been able to update the pins for R 3.4.1 on Windows.

I was recently notified by @cbrueffer that R packages were failing for R 3.4.1: conda-forge/staged-recipes#5405 (comment). I was surprised because I thought nothing had changed for R 3.4.1, but then I remembered today that PR #39 from @jakirkham was merged by @bgruening a few days ago. It was just a straightforward rerendering, but surprisingly this caused new binaries for win-64 and win-32 to be uploaded to Anaconda Cloud:

https://anaconda.org/conda-forge/r-base/files?version=3.4.1

These packages hadn't previously been uploaded because the merge commit from @ocefpaf in PR #27 did not trigger a Windows build (I have no idea why):

screen shot 2018-03-19 at 1 55 22 pm

Now that a Windows build was triggered, the build number 3 binaries appear to be failing for the same reason that the build number 2 binaries were previously failing (and were subsequently labeled as broken): #26

Action items:

  • Mark win-64/r-base-3.4.1-3.tar.bz2 and win-32/r-base-3.4.1-3.tar.bz2 as broken
  • Configure pins so that R 3.4.1 can build packages on win-64
  • Update r-base recipe to skip win-32 (we skip win-32 for all R package recipes, so it seems unnecessary to build r-base for win-32)

The r-base package is inconsistent with the rest of conda-forge packages

The use of the jinja variable {{ native }} prevents the pinning script to issue PRs to fix the different pinnings used in the package. We probably will not be able to use the same pinnings onb Windows because we don't have any control over the msys2 packages used there, but we could at least get the Linux and OS X version in sync with the rest of the stack so users can install Python and R packages in teh same env.

libRmath.so

Hi, is this package supposed to install libRmath.so?

[bug report] using R 4.0.3 with gcc_linux-64 from conda-forge results in source package installation failure.

Issue:

I am using gcc_linux-64=7.3.0 from conda-forge channel
echo $CC:
/home/USERNAME/anaconda/envs/episafety/bin/x86_64-conda_cos6-linux-gnu-cc
echo $CPP:
/home/USERNAME/anaconda/envs/episafety/bin/x86_64-conda_cos6-linux-gnu-cpp
okay you can see there is no problem

but when I tried to install some R source packages in the same environment, it gives me this error
/bin/sh: x86_64-conda-linux-gnu-cc: command not found
so it seems that r tried to find x86_64-conda-linux-gnu-cc as its compiler instead of what have been set in the CC and CPP

log

* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/Rtmp9fofpx/R.INSTALL444c87e4fae00/base64enc/src'
x86_64-conda-linux-gnu-cc -I"/home/USERNAME/anaconda/envs/episafety/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/USERNAME/anaconda/envs/episafety/include -I/home/USERNAME/anaconda/envs/episafety/include -Wl,-rpath-link,/home/USERNAME/anaconda/envs/episafety/lib   -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/USERNAME/anaconda/envs/episafety/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1606241575140/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/home/USERNAME/anaconda/envs/episafety=/usr/local/src/conda-prefix  -c base64.c -o base64.o
/bin/sh: x86_64-conda-linux-gnu-cc: command not found
make[1]: *** [/home/USERNAME/anaconda/envs/episafety/lib/R/etc/Makeconf:173: base64.o] Error 127
make[1]: Leaving directory '/tmp/Rtmp9fofpx/R.INSTALL444c87e4fae00/base64enc/src'
ERROR: compilation failed for package ‘base64enc’
* removing ‘/NAS392047/home/USERNAME/anaconda/envs/episafety/lib/R/library/base64enc’

Environment (conda list):
$ conda list
# packages in environment at /home/yujw/anaconda/envs/episafety:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
binutils_impl_linux-64    2.34                 h53a641e_7    conda-forge
binutils_linux-64         2.34                hc952b39_18    conda-forge
bwidget                   1.9.14                        0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h36c2ea0_0    conda-forge
ca-certificates           2020.12.5            ha878542_0    conda-forge
cairo                     1.16.0            h488836b_1006    conda-forge
certifi                   2020.12.5        py38h578d9bd_0    conda-forge
curl                      7.71.1               he644dc0_8    conda-forge
fontconfig                2.13.1            h1056068_1002    conda-forge
freetype                  2.10.4               he06d7ca_0    conda-forge
fribidi                   1.0.10               h516909a_0    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    defaults
gcc_linux-64              7.3.0               h553295d_18    conda-forge
gettext                   0.19.8.1          hf34092f_1004    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_1    defaults
gfortran_linux-64         7.3.0               h553295d_18    conda-forge
graphite2                 1.3.14               h23475e2_0    defaults
gsl                       2.6                  hf94e986_0    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1    defaults
gxx_linux-64              7.3.0               h553295d_18    conda-forge
harfbuzz                  2.7.2                hb1ce69c_1    conda-forge
icu                       67.1                 he1b5a44_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
krb5                      1.17.2               h926e7f8_0    conda-forge
ld_impl_linux-64          2.34                 h53a641e_7    conda-forge
libblas                   3.9.0                3_openblas    conda-forge
libcblas                  3.9.0                3_openblas    conda-forge
libcurl                   7.71.1               hcdd3856_8    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.3.0               h5dbcf3e_17    conda-forge
libgfortran-ng            7.5.0               hae1eefd_17    conda-forge
libgfortran4              7.5.0               hae1eefd_17    conda-forge
libglib                   2.66.3               hbe7bbb4_0    conda-forge
libgomp                   9.3.0               h5dbcf3e_17    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0                3_openblas    conda-forge
libnghttp2                1.41.0               h8cfc5f6_2    conda-forge
libopenblas               0.3.12          pthreads_hb3c22a3_1    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.3.0               h2ae2ef3_17    conda-forge
libtiff                   4.1.0                hc7e4089_6    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp-base              1.1.0                h516909a_3    conda-forge
libxcb                    1.14                 h7b6447c_0    defaults
libxml2                   2.9.10               h68273f3_2    conda-forge
lz4-c                     1.9.2                he1b5a44_3    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openssl                   1.1.1h               h516909a_0    conda-forge
pango                     1.42.4               h80147aa_5    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
pcre2                     10.35                h032f7d1_2    conda-forge
pip                       20.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
python                    3.8.5           h1103e12_9_cpython    conda-forge
python_abi                3.8                      1_cp38    conda-forge
r-base                    4.0.3                he481d28_2    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
setuptools                50.3.2           py38h06a4308_2    defaults
sqlite                    3.34.0               h74cdb3f_0    conda-forge
tk                        8.6.10               hed695b0_1    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
wheel                     0.36.1             pyhd3deb0d_0    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.12               h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.5                h6597ccf_2    conda-forge


Details about conda and system ( conda info ):
$ conda info

     active environment : episafety
    active env location : /home/USERNAME/anaconda/envs/episafety
            shell level : 1
       user config file : /home/USERNAME/.condarc
 populated config files : /home/USERNAME/.condarc
          conda version : 4.9.2
    conda-build version : not installed
         python version : 3.9.0.final.0
       virtual packages : __glibc=2.17=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/USERNAME/anaconda  (writable)
           channel URLs : https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/pro/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/pro/noarch
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/linux-64
                          https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/noarch
          package cache : /home/USERNAME/anaconda/pkgs
                          /home/USERNAME/.conda/pkgs
       envs directories : /home/USERNAME/anaconda/envs
                          /home/USERNAME/.conda/envs
               platform : linux-64
             user-agent : conda/4.9.2 requests/2.25.0 CPython/3.9.0 Linux/3.10.0-1062.9.1.el7.x86_64 centos/7.7.1908 glibc/2.17
                UID:GID : 1051:1061
             netrc file : None
           offline mode : False


Cannot install r-base in fresh environment

Issue:

Currently, when I try to install r-base into a fresh environment, I get the following error:

$ conda install -c conda-forge r-base

  environment variables:
                 CIO_TEST=<not set>
          CONDA_BACKUP_AR=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-ar
          CONDA_BACKUP_AS=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-as
          CONDA_BACKUP_CC=x86_64-apple-darwin13.4.0-clang
      CONDA_BACKUP_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
                          -fstack-protector-strong -O2 -pipe
   CONDA_BACKUP_CHECKSYMS=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-checksyms
       CONDA_BACKUP_CLANG=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-clang
     CONDA_BACKUP_CLANGXX=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-clang++
CONDA_BACKUP_CODESIGN_ALLOCATE=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-codesign_allocate
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/D
                          eveloper/SDKs/MacOSX10.13.sdk
    CONDA_BACKUP_CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9
         CONDA_BACKUP_CXX=x86_64-apple-darwin13.4.0-clang++
    CONDA_BACKUP_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
                          -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-
                          inlines-hidden -std=c++14 -fmessage-length=0
CONDA_BACKUP_DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
                          -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra
CONDA_BACKUP_DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
                          -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-
                          inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra
CONDA_BACKUP_DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
                          -O2 -pipe
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
                          -O2 -pipe
      CONDA_BACKUP_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
                          -O2 -pipe
CONDA_BACKUP_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
                          -O2 -pipe
    CONDA_BACKUP_GFORTRAN=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-gfortran
        CONDA_BACKUP_HOST=x86_64-apple-darwin13.4.0
        CONDA_BACKUP_INDR=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-indr
CONDA_BACKUP_INSTALL_NAME_TOOL=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-install_name_tool
          CONDA_BACKUP_LD=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-ld
     CONDA_BACKUP_LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
  CONDA_BACKUP_LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs
     CONDA_BACKUP_LIBTOOL=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-libtool
        CONDA_BACKUP_LIPO=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-lipo
          CONDA_BACKUP_NM=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-nm
      CONDA_BACKUP_NMEDIT=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-nmedit
       CONDA_BACKUP_OTOOL=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-otool
   CONDA_BACKUP_PAGESTUFF=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-pagestuff
      CONDA_BACKUP_RANLIB=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-ranlib
CONDA_BACKUP_REDO_PREBINDING=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-redo_prebinding
     CONDA_BACKUP_SEGEDIT=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-segedit
CONDA_BACKUP_SEG_ADDR_TABLE=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-seg_addr_table
    CONDA_BACKUP_SEG_HACK=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-seg_hack
        CONDA_BACKUP_SIZE=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-size
     CONDA_BACKUP_STRINGS=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-strings
       CONDA_BACKUP_STRIP=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
                          darwin13.4.0-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
        CONDA_DEFAULT_ENV=conda36
                CONDA_EXE=/Users/langmm/miniconda3/bin/conda
             CONDA_PREFIX=/Users/langmm/miniconda3/envs/conda36
           CONDA_PREFIX_1=/Users/langmm/miniconda3
    CONDA_PROMPT_MODIFIER=(conda36)
         CONDA_PYTHON_EXE=/Users/langmm/miniconda3/bin/python
               CONDA_ROOT=/Users/langmm/miniconda3
              CONDA_SHLVL=2
                     PATH=/Users/langmm/miniconda3/bin:/Users/langmm/miniconda3/envs/conda36/bin
                          :/Users/langmm/miniconda3/condabin:/Users/langmm/anaconda/bin:/usr/loc
                          al/opt/openssl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Libra
                          ry/TeX/texbin:/opt/X11/bin:/Users/langmm/Library/Android/sdk/tools:/Us
                          ers/langmm/Library/Android/sdk/tools/bin:/Users/langmm/Library/Android
                          /sdk/platform-tools:/Applications/MATLAB_R2018b.app/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : conda36
    active env location : /Users/langmm/miniconda3/envs/conda36
            shell level : 2
       user config file : /Users/langmm/.condarc
 populated config files : /Users/langmm/.condarc
          conda version : 4.7.7
    conda-build version : 3.18.7
         python version : 3.7.3.final.0
       virtual packages :
       base environment : /Users/langmm/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/langmm/miniconda3/pkgs
                          /Users/langmm/.conda/pkgs
       envs directories : /Users/langmm/miniconda3/envs
                          /Users/langmm/.conda/envs
               platform : osx-64
             user-agent : conda/4.7.7 requests/2.22.0 CPython/3.7.3 Darwin/17.5.0 OSX/10.13.4
                UID:GID : 501:20
             netrc file : None
           offline mode : False


Environment (conda list):
$ conda list

# packages in environment at /Users/langmm/miniconda3/envs/conda36:
#
# Name                    Version                   Build  Channel
appnope                   0.1.0                 py36_1000    conda-forge
backcall                  0.1.0                      py_0    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
certifi                   2019.6.16                py36_0    conda-forge
decorator                 4.4.0                      py_0    conda-forge
ipython                   7.6.1            py36h5ca1d4c_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.14.1                   py36_0    conda-forge
libcxx                    8.0.0                         4    conda-forge
libcxxabi                 8.0.0                         4    conda-forge
libffi                    3.2.1             h6de7cb9_1006    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
openssl                   1.1.1c               h01d97ff_0    conda-forge
parso                     0.5.0                      py_0    conda-forge
pexpect                   4.7.0                    py36_0    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
pip                       19.1.1                   py36_0    conda-forge
prompt_toolkit            2.0.9                      py_0    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pygments                  2.4.2                      py_0    conda-forge
python                    3.6.7             h94afb7f_1005    conda-forge
readline                  8.0                  hcfe32e1_0    conda-forge
setuptools                41.0.1                   py36_0    conda-forge
six                       1.12.0                py36_1000    conda-forge
sqlite                    3.29.0               hb7d70f7_0    conda-forge
tk                        8.6.9             h2573ce8_1002    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
wheel                     0.33.4                   py36_0    conda-forge
xz                        5.2.4             h1de35cc_1001    conda-forge
zlib                      1.2.11            h01d97ff_1005    conda-forge


Details about conda and system ( conda info ):
$ conda info

     active environment : conda36
    active env location : /Users/langmm/miniconda3/envs/conda36
            shell level : 2
       user config file : /Users/langmm/.condarc
 populated config files : /Users/langmm/.condarc
          conda version : 4.7.7
    conda-build version : 3.18.7
         python version : 3.7.3.final.0
       virtual packages : 
       base environment : /Users/langmm/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/langmm/miniconda3/pkgs
                          /Users/langmm/.conda/pkgs
       envs directories : /Users/langmm/miniconda3/envs
                          /Users/langmm/.conda/envs
               platform : osx-64
             user-agent : conda/4.7.7 requests/2.22.0 CPython/3.7.3 Darwin/17.5.0 OSX/10.13.4
                UID:GID : 501:20
             netrc file : None
           offline mode : False

System library issues with 3.5.1 build(s?)

Issue: R can't find/use system libraries with certain builds of 3.5.1

I've been having some hair-pulling issues with R and a recent build seems to be part of the issue. This version of r-base (r-base=3.5.1=he45234b_1005) seems to not be able to build/link with system libraries, and I'm not sure why. I dug through my docker containers (my container has only successfully built ONCE due to conda picking arbitrary R builds) and found the build (and Makeconf) were different.


Environment (conda list):
$ conda list
# packages in environment at /opt/conda:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1    defaults
alembic                   0.9.9                      py_0    conda-forge
asn1crypto                0.24.0                py36_1003    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     18.2.0                     py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
beautifulsoup4            4.6.3                 py36_1000    conda-forge
binutils_impl_linux-64    2.28.1               had2808c_3    defaults
binutils_linux-64         7.2.0               had2808c_27    defaults
blas                      1.1                    openblas    conda-forge
bokeh                     0.13.0                py36_1000    conda-forge
bwidget                   1.9.11                        1    defaults
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.14.12           h80bd089_1005    conda-forge
certifi                   2018.11.29            py36_1000    conda-forge
cffi                      1.11.5          py36h9745a5d_1001    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
cloudpickle               0.5.6                      py_0    conda-forge
conda                     4.6.1                    py36_0    conda-forge
conda-env                 2.6.0                         1    conda-forge
configurable-http-proxy   1.3.0                         0    conda-forge
cryptography              2.3.1           py36hb7f436b_1000    conda-forge
curl                      7.63.0            h646f8bb_1000    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cython                    0.28.5          py36hf484d3e_1000    conda-forge
cytoolz                   0.9.0.1         py36h14c3975_1001    conda-forge
dask-core                 1.1.0                      py_0    conda-forge
dbus                      1.13.0            h4e0c4b3_1000    conda-forge
decorator                 4.3.2                      py_0    conda-forge
dill                      0.2.8.2               py36_1000    conda-forge
entrypoints               0.3                   py36_1000    conda-forge
expat                     2.2.5             hf484d3e_1002    conda-forge
fastcache                 1.0.2           py36h14c3975_1001    conda-forge
fontconfig                2.13.1            h2176d3f_1000    conda-forge
freetype                  2.9.1             h94bbf69_1005    conda-forge
gcc_impl_linux-64         7.2.0                habb00fd_3    defaults
gcc_linux-64              7.2.0               h550dcbe_27    defaults
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
gfortran_impl_linux-64    7.2.0                hdf63c60_3    defaults
gfortran_linux-64         7.2.0               h550dcbe_27    defaults
glib                      2.56.2            had28632_1001    conda-forge
gmp                       6.1.2             hf484d3e_1000    conda-forge
gmpy2                     2.0.8           py36hb20f59a_1002    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gst-plugins-base          1.12.5            h3865690_1000    conda-forge
gstreamer                 1.12.5            h0cc0488_1000    conda-forge
gxx_impl_linux-64         7.2.0                hdf63c60_3    defaults
gxx_linux-64              7.2.0               h550dcbe_27    defaults
h5py                      2.7.1                    py36_3    conda-forge
harfbuzz                  1.9.0             he243708_1001    conda-forge
hdf5                      1.10.1                        2    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.8                   py36_1000    conda-forge
imageio                   2.4.1                 py36_1000    conda-forge
ipykernel                 5.1.0           py36h24bf2e0_1001    conda-forge
ipython                   7.2.0           py36h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
jedi                      0.13.2                py36_1000    conda-forge
jinja2                    2.10                       py_1    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.0.0a3               py36_1000    conda-forge
jupyter_client            5.2.4                      py_1    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyterhub                0.9.4                 py36_1000    conda-forge
jupyterlab                0.35.4                   py36_0    conda-forge
jupyterlab_server         0.2.0                      py_0    conda-forge
kiwisolver                1.0.1           py36h6bb024c_1002    conda-forge
krb5                      1.16.3            hc83ff2d_1000    conda-forge
libcurl                   7.63.0            h01ee5af_1000    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             hf484d3e_1005    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libiconv                  1.15              h14c3975_1004    conda-forge
libpng                    1.6.36            h84994c4_1000    conda-forge
libprotobuf               3.6.1             hdbcaa40_1000    conda-forge
libsodium                 1.0.16            h14c3975_1001    conda-forge
libssh2                   1.8.0             h1ad7b7a_1003    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtiff                   4.0.10            h648cc4a_1001    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
llvmlite                  0.23.0                   py36_1    conda-forge
make                      4.2.1             h14c3975_2004    conda-forge
mako                      1.0.7                      py_1    conda-forge
markupsafe                1.1.0           py36h14c3975_1000    conda-forge
matplotlib                2.2.3            py36h8e2386c_0    conda-forge
mistune                   0.8.4           py36h14c3975_1000    conda-forge
mpc                       1.1.0             hb20f59a_1006    conda-forge
mpfr                      4.0.1             ha14ba45_1000    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
networkx                  2.2                        py_1    conda-forge
nodejs                    11.7.0               hf484d3e_0    conda-forge
notebook                  5.7.2                 py36_1000    conda-forge
numba                     0.38.1                   py36_0    conda-forge
numexpr                   2.6.9           py36h637b7d7_1000    conda-forge
numpy                     1.13.3          py36_blas_openblash1522bff_1201  [blas_openblas]  conda-forge
olefile                   0.46                       py_0    conda-forge
openblas                  0.3.3             h9ac9557_1001    conda-forge
openssl                   1.0.2p            h14c3975_1002    conda-forge
packaging                 19.0                       py_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandas                    0.23.4          py36h637b7d7_1000    conda-forge
pandoc                    2.5                           1    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.40.14           hf0c64fd_1003    conda-forge
parso                     0.3.2                      py_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
pexpect                   4.6.0                 py36_1000    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
pillow                    5.4.1           py36h00a061d_1000    conda-forge
pip                       19.0.1                   py36_0    conda-forge
pixman                    0.34.0            h14c3975_1003    conda-forge
prometheus_client         0.5.0                      py_0    conda-forge
prompt_toolkit            2.0.7                      py_0    conda-forge
protobuf                  3.6.1           py36hf484d3e_1001    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                 py36_1000    conda-forge
pycosat                   0.6.3           py36h14c3975_1001    conda-forge
pycparser                 2.19                       py_0    conda-forge
pycurl                    7.43.0.2         py36hb7f436b_0    defaults
pygments                  2.3.1                      py_0    conda-forge
pyopenssl                 18.0.0                py36_1000    conda-forge
pyparsing                 2.3.1                      py_0    conda-forge
pyrsistent                0.14.9          py36h14c3975_1000    conda-forge
pysocks                   1.6.8                 py36_1002    conda-forge
python                    3.6.7             hd21baee_1001    conda-forge
python-dateutil           2.7.5                      py_0    conda-forge
python-editor             1.0.3                      py_0    conda-forge
python-oauth2             1.0.1                    py36_0    conda-forge
pytz                      2018.9                     py_0    conda-forge
pywavelets                1.0.1           py36h3010b51_1000    conda-forge
pyyaml                    3.13            py36h14c3975_1001    conda-forge
pyzmq                     17.1.2          py36h6afc9c9_1001    conda-forge
r-assertthat              0.2.0           r351h6115d3f_1001    conda-forge
r-backports               1.1.3           r351h96ca727_1000    conda-forge
r-base                    3.5.1             he45234b_1005    conda-forge
r-base64enc               0.1_3           r351h96ca727_1002    conda-forge
r-bh                      1.69.0_1         r351h6115d3f_0    conda-forge
r-bindr                   0.1.1           r351h6115d3f_1001    conda-forge
r-bindrcpp                0.2.2           r351h29659fb_1001    conda-forge
r-bit                     1.1_12          r351h14c3975_1002    conda-forge
r-bit64                   0.9_7           r351h96ca727_1000    conda-forge
r-bitops                  1.0_6           r351h96ca727_1002    conda-forge
r-blob                    1.1.1                 r351_1001    conda-forge
r-broom                   0.5.1           r351h6115d3f_1000    conda-forge
r-callr                   3.1.1           r351h6115d3f_1000    conda-forge
r-caret                   6.0_81          r351h96ca727_1000    conda-forge
r-cellranger              1.1.0           r351h6115d3f_1001    conda-forge
r-class                   7.3_15          r351h96ca727_1000    conda-forge
r-cli                     1.0.1           r351h6115d3f_1000    conda-forge
r-clipr                   0.5.0            r351h6115d3f_0    conda-forge
r-codetools               0.2_16          r351h6115d3f_1000    conda-forge
r-colorspace              1.4_0            r351h96ca727_0    conda-forge
r-config                  0.3             r351h6115d3f_1001    conda-forge
r-crayon                  1.3.4           r351h6115d3f_1001    conda-forge
r-curl                    3.3              r351h96ca727_0    conda-forge
r-dbi                     1.0.0           r351h6115d3f_1001    conda-forge
r-dbplyr                  1.3.0           r351h6115d3f_1000    conda-forge
r-devtools                1.13.6           r351h6115d3f_1    conda-forge
r-digest                  0.6.18          r351h96ca727_1000    conda-forge
r-dplyr                   0.7.8           r351h29659fb_1000    conda-forge
r-evaluate                0.12            r351h6115d3f_1000    conda-forge
r-fansi                   0.4.0           r351h96ca727_1000    conda-forge
r-forcats                 0.3.0           r351h6115d3f_1001    conda-forge
r-foreach                 1.4.4           r351h6115d3f_1001    conda-forge
r-forecast                8.2             r351hf484d3e_1001    conda-forge
r-forge                   0.1.0           r351h6115d3f_1000    conda-forge
r-fracdiff                1.4_2           r351h96ca727_1002    conda-forge
r-fs                      1.2.6           r351h29659fb_1000    conda-forge
r-generics                0.0.2           r351h6115d3f_1001    conda-forge
r-ggplot2                 3.1.0           r351h6115d3f_1000    conda-forge
r-git2r                   0.24.0           r351h47c54a8_0    conda-forge
r-glue                    1.3.0           r351h14c3975_1002    conda-forge
r-gower                   0.1.2           r351h96ca727_1002    conda-forge
r-gtable                  0.2.0           r351h6115d3f_1001    conda-forge
r-haven                   2.0.0           r351h29659fb_1000    conda-forge
r-hexbin                  1.27.2          r351ha65eedd_1002    conda-forge
r-highr                   0.7             r351h6115d3f_1001    conda-forge
r-hms                     0.4.2           r351h6115d3f_1000    conda-forge
r-htmltools               0.3.6           r351hf484d3e_1002    conda-forge
r-htmlwidgets             1.2             r351h6115d3f_1000    conda-forge
r-httpuv                  1.4.5.1         r351hf484d3e_1000    conda-forge
r-httr                    1.4.0           r351h6115d3f_1000    conda-forge
r-ipred                   0.9_8           r351h96ca727_1000    conda-forge
r-irdisplay               0.7                   r351_1000    conda-forge
r-irkernel                0.8.15          r351h6115d3f_1001    conda-forge
r-iterators               1.0.10          r351h6115d3f_1001    conda-forge
r-jsonlite                1.6             r351h96ca727_1000    conda-forge
r-kernsmooth              2.23_15         r351ha65eedd_1002    conda-forge
r-knitr                   1.21            r351h6115d3f_1000    conda-forge
r-labeling                0.3             r351h6115d3f_1001    conda-forge
r-later                   0.7.5           r351h29659fb_1000    conda-forge
r-lattice                 0.20_38         r351h96ca727_1000    conda-forge
r-lava                    1.6.4           r351h6115d3f_1000    conda-forge
r-lazyeval                0.2.1           r351h96ca727_1002    conda-forge
r-lmtest                  0.9_36          r351ha65eedd_1000    conda-forge
r-lubridate               1.7.4           r351h29659fb_1001    conda-forge
r-magrittr                1.5             r351h6115d3f_1001    conda-forge
r-markdown                0.9             r351h96ca727_1000    conda-forge
r-mass                    7.3_51.1        r351h96ca727_1000    conda-forge
r-matrix                  1.2_15          r351h96ca727_1000    conda-forge
r-memoise                 1.1.0           r351h6115d3f_1001    conda-forge
r-mgcv                    1.8_26          r351h96ca727_1000    conda-forge
r-mime                    0.6             r351h96ca727_1000    conda-forge
r-modelmetrics            1.1.0           r351h29659fb_1002    conda-forge
r-modelr                  0.1.2           r351h6115d3f_1001    conda-forge
r-munsell                 0.5.0           r351h6115d3f_1001    conda-forge
r-nlme                    3.1_137         r351ha65eedd_1000    conda-forge
r-nnet                    7.3_12          r351h96ca727_1002    conda-forge
r-numderiv                2016.8_1        r351h6115d3f_1001    conda-forge
r-nycflights13            1.0.0                 r351_1000    conda-forge
r-openssl                 1.1             r351hff1dc39_1000    conda-forge
r-pbdzmq                  0.3_3           r351h193a840_1000    conda-forge
r-pillar                  1.3.1           r351h6115d3f_1000    conda-forge
r-pkgconfig               2.0.2           r351h6115d3f_1001    conda-forge
r-plogr                   0.2.0           r351h6115d3f_1001    conda-forge
r-plyr                    1.8.4           r351h29659fb_1002    conda-forge
r-prettyunits             1.0.2           r351h6115d3f_1001    conda-forge
r-processx                3.2.1           r351h96ca727_1000    conda-forge
r-prodlim                 2018.04.18      r351h29659fb_1002    conda-forge
r-progress                1.2.0           r351h6115d3f_1002    conda-forge
r-promises                1.0.1           r351h29659fb_1000    conda-forge
r-ps                      1.3.0           r351h96ca727_1000    conda-forge
r-purrr                   0.2.5           r351h96ca727_1002    conda-forge
r-quadprog                1.5_5           r351ha65eedd_1002    conda-forge
r-quantmod                0.4_13          r351h6115d3f_1000    conda-forge
r-r2d3                    0.2.3           r351h6115d3f_1000    conda-forge
r-r6                      2.3.0           r351h6115d3f_1000    conda-forge
r-randomforest            4.6_14          r351ha65eedd_1000    conda-forge
r-rappdirs                0.3.1           r351h96ca727_1002    conda-forge
r-rcolorbrewer            1.1_2           r351h6115d3f_1001    conda-forge
r-rcpp                    1.0.0           r351h29659fb_1000    conda-forge
r-rcpparmadillo           0.9.100.5.0     r351h29659fb_1000    conda-forge
r-rcpproll                0.3.0           r351h29659fb_1000    conda-forge
r-rcurl                   1.95_4.11       r351h96ca727_1003    conda-forge
r-readr                   1.3.1           r351h29659fb_1000    conda-forge
r-readxl                  1.2.0           r351h29659fb_1000    conda-forge
r-recipes                 0.1.4           r351h6115d3f_1000    conda-forge
r-rematch                 1.0.1           r351h6115d3f_1001    conda-forge
r-repr                    0.19.1          r351h6115d3f_1000    conda-forge
r-reprex                  0.2.1           r351h6115d3f_1000    conda-forge
r-reshape2                1.4.3           r351h29659fb_1003    conda-forge
r-rlang                   0.3.1            r351h96ca727_0    conda-forge
r-rmarkdown               1.11            r351h6115d3f_1000    conda-forge
r-rpart                   4.1_13          r351h96ca727_1002    conda-forge
r-rprojroot               1.3_2           r351h6115d3f_1001    conda-forge
r-rsqlite                 2.1.1           r351h29659fb_1000    conda-forge
r-rstudioapi              0.9.0            r351h6115d3f_0    conda-forge
r-rvest                   0.3.2           r351h6115d3f_1001    conda-forge
r-scales                  1.0.0           r351h29659fb_1001    conda-forge
r-selectr                 0.4_1           r351h6115d3f_1000    conda-forge
r-shiny                   1.2.0                 r351_1000    conda-forge
r-sourcetools             0.1.7           r351hf484d3e_1000    conda-forge
r-sparklyr                0.9.4            r351h6115d3f_0    conda-forge
r-squarem                 2017.10_1       r351h6115d3f_1001    conda-forge
r-stringi                 1.2.4           r351h29659fb_1001    conda-forge
r-stringr                 1.3.1           r351h6115d3f_1001    conda-forge
r-survival                2.43_3          r351h96ca727_1000    conda-forge
r-tibble                  2.0.1            r351h96ca727_0    conda-forge
r-tidyr                   0.8.2           r351h29659fb_1002    conda-forge
r-tidyselect              0.2.5           r351h29659fb_1000    conda-forge
r-tidyverse               1.2.1           r351h6115d3f_1001    conda-forge
r-timedate                3043.102        r351h6115d3f_1000    conda-forge
r-tinytex                 0.10             r351h6115d3f_0    conda-forge
r-tseries                 0.10_46         r351h9ac9557_1000    conda-forge
r-ttr                     0.23_4          r351ha65eedd_1000    conda-forge
r-utf8                    1.1.4           r351h96ca727_1000    conda-forge
r-uuid                    0.1_2           r351h96ca727_1001    conda-forge
r-viridislite             0.3.0           r351h6115d3f_1001    conda-forge
r-whisker                 0.3_2           r351h6115d3f_1001    conda-forge
r-withr                   2.1.2           r351h6115d3f_1000    conda-forge
r-xfun                    0.4             r351h6115d3f_1000    conda-forge
r-xml2                    1.2.0           r351h29659fb_1002    conda-forge
r-xtable                  1.8_3                 r351_2000    conda-forge
r-xts                     0.11_1          r351h96ca727_1000    conda-forge
r-yaml                    2.2.0           r351h96ca727_1001    conda-forge
r-zoo                     1.8_4           r351h96ca727_1000    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
requests                  2.21.0                py36_1000    conda-forge
rpy2                      2.9.4           py36r351h941a26a_1    conda-forge
ruamel_yaml               0.15.71         py36h14c3975_1000    conda-forge
scikit-image              0.14.2           py36hf484d3e_0    conda-forge
scikit-learn              0.20.2          py36_blas_openblashebff5e3_1400  [blas_openblas]  conda-forge
scipy                     1.1.0           py36_blas_openblash1522bff_1202  [blas_openblas]  conda-forge
seaborn                   0.9.0                      py_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                40.7.0                   py36_0    conda-forge
sip                       4.18.1          py36hf484d3e_1000    conda-forge
six                       1.12.0                py36_1000    conda-forge
sqlalchemy                1.2.16          py36h14c3975_1000    conda-forge
sqlite                    3.26.0            h67949de_1000    conda-forge
statsmodels               0.9.0           py36h3010b51_1000    conda-forge
sympy                     1.1.1                    py36_0    conda-forge
terminado                 0.8.1                 py36_1001    conda-forge
testpath                  0.4.2                 py36_1000    conda-forge
tini                      0.18.0            h14c3975_1001    conda-forge
tk                        8.6.9             h84994c4_1000    conda-forge
tktable                   2.10                 h14c3975_0    defaults
toolz                     0.9.0                      py_1    conda-forge
tornado                   5.1.1           py36h14c3975_1000    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
tzlocal                   1.5.1                      py_0    conda-forge
urllib3                   1.24.1                py36_1000    conda-forge
vincent                   0.4.4                      py_1    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.32.3                   py36_0    conda-forge
widgetsnbextension        3.4.2                 py36_1000    conda-forge
xlrd                      1.2.0                      py_0    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h14c3975_1004    conda-forge
xorg-libsm                1.2.3             h4937e3b_1000    conda-forge
xorg-libx11               1.6.6             h14c3975_1000    conda-forge
xorg-libxau               1.0.8             h14c3975_1006    conda-forge
xorg-libxdmcp             1.1.2             h14c3975_1007    conda-forge
xorg-libxext              1.3.3             h14c3975_1004    conda-forge
xorg-libxrender           0.9.10            h14c3975_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
yaml                      0.1.7             h14c3975_1001    conda-forge
zeromq                    4.2.5             hf484d3e_1006    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge

Details about conda and system ( conda info ):
$ conda info
     active environment : None
       user config file : /home/waskd6/.condarc
 populated config files : /opt/conda/.condarc
          conda version : 4.6.1
    conda-build version : not installed
         python version : 3.6.7.final.0
       base environment : /opt/conda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda/pkgs
                          /home/waskd6/.conda/pkgs
       envs directories : /opt/conda/envs
                          /home/waskd6/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.1 requests/2.21.0 CPython/3.6.7 Linux/3.10.0-957.1.3.el7.x86_64 ubuntu/18.04.1 glibc/2.27
                UID:GID : 848809:848809
             netrc file : None
           offline mode : False

Using rgdal as an example (r-rgdal is broken in main right now, don't get me started):
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages("rgdal", repos="https://cran.rstudio.com/")
configure: R_HOME: /opt/conda/lib/R
configure: CC: x86_64-conda_cos6-linux-gnu-cc
configure: CXX: x86_64-conda_cos6-linux-gnu-c++
configure: C++11 support available
configure: rgdal: 1.3-6
checking for /usr/bin/svnversion... no
configure: svn revision: 773
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.2.3
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libarmadillo.so.8, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libproj.so.12, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libpoppler.so.73, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libjson-c.so.3, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libfreexl.so.1, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libqhull.so.7, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libgeos_c.so.1, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libwebp.so.6, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libepsilon.so.1, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libodbc.so.2, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libodbcinst.so.2, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libkmlbase.so.1, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libkmldom.so.1, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libkmlengine.so.1, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libxerces-c-3.2.so, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libopenjp2.so.7, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.2.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libnetcdf.so.13, needed by /usr/lib/libgdal.so, not found (try using -rpath or -rpath-link)
.
.
.
/usr/lib/libgdal.so: undefined reference to `opj_read_header'
/usr/lib/libgdal.so: undefined reference to `HO_TestSOSI(char const*, long*)'
/usr/lib/libgdal.so: undefined reference to `nc_get_var1_ulonglong'
/usr/lib/libgdal.so: undefined reference to `sqlite3_bind_int'
/usr/lib/libgdal.so: undefined reference to `PQresultStatus'
/usr/lib/libgdal.so: undefined reference to `GEOSSymDifference_r'
/usr/lib/libgdal.so: undefined reference to `TIFFCreateDirectory@LIBTIFF_4.0'
/usr/lib/libgdal.so: undefined reference to `TIFFReadScanline@LIBTIFF_4.0'
/usr/lib/libgdal.so: undefined reference to `kmlengine::Href::Parse(std::__cxx11::basic_string<char, std::char_traits<char>
, std::allocator<char> > const&)'
/usr/lib/libgdal.so: undefined reference to `PQgetvalue'
/usr/lib/libgdal.so: undefined reference to `nc_inq_unlimdim'
/usr/lib/libgdal.so: undefined reference to `xercesc_3_2::XSComplexTypeDefinition::getDerivationMethod() const'
/usr/lib/libgdal.so: undefined reference to `xercesc_3_2::XMLUni::fgXercesSchemaFullChecking'
/usr/lib/libgdal.so: undefined reference to `PQclear'
/usr/lib/libgdal.so: undefined reference to `sqlite3_column_blob'
/usr/lib/libgdal.so: undefined reference to `opj_set_decode_area'
/usr/lib/libgdal.so: undefined reference to `SQLFetchScroll'
/usr/lib/libgdal.so: undefined reference to `kmldom::AsPlacemark(boost::intrusive_ptr<kmldom::Element>)'
/usr/lib/libgdal.so: undefined reference to `nc_get_att_uint'
.
.
.
collect2: error: ld returned 1 exit status
configure: Install failure: compilation and/or linkage problems.
It goes on for a couple dozen kB like that

Switching to r-base=3.5.1=h391c2eb_5 fixes the issue and gives the following delta to the env:

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - r-base==3.5.1=h391c2eb_5


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    gsl-2.2.1                  |blas_openblashddceaf2_6         2.1 MB  conda-forge
    r-base-3.5.1               |       h391c2eb_5        37.6 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        39.8 MB

The following NEW packages will be INSTALLED:

  gsl                conda-forge/linux-64::gsl-2.2.1-blas_openblashddceaf2_6

The following packages will be DOWNGRADED:

  r-base                                3.5.1-he45234b_1005 --> 3.5.1-h391c2eb_5

And the build works!
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages("rgdal", repos="https://cran.rstudio.com/")
trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.3-6.tar.gz'
Content type 'application/x-gzip' length 1666975 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /opt/conda/lib/R
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.3-6
checking for /usr/bin/svnversion... no
configure: svn revision: 773
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.2.3
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... yes
checking GDAL: /usr/share/gdal/2.2/pcs.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 4.9.3
checking proj_api.h presence and usability... yes
checking PROJ version >= 4.8.0... yes
checking projects.h presence and usability... yes
checking PROJ.4: epsg found and readable... yes
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags:  -I/usr/include/gdal
configure: Package LIBS:  -L/usr/lib -lgdal -larmadillo -lproj -lpoppler -ljson-c -L/usr/lib -lfreexl -lqhull -lqhull -L/usr/lib/x86_64-linux-gnu -lgeos_c -lwebp -L/usr/lib -lepsilon -lodbc -lodbcinst -lkmlbase -lkmldom -lkmlengine -lkmlxsd -lkmlregionator -lexpat -lxerces-c -lpthread -lopenjp2 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl -L/usr/lib/x86_64-linux-gnu/hdf5/serial/lib -lhdf5 -lmfhdfalt -ldfalt -logdi -lgif -ljpeg -lgeotiff -ltiff -lpng -L/usr/lib/x86_64-linux-gnu -lpq -llzma -lz -lpthread -lm -lrt -ldl -ldapclient -ldapserver -ldap -L/usr/lib -lspatialite -lpcre -lcurl -lfyba -lfygm -lfyut -lxml2 -L/usr/lib/x86_64-linux-gnu -lmysqlclient -lpthread -lz -lm -lrt -latomic -ldl -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -c OGR_write.cpp -o OGR_write.o
g++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -c gdal-bindings.cpp -o gdal-bindings.o
gcc -std=gnu99 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -m64 -fPIC  -c init.c -o init.o
gcc -std=gnu99 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -m64 -fPIC  -c inverser.c -o inverser.o
gcc -std=gnu99 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -m64 -fPIC  -c local_stubs.c -o local_stubs.o
g++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -c ogr_geom.cpp -o ogr_geom.o
gcc -std=gnu99 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -m64 -fPIC  -c ogr_polygons.c -o ogr_polygons.o
g++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -c ogr_proj.cpp -o ogr_proj.o
g++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -c ogrdrivers.cpp -o ogrdrivers.o
g++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -c ogrsource.cpp -o ogrsource.o
g++ -std=gnu++11 -I"/opt/conda/lib/R/include" -DNDEBUG -I/usr/include/gdal -I"/opt/conda/lib/R/library/sp/include" -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib   -fpic  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -c projectit.cpp -o projectit.o
g++ -std=gnu++11 -shared -L/opt/conda/lib/R/lib -Wl,-rpath,/opt/conda/lib -L/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib -lgdal -larmadillo -lproj -lpoppler -ljson-c -L/usr/lib -lfreexl -lqhull -lqhull -L/usr/lib/x86_64-linux-gnu -lgeos_c -lwebp -L/usr/lib -lepsilon -lodbc -lodbcinst -lkmlbase -lkmldom -lkmlengine -lkmlxsd -lkmlregionator -lexpat -lxerces-c -lpthread -lopenjp2 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf-lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl -L/usr/lib/x86_64-linux-gnu/hdf5/serial/lib -lhdf5 -lmfhdfalt -ldfalt -logdi -lgif -ljpeg -lgeotiff -ltiff -lpng -L/usr/lib/x86_64-linux-gnu -lpq -llzma -lz -lpthread -lm -lrt -ldl -ldapclient -ldapserver -ldap -L/usr/lib -lspatialite -lpcre -lcurl -lfyba -lfygm -lfyut -lxml2 -L/usr/lib/x86_64-linux-gnu -lmysqlclient -lpthread -lz -lm -lrt -latomic -ldl -lproj -L/opt/conda/lib/R/lib -lR
installing to /opt/conda/lib/R/library/rgdal/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rgdal)

The downloaded source packages are in
        ‘/tmp/RtmposG5Ml/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

I'm pretty new to anaconda, so I may just be misunderstanding something, but this seems bad. Here are the Makeconfs, which are probably key:


r-base=3.5.1=he45234b_1005

# etc/Makeconf.  Generated from Makeconf.in by configure.
#
# ${R_HOME}/etc/Makeconf
#
# R was configured using the following call
# (not including env. vars and site configuration)
# configure  '--prefix=/opt/conda' '--host=x86_64-conda_cos6-linux-gnu' '--build=x86_64-conda_cos6-linux-gnu' '--enable-shared' '--enable-R-shlib' '--enable-BLAS-shlib' '--disable-prebuilt-html' '--enable-memory-profiling' '--with-tk-config=/opt/conda/lib/tkConfig.sh' '--with-tcl-config=/opt/conda/lib/tclConfig.sh' '--with-x' '--with-pic' '--with-cairo' '--with-readline' '--with-recommended-packages=no' '--without-libintl-prefix' 'LIBnn=lib' 'build_alias=x86_64-conda_cos6-linux-gnu' 'host_alias=x86_64-conda_cos6-linux-gnu' 'PKG_CONFIG_PATH=/opt/conda/lib/pkgconfig' 'CC=x86_64-conda_cos6-linux-gnu-cc' 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/opt/conda/lib -L/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/opt/conda/include-Wl,-rpath-link,/opt/conda/lib' 'CPP=/home/conda/feedstock_root/build_artifacts/r-base_1544256230819/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp' 'F77=x86_64-conda_cos6-linux-gnu-gfortran' 'FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix' 'CXX=x86_64-conda_cos6-linux-gnu-c++' 'CXXFLAGS=-fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix' 'OBJC=x86_64-conda_cos6-linux-gnu-cc' 'FC=x86_64-conda_cos6-linux-gnu-gfortran'

## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk

AR = x86_64-conda_cos6-linux-gnu-ar
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas
C_VISIBILITY = -fvisibility=hidden
CC = x86_64-conda_cos6-linux-gnu-cc
CFLAGS = -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix $(LTO)
CPICFLAGS = -fpic
CPPFLAGS = -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib
CXX = x86_64-conda_cos6-linux-gnu-c++
CXXCPP = $(CXX) -E
CXXFLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix $(LTO)
CXXPICFLAGS = -fpic
CXX98 = x86_64-conda_cos6-linux-gnu-c++
CXX98FLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
CXX98PICFLAGS = -fpic
CXX98STD = -std=gnu++98
CXX11 = x86_64-conda_cos6-linux-gnu-c++
CXX11FLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = x86_64-conda_cos6-linux-gnu-c++
CXX14FLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = x86_64-conda_cos6-linux-gnu-c++
CXX17FLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
## NB, set FC before F77 as on Solaris make, setting FC sets F77
FC = x86_64-conda_cos6-linux-gnu-gfortran
FCFLAGS = -g -O2 $(LTO)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS =
F77 = x86_64-conda_cos6-linux-gnu-gfortran
F77_VISIBILITY = -fvisibility=hidden
FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix $(LTO)
FLIBS =  -lgfortran -lm -lgomp -lquadmath -lpthread
FCPICFLAGS = -fpic
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS =
JAR =
JAVA =
JAVAC =
JAVAH =
## JAVA_HOME might be used in the next three.
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME =
JAVA_CPPFLAGS =
JAVA_LIBS =
JAVA_LD_LIBRARY_PATH =
LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRlapack
## we only need this is if it is external, as otherwise link to R
LIBINTL=
LIBM = -lm
LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)"
LIBR1 = -lR
LIBR = -L"$(R_HOME)/lib$(R_ARCH)" -lR
LIBS =  -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -liconv -licuuc -licui18n
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
LDFLAGS = -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/opt/conda/lib -L/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib
LTO =
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp
RPATH_LDFLAGS = -Wl,-rpath,$(abs_top_builddir)/lib -Wl,-rpath,/opt/conda/lib
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) $(RPATH_LDFLAGS)
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
OBJC = x86_64-conda_cos6-linux-gnu-cc
OBJCFLAGS = -g -O2 -fobjc-exceptions $(LTO)
OBJC_LIBS =
OBJCXX =
R_ARCH =
RANLIB = x86_64-conda_cos6-linux-gnu-ranlib
SAFE_FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -msse2 -mfpmath=sse
SED = /bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX98LD = $(CXX98) $(CXX98STD)
SHLIB_CXX98LDFLAGS = -shared
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -shared
SHLIB_FFLAGS =
SHLIB_LD = $(CC)
SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS)
SHLIB_LIBADD =
## We want to ensure libR is picked up from $(R_HOME)/lib
## before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FCFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS =
STRIP_LIBS = x86_64-conda_cos6-linux-gnu-strip --strip-unneeded
STRIP_STATIC_LIBS = x86_64-conda_cos6-linux-gnu-strip --strip-debug
TCLTK_CPPFLAGS = -I/opt/conda/include -I/opt/conda/include
TCLTK_LIBS = -L/opt/conda/lib -ltcl8.6 -L/opt/conda/lib -ltk8.6 -lX11
YACC = yacc

## legacy
CXX1X = x86_64-conda_cos6-linux-gnu-c++
CXX1XFLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
CXX1XPICFLAGS = -fpic
CXX1XSTD = -std=gnu++11
SHLIB_CXX1XLD = $(CXX11) $(CXX11STD)
SHLIB_CXX1XLDFLAGS = -shared


## for linking to libR.a
STATIC_LIBR = # -Wl,--whole-archive "$(R_HOME)/lib$(R_ARCH)/libR.a" -Wl,--no-whole-archive $(BLAS_LIBS) $(FLIBS)  $(LIBINTL) -lreadline  $(LIBS)

R_XTRA_CFLAGS =
R_XTRA_CPPFLAGS =  -I"$(R_INCLUDE_DIR)" -DNDEBUG
R_XTRA_CXXFLAGS =
R_XTRA_FFLAGS =

ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS)
ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
## LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR)# $(LIBINTL)

.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o

.c.o:
        $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
        @echo "making $@ from $<"
        @$(CC) -MM $(ALL_CPPFLAGS) $< > $@
.cc.o:
        $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
        $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
        @echo "making $@ from $<"
        @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.cpp.d:
        @echo "making $@ from $<"
        @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.m.o:
        $(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.m.d:
        @echo "making $@ from $<"
        @x86_64-conda_cos6-linux-gnu-cc -MM $(ALL_CPPFLAGS) $< > $@
.mm.o:
        $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
        $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
        $(F77) $(ALL_FFLAGS) -c $< -o $@
.f95.o:
        $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c  $< -o $@
.f90.o:
        $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c  $< -o $@

r-base=3.5.1=h391c2eb_5

# etc/Makeconf.  Generated from Makeconf.in by configure.
#
# ${R_HOME}/etc/Makeconf
#
# R was configured using the following call
# (not including env. vars and site configuration)
# configure  '--prefix=/opt/conda' '--host=' '--build=x86_64-conda_cos6-linux-gnu' '--enable-shared' '--enable-R-shlib' '--enable-BLAS-shlib' '--disable-prebuilt-html' '--enable-memory-profiling' '--with-tk-config=/opt/conda/lib/tkConfig.sh' '--with-tcl-config=/opt/conda/lib/tclConfig.sh' '--with-x' '--with-pic' '--with-cairo' '--with-readline' '--with-recommended-packages=no' '--without-libintl-prefix' 'LIBnn=lib' 'build_alias=x86_64-conda_cos6-linux-gnu' 'host_alias=' 'PKG_CONFIG_PATH=/opt/conda/lib/pkgconfig' 'CC=gcc' 'CFLAGS= -m64 -fPIC' 'LDFLAGS= -Wl,-rpath,/opt/conda/lib -L/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib' 'CPPFLAGS=  -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib' 'F77=gfortran' 'CXX=g++' 'CXXFLAGS= -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC' 'OBJC=gcc' 'FC=gfortran'

## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk

AR = ar
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas
C_VISIBILITY = -fvisibility=hidden
CC = gcc -std=gnu99
CFLAGS =  -m64 -fPIC $(LTO)
CPICFLAGS = -fpic
CPPFLAGS =   -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib
CXX = g++ 
CXXCPP = $(CXX) -E
CXXFLAGS =  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC $(LTO)
CXXPICFLAGS = -fpic
CXX98 = g++
CXX98FLAGS =  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC
CXX98PICFLAGS = -fpic
CXX98STD = -std=gnu++98
CXX11 = g++
CXX11FLAGS =  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = 
CXX14FLAGS = 
CXX14PICFLAGS = 
CXX14STD = 
CXX17 = 
CXX17FLAGS = 
CXX17PICFLAGS = 
CXX17STD = 
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C = 
ECHO_N = -n
ECHO_T = 
## NB, set FC before F77 as on Solaris make, setting FC sets F77
FC = gfortran
FCFLAGS = -g -O2 $(LTO)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS = 
F77 = gfortran
F77_VISIBILITY = -fvisibility=hidden
FFLAGS = -g -O2 $(LTO)
FLIBS =  -lgfortran -lm -lquadmath
FCPICFLAGS = -fpic
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS = 
FOUNDATION_LIBS = 
JAR = 
JAVA = 
JAVAC = 
JAVAH = 
## JAVA_HOME might be used in the next three.  
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = 
JAVA_CPPFLAGS = 
JAVA_LIBS = 
JAVA_LD_LIBRARY_PATH = 
LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRlapack
## we only need this is if it is external, as otherwise link to R
LIBINTL= 
LIBM = -lm
LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)"
LIBR1 = -lR
LIBR = -L"$(R_HOME)/lib$(R_ARCH)" -lR
LIBS =  -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -liconv -licuuc -licui18n
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
LDFLAGS =  -Wl,-rpath,/opt/conda/lib -L/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib
LTO = 
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp
RPATH_LDFLAGS = -Wl,-rpath,$(abs_top_builddir)/lib -Wl,-rpath,/opt/conda/lib
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) $(RPATH_LDFLAGS)
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
OBJC = 
OBJCFLAGS =  $(LTO)
OBJC_LIBS = 
OBJCXX = 
R_ARCH = 
RANLIB = ranlib
SAFE_FFLAGS = -g -O2 -msse2 -mfpmath=sse
SED = /bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS = 
SHLIB_CXXFLAGS = 
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX98LD = $(CXX98) $(CXX98STD)
SHLIB_CXX98LDFLAGS = -shared
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -shared
SHLIB_FFLAGS = 
SHLIB_LD = $(CC)
SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS)
SHLIB_LIBADD = 
## We want to ensure libR is picked up from $(R_HOME)/lib
## before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FCFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS = -fopenmp
STRIP_LIBS = strip --strip-unneeded
STRIP_STATIC_LIBS = strip --strip-debug
TCLTK_CPPFLAGS = -I/opt/conda/include -I/opt/conda/include 
TCLTK_LIBS = -L/opt/conda/lib -ltcl8.6 -L/opt/conda/lib -ltk8.6 -lX11
YACC = yacc

## legacy
CXX1X = g++
CXX1XFLAGS =  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC
CXX1XPICFLAGS = -fpic
CXX1XSTD = -std=gnu++11
SHLIB_CXX1XLD = $(CXX11) $(CXX11STD)
SHLIB_CXX1XLDFLAGS = -shared


## for linking to libR.a
STATIC_LIBR = # -Wl,--whole-archive "$(R_HOME)/lib$(R_ARCH)/libR.a" -Wl,--no-whole-archive $(BLAS_LIBS) $(FLIBS)  $(LIBINTL) -lreadline  $(LIBS)

R_XTRA_CFLAGS = 
R_XTRA_CPPFLAGS =  -I"$(R_INCLUDE_DIR)" -DNDEBUG
R_XTRA_CXXFLAGS = 
R_XTRA_FFLAGS = 

ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS)
ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
## LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR)# $(LIBINTL)

.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o

.c.o:
	$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
	@echo "making $@ from $<"
	@$(CC) -MM $(ALL_CPPFLAGS) $< > $@
.m.d:
	@echo > $@
.cc.o:
	$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
	$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
	@echo "making $@ from $<"
	@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.cpp.d:
	@echo "making $@ from $<"
	@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.m.o:
	$(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.mm.o:
	$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
	$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
	$(F77) $(ALL_FFLAGS) -c $< -o $@
.f95.o:
	$(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c  $< -o $@
.f90.o:
	$(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c  $< -o $@

windows build failure

Fails with,

2021-01-27T04:17:32.3041470Z starting package maintenance...
2021-01-27T04:17:32.3042999Z installation directory: D:\bld\r-base-split_1611719175201\work\miktex\texmfs\install
2021-01-27T04:17:32.3043690Z package repository: https://mirror.koddos.net/CTAN/systems/win32/miktex/tm/packages/
2021-01-27T04:17:32.3044349Z package repository digest: a12a9bc1e37031628ebb2a1c20736606
2021-01-27T04:17:32.3044859Z going to download 478244 bytes
2021-01-27T04:17:32.3045347Z going to install 192 file(s) (1 package(s))
2021-01-27T04:17:32.3045971Z downloading https://mirror.koddos.net/CTAN/systems/win32/miktex/tm/packages/inconsolata.tar.lzma...
2021-01-27T04:17:32.3046935Z ======================================================================
2021-01-27T04:17:32.3047362Z 
2021-01-27T04:17:32.3047719Z 
2021-01-27T04:17:32.3439557Z ! LaTeX Error: File `inconsolata.sty' not found.
2021-01-27T04:17:32.3440999Z 
2021-01-27T04:17:32.3441462Z Type X to quit or <RETURN> to proceed,
2021-01-27T04:17:32.3441938Z or enter new name. (Default extension: sty)
2021-01-27T04:17:32.3442344Z 
2021-01-27T04:17:32.3451138Z Unfortunately, the package inconsolata could not be installed.
2021-01-27T04:17:32.3467188Z Please check the log file:
2021-01-27T04:17:32.3477145Z D:\bld\r-base-split_1611719175201\work\miktex\texmfs\data\miktex\log\pdflatex.log

No PNG support in R 3.4.1-hff14c37_5

Issue: I just created a new environment with
conda create -n bioc r-base=3.4.1 rstudio r-tidyverse bioconductor-deseq2 bioconductor-edger bioconductor-biostrings bioconductor-bsgenome
And there isn't PNG support

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE       FALSE       FALSE        TRUE        TRUE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE        TRUE       FALSE        TRUE        TRUE        TRUE 

I tested an environment with R=3.4.3-4 and png was supported, but rstudio needs r-base 3.4.1-hff14c37_5 which apparently has this problem.

r-base: 3.4.1-4 conda-forge --> 3.4.1-hff14c37_5 conda-forge


Environment (conda list):
$ conda list
# packages in environment at /media/mibu/Storage_SSD/Miniconda3/envs/bioconductor:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0                     mro_2  
backcall                  0.1.0                      py_0    conda-forge
binutils_impl_linux-64    2.28.1               had2808c_3  
binutils_linux-64         7.2.0               had2808c_27  
bioconductor-annotate     1.56.0                 r3.4.1_0    bioconda
bioconductor-annotationdbi 1.40.0                 r3.4.1_0    bioconda
bioconductor-biobase      2.38.0                 r3.4.1_0    bioconda
bioconductor-biocgenerics 0.24.0                 r3.4.1_0    bioconda
bioconductor-biocparallel 1.12.0                 r3.4.1_0    bioconda
bioconductor-biostrings   2.46.0                 r3.4.1_0    bioconda
bioconductor-bsgenome     1.46.0                 r3.4.1_0    bioconda
bioconductor-delayedarray 0.4.1                  r3.4.1_0    bioconda
bioconductor-deseq2       1.18.1                 r3.4.1_1    bioconda
bioconductor-edger        3.20.7                 r3.4.1_0    bioconda
bioconductor-genefilter   1.60.0                 r3.4.1_0    bioconda
bioconductor-geneplotter  1.56.0                 r3.4.1_0    bioconda
bioconductor-genomeinfodb 1.14.0                 r3.4.1_0    bioconda
bioconductor-genomeinfodbdata 1.0.0                  r3.4.1_1    bioconda
bioconductor-genomicalignments 1.14.1                 r3.4.1_0    bioconda
bioconductor-genomicranges 1.30.3                 r3.4.1_0    bioconda
bioconductor-iranges      2.12.0                 r3.4.1_0    bioconda
bioconductor-limma        3.34.9                 r3.4.1_0    bioconda
bioconductor-rsamtools    1.30.0                 r3.4.1_0    bioconda
bioconductor-rtracklayer  1.38.3                 r3.4.1_0    bioconda
bioconductor-s4vectors    0.16.0                 r3.4.1_0    bioconda
bioconductor-summarizedexperiment 1.8.0                  r3.4.1_0    bioconda
bioconductor-tximport     1.6.0                  r3.4.1_0    bioconda
bioconductor-xvector      0.18.0                 r3.4.1_0    bioconda
bioconductor-zlibbioc     1.24.0                 r3.4.1_0    bioconda
bleach                    1.4.2                    py36_0    bioconda
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2018.4.16                     0    conda-forge
cairo                     1.14.12              h77bcde2_0  
certifi                   2018.4.16                py36_0    conda-forge
curl                      7.60.0                        0    conda-forge
cyrus-sasl                2.1.26                        1    conda-forge
dbus                      1.13.0               h3a4f0e9_0    conda-forge
decorator                 4.3.0                      py_0    conda-forge
entrypoints               0.2.3                    py36_1    conda-forge
expat                     2.2.5                hfc679d8_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 h6964260_0  
font-ttf-inconsolata      2.001                hcb22688_0  
font-ttf-source-code-pro  2.030                h7457263_0  
font-ttf-ubuntu           0.83                 h8b1ccd4_0  
fontconfig                2.12.6                        0    conda-forge
fonts-anaconda            1                    h8fa9717_0  
freetype                  2.8.1                         0    conda-forge
fribidi                   1.0.4                h14c3975_0  
gcc_impl_linux-64         7.2.0                habb00fd_3  
gcc_linux-64              7.2.0               h550dcbe_27  
gfortran_impl_linux-64    7.2.0                hdf63c60_3  
gfortran_linux-64         7.2.0               h550dcbe_27  
glib                      2.53.6               h5d9569c_2  
gmp                       6.1.2                hfc679d8_0    conda-forge
graphite2                 1.3.11               hfc679d8_0    conda-forge
gsl                       2.1                           2    conda-forge
gst-plugins-base          1.8.0                         0    conda-forge
gstreamer                 1.8.0                         1    conda-forge
gxx_impl_linux-64         7.2.0                hdf63c60_3  
gxx_linux-64              7.2.0               h550dcbe_27  
harfbuzz                  1.7.6                hc5b324e_0  
html5lib                  1.0.1                      py_0    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
ipykernel                 4.8.2                    py36_0    conda-forge
ipython                   6.4.0                    py36_0    conda-forge
ipython_genutils          0.2.0                    py36_0    conda-forge
jedi                      0.12.0                   py36_0    conda-forge
jinja2                    2.10                     py36_0    conda-forge
jpeg                      9c                   h470a237_0    conda-forge
jsonschema                2.6.0                    py36_1    conda-forge
jupyter_client            5.2.3                    py36_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
krb5                      1.14.6                        0    conda-forge
libedit                   3.1.20170329         haf1bffa_0    conda-forge
libffi                    3.2.1                         3    conda-forge
libgcc                    7.2.0                h69d50b8_2  
libgcc-ng                 7.2.0                hdf63c60_3  
libgfortran-ng            7.2.0                hdf63c60_3  
libiconv                  1.15                 h470a237_1    conda-forge
libntlm                   1.4                  h470a237_1    conda-forge
libpng                    1.6.34               ha92aebf_1    conda-forge
libsodium                 1.0.16                        0    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3  
libtiff                   4.0.9                he6b73bb_1    conda-forge
libuuid                   1.0.3                         1    conda-forge
libxcb                    1.13                 h470a237_0    conda-forge
libxml2                   2.9.8                h422b904_1    conda-forge
markupsafe                1.0                      py36_0    conda-forge
mistune                   0.8.3                    py36_1    conda-forge
mro-base                  3.4.3                h1c2f66e_0  
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                    py36_0    conda-forge
ncurses                   6.1                           0    conda-forge
notebook                  5.5.0                    py36_0    conda-forge
openssl                   1.0.2o                        0    conda-forge
pandoc                    2.2.1                         0    conda-forge
pandocfilters             1.4.2                    py36_0    conda-forge
pango                     1.42.0               h377f3fa_0  
parso                     0.3.0                      py_0    conda-forge
pcre                      8.39                          0    conda-forge
pexpect                   4.6.0                    py36_0    conda-forge
pickleshare               0.7.4                    py36_0    conda-forge
pip                       9.0.3                    py36_0    conda-forge
pixman                    0.34.0                        2    conda-forge
prompt_toolkit            1.0.15                   py36_0    conda-forge
ptyprocess                0.6.0                    py36_0    conda-forge
pygments                  2.2.0                    py36_0    conda-forge
python                    3.6.4                hc3d631a_1  
python-dateutil           2.7.3                      py_0    conda-forge
pyzmq                     17.0.0                   py36_4    conda-forge
qt                        5.6.2                         7    conda-forge
r-abind                   1.4_5                  r3.4.1_0    conda-forge
r-acepack                 1.4.1                  r3.4.1_0    conda-forge
r-assertthat              0.2.0                  r3.4.1_0    conda-forge
r-backports               1.1.2                  r3.4.1_0    conda-forge
r-base                    3.4.1                hff14c37_5    conda-forge
r-base64enc               0.1_3                  r3.4.1_0    conda-forge
r-bh                      1.66.0_1               r3.4.1_0    conda-forge
r-bindr                   0.1.1                  r3.4.1_0    conda-forge
r-bindrcpp                0.2                    r3.4.1_0    conda-forge
r-bit                     1.1_12                 r3.4.1_0    conda-forge
r-bit64                   0.9_5                  r3.4.1_0    conda-forge
r-bitops                  1.0_6                  r3.4.1_0    conda-forge
r-blob                    1.1.1                  r3.4.1_0    conda-forge
r-boot                    1.3_20                 r3.4.1_0    conda-forge
r-broom                   0.4.4                  r3.4.1_0    conda-forge
r-caret                   6.0_79                 r3.4.1_0    conda-forge
r-catools                 1.17.1                 r3.4.1_0    conda-forge
r-cellranger              1.1.0                  r3.4.1_0    conda-forge
r-checkmate               1.8.5                  r3.4.1_0    conda-forge
r-class                   7.3_14                 r3.4.1_0    conda-forge
r-cli                     1.0.0                  r3.4.1_0    conda-forge
r-cluster                 2.0.6                  r3.4.1_0    conda-forge
r-codetools               0.2_15                 r3.4.1_0    conda-forge
r-colorspace              1.3_2                  r3.4.1_0    conda-forge
r-config                  0.2                    r3.4.1_0    conda-forge
r-crayon                  1.3.4                  r3.4.1_0    conda-forge
r-curl                    3.2                    r3.4.1_0    conda-forge
r-cvst                    0.2_1                  r3.4.1_0    conda-forge
r-data.table              1.10.4                 r3.4.1_0    bioconda
r-dbi                     1.0.0                    r341_0    conda-forge
r-dbplyr                  1.2.1                    r341_1    conda-forge
r-ddalpha                 1.3.4                    r341_0    conda-forge
r-deoptimr                1.0_8                  r3.4.1_0    bioconda
r-dichromat               2.0_0                  r3.4.1_0    conda-forge
r-digest                  0.6.15                 r3.4.1_0    conda-forge
r-dimred                  0.1.0                  r3.4.1_0    conda-forge
r-dplyr                   0.7.4                  r3.4.1_0    conda-forge
r-drr                     0.0.3                  r3.4.1_0    conda-forge
r-essentials              3.4.1                  r3.4.1_0    conda-forge
r-evaluate                0.10.1                 r3.4.1_0    conda-forge
r-forcats                 0.3.0                  r3.4.1_0    conda-forge
r-foreach                 1.4.4                  r3.4.1_0    conda-forge
r-foreign                 0.8_67                 r3.4.1_0    conda-forge
r-formatr                 1.5                    r3.4.1_0    conda-forge
r-formula                 1.2_1                  r3.4.1_0    conda-forge
r-futile.logger           1.4.3                  r3.4.1_0    conda-forge
r-futile.options          1.0.0                  r3.4.1_0    conda-forge
r-gdata                   2.18.0                 r3.4.1_0    conda-forge
r-geometry                0.3_6                  r3.4.1_0    conda-forge
r-getopt                  1.20.2                 r3.4.1_0    conda-forge
r-ggplot2                 2.2.1                  r3.4.1_0    conda-forge
r-gistr                   0.4.2                    r341_0    conda-forge
r-glmnet                  2.0_5                  r3.4.1_0    conda-forge
r-glue                    1.2.0                  r3.4.1_0    conda-forge
r-gower                   0.1.2                  r3.4.1_0    conda-forge
r-gplots                  3.0.1                  r3.4.1_0    conda-forge
r-gridextra               2.3                    r3.4.1_0    conda-forge
r-gtable                  0.2.0                  r3.4.1_0    conda-forge
r-gtools                  3.8.1                    r341_0    conda-forge
r-haven                   1.1.2                    r341_0    conda-forge
r-hexbin                  1.27.2                 r3.4.1_0    conda-forge
r-highr                   0.7                      r341_0    conda-forge
r-hmisc                   4.0_3                  r3.4.1_0    conda-forge
r-hms                     0.3                    r3.4.1_0    conda-forge
r-htmltable               1.9                    r3.4.1_0    conda-forge
r-htmltools               0.3.6                  r3.4.1_0    conda-forge
r-htmlwidgets             1.0                    r3.4.1_0    conda-forge
r-httpuv                  1.3.6.2                r3.4.1_0    conda-forge
r-httr                    1.3.1                  r3.4.1_0    conda-forge
r-ipred                   0.9_6                  r3.4.1_0    conda-forge
r-irdisplay               0.4.4                  r3.4.1_0    conda-forge
r-irkernel                0.8.11                 r3.4.1_0    conda-forge
r-iterators               1.0.9                  r3.4.1_0    conda-forge
r-jsonlite                1.5                    r3.4.1_0    conda-forge
r-kernlab                 0.9_25                 r3.4.1_0    conda-forge
r-kernsmooth              2.23_15                r3.4.1_0    conda-forge
r-knitr                   1.20                   r3.4.1_0    conda-forge
r-labeling                0.3                    r3.4.1_0    conda-forge
r-lambda.r                1.2                    r3.4.1_0    conda-forge
r-lattice                 0.20_34                r3.4.1_0    conda-forge
r-latticeextra            0.6_28                 r3.4.1_0    conda-forge
r-lava                    1.6.1                  r3.4.1_0    conda-forge
r-lazyeval                0.2.1                  r3.4.1_0    conda-forge
r-locfit                  1.5_9.1                r3.4.1_0    conda-forge
r-lubridate               1.7.4                  r3.4.1_0    conda-forge
r-magic                   1.5_6                  r3.4.1_0    conda-forge
r-magrittr                1.5                    r3.4.1_0    conda-forge
r-maps                    3.3.0                  r3.4.1_0    conda-forge
r-markdown                0.8                    r3.4.1_1    conda-forge
r-mass                    7.3_48                 r3.4.1_0    conda-forge
r-matrix                  1.2_14                 r3.4.1_0    conda-forge
r-matrixstats             0.53.1                   r341_0    conda-forge
r-memoise                 1.1.0                  r3.4.1_0    conda-forge
r-mgcv                    1.8_24                   r341_0    conda-forge
r-mime                    0.5                    r3.4.1_0    conda-forge
r-miniui                  0.1.1                  r3.4.1_0    conda-forge
r-mnormt                  1.5_5                  r3.4.1_0    conda-forge
r-modelmetrics            1.1.0                  r3.4.1_0    conda-forge
r-modelr                  0.1.2                    r341_0    conda-forge
r-mongolite               1.4             mro343h086d26f_0  
r-munsell                 0.5.0                    r341_0    conda-forge
r-nlme                    3.1_131                r3.4.1_0    conda-forge
r-nnet                    7.3_12                 r3.4.1_0    conda-forge
r-numderiv                2016.8_1               r3.4.1_0    conda-forge
r-odbc                    1.1.3           mro343h599a50d_0  
r-openssl                 1.0.1                  r3.4.1_0    conda-forge
r-packrat                 0.4.9                  r3.4.1_0    conda-forge
r-pbdzmq                  0.3_2                  r3.4.1_0    conda-forge
r-pillar                  1.2.2            r341h6115d3f_1    conda-forge
r-pkgconfig               2.0.1                  r3.4.1_0    conda-forge
r-pki                     0.1_3                  r3.4.1_0    conda-forge
r-plogr                   0.1_1                  r3.4.1_0    conda-forge
r-pls                     2.6_0                  r3.4.1_0    conda-forge
r-plyr                    1.8.4                  r3.4.1_0    conda-forge
r-prettyunits             1.0.2                  r3.4.1_0    conda-forge
r-prodlim                 2018.04.18             r3.4.1_0    conda-forge
r-profvis                 0.3.4           mro343h086d26f_0  
r-pryr                    0.1.4                  r3.4.1_0    conda-forge
r-psych                   1.5.8                  r3.4.1_0    bioconda
r-purrr                   0.2.4                  r3.4.1_0    conda-forge
r-quantmod                0.4_8                  r3.4.1_0    conda-forge
r-r6                      2.2.2                  r3.4.1_0    conda-forge
r-randomforest            4.6_12                 r3.4.1_0    conda-forge
r-rappdirs                0.3.1                  r3.4.1_0    conda-forge
r-rbokeh                  0.5.0                  r3.4.1_0    conda-forge
r-rcolorbrewer            1.1_2                  r3.4.1_0    conda-forge
r-rcpp                    0.12.15                r3.4.1_0    conda-forge
r-rcpparmadillo           0.8.500.0              r3.4.1_0    conda-forge
r-rcpproll                0.2.2                  r3.4.1_0    conda-forge
r-rcurl                   1.95_4.8               r3.4.1_0    conda-forge
r-readr                   1.1.1                  r3.4.1_0    conda-forge
r-readxl                  1.1.0                    r341_0    conda-forge
r-recipes                 0.1.3                    r341_0    conda-forge
r-recommended             3.4.1                  r3.4.1_0    conda-forge
r-rematch                 1.0.1                  r3.4.1_0    conda-forge
r-repr                    0.15                     r341_0    conda-forge
r-reshape2                1.4.3                  r3.4.1_0    conda-forge
r-rjava                   0.9_9           mro343h086d26f_0  
r-rjdbc                   0.2_5           mro343h889e2dd_0  
r-rjson                   0.2.15                 r3.4.1_0    conda-forge
r-rjsonio                 1.3_0                  r3.4.1_0    conda-forge
r-rlang                   0.2.1                    r341_0    conda-forge
r-rmarkdown               1.9                      r341_0    conda-forge
r-robustbase              0.92_7                 r3.4.1_0    conda-forge
r-rpart                   4.1_13                 r3.4.1_0    conda-forge
r-rprojroot               1.3_2                  r3.4.1_0    conda-forge
r-rsconnect               0.8.5           mro343h889e2dd_0  
r-rsqlite                 2.0                    r3.4.1_0    conda-forge
r-rstudioapi              0.7                    r3.4.1_0    conda-forge
r-rvest                   0.3.2                  r3.4.1_0    conda-forge
r-scales                  0.5.0                  r3.4.1_0    conda-forge
r-selectr                 0.3_1                  r3.4.1_0    conda-forge
r-sfsmisc                 1.1_1                  r3.4.1_0    conda-forge
r-shiny                   1.0.5                  r3.4.1_0    conda-forge
r-snow                    0.4_2                  r3.4.1_0    conda-forge
r-sourcetools             0.1.6                  r3.4.1_0    conda-forge
r-sparklyr                0.8.2                  r3.4.1_0    conda-forge
r-spatial                 7.3_11                 r3.4.1_0    conda-forge
r-squarem                 2017.10_1              r3.4.1_0    conda-forge
r-stringi                 1.1.7                  r3.4.1_1    conda-forge
r-stringr                 1.3.0                  r3.4.1_0    conda-forge
r-survival                2.40_1                 r3.4.1_0    conda-forge
r-tibble                  1.4.2                  r3.4.1_0    conda-forge
r-tidyr                   0.8.1                    r341_0    conda-forge
r-tidyselect              0.2.4                  r3.4.1_0    conda-forge
r-tidyverse               1.1.1                  r3.4.1_0    conda-forge
r-timedate                3012.100               r3.4.1_0    conda-forge
r-ttr                     0.23_1                 r3.4.1_0    conda-forge
r-utf8                    1.1.3                  r3.4.1_0    conda-forge
r-uuid                    0.1_2                  r3.4.1_0    conda-forge
r-viridis                 0.5.1                  r3.4.1_0    conda-forge
r-viridislite             0.3.0                  r3.4.1_0    conda-forge
r-withr                   2.1.1                  r3.4.1_0    conda-forge
r-xml                     3.98_1.6               r3.4.1_0    conda-forge
r-xml2                    1.2.0                    r341_0    conda-forge
r-xtable                  1.8_2                  r3.4.1_0    conda-forge
r-xts                     0.10_1                 r3.4.1_0    conda-forge
r-yaml                    2.1.18                 r3.4.1_0    conda-forge
r-zoo                     1.8_1                  r3.4.1_0    conda-forge
readline                  7.0                  ha6073c6_4  
rstudio                   1.1.383              h2c9cdda_2  
send2trash                1.5.0                      py_0    conda-forge
setuptools                39.2.0                   py36_0    conda-forge
simplegeneric             0.8.1                    py36_0    conda-forge
six                       1.11.0                   py36_1    conda-forge
sqlite                    3.20.1                        0    conda-forge
terminado                 0.8.1                    py36_0    conda-forge
testpath                  0.3.1                    py36_0    conda-forge
tk                        8.6.7                         0    conda-forge
tornado                   5.0.2                    py36_0    conda-forge
traitlets                 4.3.2                    py36_0    conda-forge
unixodbc                  2.3.5                h09ba92c_1    conda-forge
wcwidth                   0.1.7                    py36_0    conda-forge
webencodings              0.5                      py36_0    conda-forge
wget                      1.19.5               h1ad7b7a_0  
wheel                     0.31.0                   py36_0    conda-forge
xorg-kbproto              1.0.7                h470a237_2    conda-forge
xorg-libice               1.0.9                         2    conda-forge
xorg-libsm                1.2.2                         2    conda-forge
xorg-libx11               1.6.5                         0    conda-forge
xorg-libxau               1.0.8                h470a237_4    conda-forge
xorg-libxdmcp             1.1.2                h470a237_4    conda-forge
xorg-libxext              1.3.3                         2    conda-forge
xorg-libxrender           0.9.10                        0    conda-forge
xorg-renderproto          0.11.1               h470a237_2    conda-forge
xorg-xextproto            7.3.0                h470a237_2    conda-forge
xorg-xproto               7.0.31               h470a237_7    conda-forge
xz                        5.2.3                         0    conda-forge
zeromq                    4.2.5                hfc679d8_3    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge


Details about conda and system ( conda info ):
$ conda info
active environment : bioc
    active env location : /media/mibu/Storage_SSD/Miniconda3/envs/bioc
            shell level : 1
       user config file : /home/mibu/.condarc
 populated config files : /home/mibu/.condarc
          conda version : 4.5.5
    conda-build version : not installed
         python version : 3.6.5.final.0
       base environment : /media/mibu/Storage_SSD/Miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /media/mibu/Storage_SSD/Miniconda3/pkgs
                          /home/mibu/.conda/pkgs
       envs directories : /media/mibu/Storage_SSD/Miniconda3/envs
                          /home/mibu/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.5 requests/2.18.4 CPython/3.6.5 Linux/4.14.52-1-MANJARO manjaro/17.1.11 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False


Add {{ compiler('c') }} to runtime dependencies

I think it might be a good idea to add {{ compiler('c') }} to the runtime dependencies of r-base. This way, we could ensure that people can install R packages from within R while getting a compatible build environment. This could solve problems like this one.

I know this is somehow an unusual move, but it is very common to manually install stuff in R and people are suprised when it does not work, which causes quite some trouble for e.g. the bioconductor community.

@mingwandroid @bgruening thoughts?

Packages installed via `install.packages` in R conflict with packages installed via `conda`.

Issue:

Packages installed via install.packages in R conflict with packages installed via conda.

Reproduction steps

Here is an example to demonstrate this problem:

  1. Create and activate a conda environment with the r-brio package:
 ~ $ mamba create -n rtest1 r-base r-brio 
<snip>
Executing transaction: done
<snip>
 ~ $ conda activate rtest1
  1. Use R to install the brio package
~ $ Rscript -e "install.packages('brio', repos='https://cran.rstudio.com')"
trying URL 'https://cran.rstudio.com/src/contrib/brio_1.1.2.tar.gz'
Content type 'application/x-gzip' length 12069 bytes (11 KB)
==================================================
downloaded 11 KB

* installing *source* package ‘brio’ ...
<snip>
* DONE (brio)
  1. Try to create another conda environment with the r-brio package and watch the carnage
 ~ $ mamba create -n rtest2 r-base r-brio 
<snip>
Verifying transaction: / 
SafetyError: The package for r-base located at /home/izahn/.conda/pkgs/r-base-4.0.5-h8cab1ac_0
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
  reported size: 2946 bytes
  actual size: 3102 bytes

done
Executing transaction: done

Cleanup

The mess (intentionally) created above can be cleaned up be deleting the environments and cleaning out unused packages:

 ~ [1] $ conda deactivate
 ~ $ mamba env remove -n rtest1

Remove all packages in environment /home/izahn/.conda/envs/rtest1:

 ~ $ mamba env remove -n rtest2

Remove all packages in environment /home/izahn/.conda/envs/rtest2:

 ~ $ conda clean --yes --all

Proposed solution

I propose that we fix this problem by creating the site-library directory when building the r-base package. Here is a demonstration showing that this solves the problem:

  1. Create conda environment with r-brio as before
 ~ $ mamba create -n rtest1 r-base r-brio

<snip>

Finished r-base                               (00m:03s)              24 MB     28 MB/s
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
  1. Create the site-library directory this is the crucial step
 ~ $ mkdir ~/.conda/envs/rtest1/lib/R/site-library
  1. Activate environment and install brio with install.packages, as before
 ~ $ conda activate rtest1
 ~ $ Rscript -e "install.packages('brio', repos='https://cran.rstudio.com')"  
Installing package into ‘/home/izahn/.conda/envs/rtest1/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/brio_1.1.2.tar.gz'
Content type 'application/x-gzip' length 12069 bytes (11 KB)
==================================================
downloaded 11 KB

* installing *source* package ‘brio’ ...
<snip>
* DONE (brio)
  1. Create another conda environment including r-brio -- all good!
 ~ $ mamba create -n rtest2 r-base r-brio 
<snip>
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate rtest2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

I'm happy to make a PR including the proposed change, but I wanted to propose and discuss it here first to see if there are any objections or concerns.


Details about conda and system ( conda info ):
$ conda info

 active environment : mamba
active env location : /home/izahn/.conda/envs/mamba
        shell level : 1
   user config file : /home/izahn/.condarc

populated config files : /opt/mambaforge/.condarc
/home/izahn/.condarc
conda version : 4.10.1
conda-build version : not installed
python version : 3.9.2.final.0
virtual packages : __linux=5.12.2=0
__glibc=2.33=0
__unix=0=0
__archspec=1=x86_64
base environment : /opt/mambaforge (read only)
conda av data dir : /opt/mambaforge/etc/conda
conda av metadata url : https://repo.anaconda.com/pkgs/main
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/izahn/.conda/pkgs
envs directories : /home/izahn/.conda/envs
/opt/mambaforge/envs
platform : linux-64
user-agent : conda/4.10.1 requests/2.25.1 CPython/3.9.2 Linux/5.12.2-arch1-1 arch/rolling glibc/2.33
UID:GID : 1000:1000
netrc file : None
offline mode : False

Proposal: Drop support for R 3.3.2

Summary

I propose we stop building conda-forge R packages for R 3.3.2.

cc: @conda-forge/r-base @isuruf

Motivation

  • We are struggling to update the pins for R 3.3.2. If we can't update the pins, then we are unable to add some non-R dependencies for the recipes, which I consider one of the main advantages of using conda for R. I've made some attempts to patch R 3.3.2, but my efforts were motivated more by curiosity than any practical need: #28 #31 #32 #33

  • R 3.3.2 is getting dated and more and more R packages don't even support it, e.g. libcoin and uniqueAtomMat

  • The defaults channel is adding a dependency to all R packages (#34). Dropping support for R 3.3.2 packages will reduce the number that need to be rebuilt.

  • I have gone through and rerendered all the R feedstocks that needed to be built for R 3.3.2 (with help from @rvalieris). Any R feedstock not built for R 3.3.2 at this point is because either it or a dependency is failing to build for a non-trivial reason.

  • Based on the development patterns of the R core team, we can expect R 3.5.1 to be released near the end of June 2018, at which point we can start building the R packages for both 3.4.1 and 3.5.1.

Actions to be taken

If we decide to drop support for R 3.3.2, we'll need to do the following:

RStudio fails with R 3.4.1

Issue:
Although RStudio works with the latest r-base:

$ conda install -c conda-forge -c r r-base rstudio
$ rstudio

I find that it fails with version 3.4.1:

$ conda install -c conda-forge -c r r=3.4.1 rstudio
$ rstudio

Environment (conda list):
$ conda list
# packages in environment at /Users/david.hall/miniconda3/envs/test2:
#
# Name                    Version                   Build  Channel
ca-certificates           2018.8.24            ha4d7672_0    conda-forge
cairo                     1.14.12              he6fea26_5    conda-forge
clangdev                  6.0.1                 default_1    conda-forge
curl                      7.61.0               h93b3f91_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 h6964260_0
font-ttf-inconsolata      2.001                hcb22688_0
font-ttf-source-code-pro  2.030                h7457263_0
font-ttf-ubuntu           0.83                 h8b1ccd4_0
fontconfig                2.13.0               hce039c3_5    conda-forge
fonts-anaconda            1                    h8fa9717_0
freetype                  2.9.1                h6debe1e_1    conda-forge
gettext                   0.19.8.1                      0    conda-forge
glib                      2.55.0               h464dc38_2    conda-forge
graphite2                 1.3.12               h7d4d677_1    conda-forge
gsl                       2.1                           2    conda-forge
harfbuzz                  1.8.8                h08d66d9_0    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
jpeg                      9c                   h470a237_0    conda-forge
krb5                      1.14.6                        0    conda-forge
libcxx                    6.0.1                         0    conda-forge
libedit                   3.1.20170329                  0    conda-forge
libffi                    3.2.1                hfc679d8_4    conda-forge
libgcc                    4.8.5                         1    conda-forge
libiconv                  1.15                 h470a237_2    conda-forge
libpng                    1.6.34               ha92aebf_1    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libtiff                   4.0.9                he6b73bb_1    conda-forge
libxml2                   2.9.8                h422b904_3    conda-forge
llvm-meta                 6.0.1                         0    conda-forge
llvmdev                   6.0.1                hf8ce74a_2    conda-forge
ncurses                   5.9                          10    conda-forge
openssl                   1.0.2o               h470a237_1    conda-forge
pandoc                    2.2.2                hde52d81_1    conda-forge
pango                     1.40.14              he752989_2    conda-forge
pcre                      8.39                          0    conda-forge
pixman                    0.34.0                        2    conda-forge
r                         3.4.1                  r3.4.1_0    conda-forge
r-base                    3.4.1                         4    conda-forge
r-boot                    1.3_19                 r3.4.1_0    r
r-class                   7.3_14                 r3.4.1_0    r
r-cluster                 2.0.6                  r3.4.1_0    r
r-codetools               0.2_15                 r3.4.1_0    r
r-foreign                 0.8_68                 r3.4.1_0    r
r-kernsmooth              2.23_15                r3.4.1_0    r
r-lattice                 0.20_35                r3.4.1_0    r
r-mass                    7.3_47                 r3.4.1_0    r
r-matrix                  1.2_10                 r3.4.1_0    r
r-mgcv                    1.8_17                 r3.4.1_0    r
r-nlme                    3.1_131                r3.4.1_0    r
r-nnet                    7.3_12                 r3.4.1_0    r
r-recommended             3.4.1                  r3.4.1_0    r
r-rpart                   4.1_11                 r3.4.1_0    r
r-spatial                 7.3_11                 r3.4.1_0    r
r-survival                2.41_3                 r3.4.1_0    r
readline                  7.0                           0    conda-forge
rstudio                   1.1.456              h04f5b5a_0    r
tk                        8.6.8                         0    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ):
$ conda info

     active environment : test2
    active env location : /Users/david.hall/miniconda3/envs/test2
            shell level : 1
       user config file : /Users/david.hall/.condarc
 populated config files : /Users/david.hall/.condarc
          conda version : 4.5.11
    conda-build version : 3.12.1
         python version : 3.6.5.final.0
       base environment : /Users/david.hall/miniconda3  (writable)
           channel URLs : s3://dataeng-conda/osx-64
                          s3://dataeng-conda/noarch
                          https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/osx-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /Users/david.hall/miniconda3/pkgs
                          /Users/david.hall/.conda/pkgs
       envs directories : /Users/david.hall/miniconda3/envs
                          /Users/david.hall/.conda/envs
               platform : osx-64
             user-agent : conda/4.5.11 requests/2.18.4 CPython/3.6.5 Darwin/17.7.0 OSX/10.13.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False

deactivate-r-base.sh not installed with `r-base`

Issue:

Conda environment with r-base sets environment variable RSTUDIO_WHICH_R from $CONDA_PREFIX/etc/conda/activate.d/activate-r-base.sh, but does not reset to initial state upon deactivation.
This state will keep RSTUDIO_WHICH_R set to a specific environment install or R, which can crash rstudio in some cases.

Although the deactivate script exists in the repo, its installation was removed from build.sh a few months ago.

PR #69 is intended to fix this.


Environment (conda list):
$ conda list
# packages in environment at /local/conda/envs/R-test:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1
binutils_impl_linux-64    2.31.1               h6176602_1    conda-forge
binutils_linux-64         2.31.1               h6176602_3    conda-forge
bwidget                   1.9.11                        1
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.14.12           h80bd089_1005    conda-forge
curl                      7.64.0               h646f8bb_0    conda-forge
fontconfig                2.13.1            h2176d3f_1000    conda-forge
freetype                  2.9.1             h94bbf69_1005    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_3    conda-forge
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_1    conda-forge
gfortran_linux-64         7.3.0                h553295d_3    conda-forge
glib                      2.56.2            had28632_1001    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1    conda-forge
gxx_linux-64              7.3.0                h553295d_3    conda-forge
harfbuzz                  1.9.0             he243708_1001    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.16.3            hc83ff2d_1000    conda-forge
libcurl                   7.64.0               h01ee5af_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             hf484d3e_1005    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgfortran-ng            7.3.0                hdf63c60_0
libiconv                  1.15              h14c3975_1004    conda-forge
libpng                    1.6.36            h84994c4_1000    conda-forge
libssh2                   1.8.0             h1ad7b7a_1003    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtiff                   4.0.10            h648cc4a_1001    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
make                      4.2.1             h14c3975_2004    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openssl                   1.0.2p            h14c3975_1002    conda-forge
pango                     1.40.14           hf0c64fd_1003    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
pixman                    0.34.0            h14c3975_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
r-base                    3.5.1             he45234b_1005    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
tk                        8.6.9             h84994c4_1000    conda-forge
tktable                   2.10                 h14c3975_0
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h14c3975_1004    conda-forge
xorg-libsm                1.2.3             h4937e3b_1000    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.2             h14c3975_1007    conda-forge
xorg-libxext              1.3.3             h14c3975_1004    conda-forge
xorg-libxrender           0.9.10            h14c3975_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge

Details about conda and system ( conda info ):
$ conda info

     active environment : R-test
    active env location : /local/conda/envs/R-test
            shell level : 1
       user config file : /some/remote/.condarc
 populated config files : /local/conda/.condarc
                          /some/remote/.condarc
          conda version : 4.5.12
    conda-build version : not installed
         python version : 3.6.6.final.0
       base environment : /local/conda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /some/remote/pkgs_cache
       envs directories : /local/conda/envs
                          /some/remote/conda_envs
               platform : linux-64
             user-agent : conda/4.5.12 requests/2.19.1 CPython/3.6.6 Linux/3.10.0-862.11.6.el7.x86_64 centos/7 glibc/2.17
                UID:GID : 21075:21000
             netrc file : None
           offline mode : False

R on ARM Mac M1:load failed for ‘stats’ and Rlog1p error

Issue:


Environment (conda list):
$ conda list
# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
bwidget                   1.9.14               hce30654_0    conda-forge
bzip2                     1.0.8                h27ca646_4    conda-forge
c-ares                    1.17.1               h27ca646_1    conda-forge
ca-certificates           2020.12.5            h4653dfc_0    conda-forge
cairo                     1.16.0            h11c81c9_1007    conda-forge
cctools_osx-arm64         949.0.1             h1c8944f_20    conda-forge
clang                     11.1.0               hce30654_0    conda-forge
clang-11                  11.1.0          default_h87665d4_0    conda-forge
clang_osx-arm64           11.1.0               h54d7cd3_0    conda-forge
clangxx                   11.1.0          default_hbe4449c_0    conda-forge
clangxx_osx-arm64         11.1.0               hb84c830_0    conda-forge
compiler-rt               11.1.0               h7d99272_0    conda-forge
compiler-rt_osx-arm64     11.1.0               h103ad0d_0    conda-forge
curl                      7.75.0               hb25ae9e_0    conda-forge
fontconfig                2.13.1            h751047c_1004    conda-forge
freetype                  2.10.4               h17b34a0_1    conda-forge
fribidi                   1.0.10               h27ca646_0    conda-forge
gettext                   0.19.8.1          hea66d9f_1005    conda-forge
gfortran_impl_osx-arm64   11.0.1.dev0         h4f36874_20    conda-forge
gfortran_osx-arm64        11.0.1.dev0         h57527a5_14    conda-forge
gmp                       6.2.1                h9f76cd9_0    conda-forge
graphite2                 1.3.13            h9f76cd9_1001    conda-forge
gsl                       2.6                  hc8a51ae_2    conda-forge
harfbuzz                  2.8.0                h2a75196_0    conda-forge
icu                       68.1                 h17758a7_0    conda-forge
isl                       0.22.1               hb904e53_2    conda-forge
jpeg                      9d                   h27ca646_0    conda-forge
krb5                      1.17.2               h17618d6_0    conda-forge
ld64_osx-arm64            530                 h8a2aa15_20    conda-forge
ldid                      2.1.2                h34db0f2_2    conda-forge
libblas                   3.9.0                8_openblas    conda-forge
libcblas                  3.9.0                8_openblas    conda-forge
libclang-cpp11.1          11.1.0          default_h87665d4_0    conda-forge
libcurl                   7.75.0               h222edf9_0    conda-forge
libcxx                    11.1.0               h168391b_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libffi                    3.3                  h9f76cd9_2    conda-forge
libgfortran               5.0.0.dev0      11_0_1_hf114ba7_20    conda-forge
libgfortran-devel_osx-arm64 11.0.1.dev0         hf114ba7_20    conda-forge
libgfortran5              11.0.1.dev0         hf114ba7_20    conda-forge
libglib                   2.66.7               haaa185a_1    conda-forge
libiconv                  1.16                 h642e427_0    conda-forge
liblapack                 3.9.0                8_openblas    conda-forge
libllvm11                 11.1.0               h4468dd5_0    conda-forge
libnghttp2                1.43.0               hf3018f0_0    conda-forge
libopenblas               0.3.12          openmp_h2ecc587_1    conda-forge
libpng                    1.6.37               hf7e6567_2    conda-forge
libssh2                   1.9.0                hb80f160_6    conda-forge
libtiff                   4.2.0                h70663a0_0    conda-forge
libwebp-base              1.2.0                h27ca646_1    conda-forge
libxml2                   2.9.10               h8f9ca65_3    conda-forge
llvm-openmp               11.0.1               hb3022d6_0    conda-forge
llvm-tools                11.1.0               h4468dd5_0    conda-forge
lz4-c                     1.9.3                h9f76cd9_0    conda-forge
make                      4.3                  he57ea6c_1    conda-forge
mpc                       1.1.0             hb760245_1009    conda-forge
mpfr                      4.0.2                hbc63f68_1    conda-forge
ncurses                   6.2                  h9aa5885_4    conda-forge
openssl                   1.1.1j               h27ca646_0    conda-forge
pango                     1.42.4               h9aa5ae2_5    conda-forge
pcre                      8.44                 hb904e53_0    conda-forge
pcre2                     10.36                hdd8d5aa_1    conda-forge
pixman                    0.40.0               h27ca646_0    conda-forge
r                         4.0                    r40_1004    conda-forge
r-base                    4.0.3                hebbb28a_7    conda-forge
r-boot                    1.3_27            r40hc72bb7e_0    conda-forge
r-class                   7.3_18            r40h4d528fc_0    conda-forge
r-cluster                 2.1.1             r40h09a9d6b_0    conda-forge
r-codetools               0.2_18            r40hc72bb7e_0    conda-forge
r-foreign                 0.8_81            r40h4d528fc_0    conda-forge
r-kernsmooth              2.23_18           r40hd851986_0    conda-forge
r-lattice                 0.20_41           r40h4d528fc_3    conda-forge
r-mass                    7.3_53.1          r40h4d528fc_0    conda-forge
r-matrix                  1.3_2             r40hdd02fd4_0    conda-forge
r-mgcv                    1.8_34            r40hdd02fd4_0    conda-forge
r-nlme                    3.1_152           r40h09a9d6b_0    conda-forge
r-nnet                    7.3_15            r40h4d528fc_0    conda-forge
r-recommended             4.0                    r40_1004    conda-forge
r-rpart                   4.1_15            r40h4d528fc_2    conda-forge
r-spatial                 7.3_13            r40h4d528fc_0    conda-forge
r-survival                3.2_10            r40h4d528fc_0    conda-forge
readline                  8.0                  hc8eb9b7_2    conda-forge
tapi                      1100.0.11            he4954df_0    conda-forge
tk                        8.6.10               hf7e6567_1    conda-forge
tktable                   2.10                 h4161312_3    conda-forge
xz                        5.2.5                h642e427_1    conda-forge
zlib                      1.2.11            h31e879b_1009    conda-forge
zstd                      1.4.9                h5b28eab_0    conda-forge

Details about conda and system ( conda info ):
$ conda info
     active environment : r4
    active env location : /Users/yifanyang/miniforge3/envs/r4
            shell level : 2
       user config file : /Users/yifanyang/.condarc
 populated config files : /Users/yifanyang/miniforge3/.condarc
          conda version : 4.9.2
    conda-build version : not installed
         python version : 3.9.2.final.0
       virtual packages : __osx=11.2=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /Users/yifanyang/miniforge3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/yifanyang/miniforge3/pkgs
                          /Users/yifanyang/.conda/pkgs
       envs directories : /Users/yifanyang/miniforge3/envs
                          /Users/yifanyang/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.9.2 requests/2.25.1 CPython/3.9.2 Darwin/20.3.0 OSX/11.2
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Issue 1 (see solution later):

When I start the R console, it shows

Error: package or namespace load failed forstatsin dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/yifanyang/miniforge3/envs/r4/lib/R/library/stats/libs/stats.dylib':
  dlopen(/Users/yifanyang/miniforge3/envs/r4/lib/R/library/stats/libs/stats.dylib, 6): Symbol not found: ___kmpc_for_static_fini
  Referenced from: /Users/yifanyang/miniforge3/envs/r4/lib/R/library/stats/libs/stats.dylib
  Expected in: /Users/yifanyang/miniforge3/envs/r4/lib/libomp.dylib
 in /Users/yifanyang/miniforge3/envs/r4/lib/R/library/stats/libs/stats.dylib
During startup - Warning message:
packagestatsin options("defaultPackages") was not found 

Issue 2 (Details RcppArmadillo330)

When using Rcpp, it will fail on std::log1p, i.e. HAVE_WORKING_LOG1P is not detected in R configuration stage.

> library(Rcpp)
> cppFunction("double e330(double x){return std::log1p(x);}", verbose=T)

Generated code for function definition: 
--------------------------------------------------------

#include <Rcpp.h>

using namespace Rcpp;

// [[Rcpp::export]]
double e330(double x){return std::log1p(x);}

Generated extern "C" functions 
--------------------------------------------------------


#include <Rcpp.h>
// e330
double e330(double x);
RcppExport SEXP sourceCpp_1_e330(SEXP xSEXP) {
BEGIN_RCPP
    Rcpp::RObject rcpp_result_gen;
    Rcpp::RNGScope rcpp_rngScope_gen;
    Rcpp::traits::input_parameter< double >::type x(xSEXP);
    rcpp_result_gen = Rcpp::wrap(e330(x));
    return rcpp_result_gen;
END_RCPP
}

Generated R functions 
-------------------------------------------------------

`.sourceCpp_1_DLLInfo` <- dyn.load('/private/var/folders/jg/3j5kv0dd3sq5v45cqptp8p2r0000gn/T/Rtmpk6XFNs/sourceCpp-aarch64-apple-darwin20.0.0-1.0.6/sourcecpp_17c1e234ba86d/sourceCpp_2.dylib')

e330 <- Rcpp:::sourceCppFunction(function(x) {}, FALSE, `.sourceCpp_1_DLLInfo`, 'sourceCpp_1_e330')

rm(`.sourceCpp_1_DLLInfo`)

Building shared library
--------------------------------------------------------

DIR: /private/var/folders/jg/3j5kv0dd3sq5v45cqptp8p2r0000gn/T/Rtmpk6XFNs/sourceCpp-aarch64-apple-darwin20.0.0-1.0.6/sourcecpp_17c1e234ba86d

/Users/yifanyang/miniforge3/envs/r4/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.dylib' 'file17c1e6c5c9ec.cpp' 
arm64-apple-darwin20.0.0-clang++ -std=gnu++11 -I"/Users/yifanyang/miniforge3/envs/r4/lib/R/include" -DNDEBUG   -I"/Users/yifanyang/miniforge3/envs/r4/lib/R/library/Rcpp/include" -I"/private/var/folders/jg/3j5kv0dd3sq5v45cqptp8p2r0000gn/T/Rtmpk6XFNs/sourceCpp-aarch64-apple-darwin20.0.0-1.0.6" -D_FORTIFY_SOURCE=2 -isystem /Users/yifanyang/miniforge3/envs/r4/include -mmacosx-version-min=11.0 -I/Users/yifanyang/miniforge3/envs/r4/include   -fPIC  -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -isystem /Users/yifanyang/miniforge3/envs/r4/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1615277992527/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/Users/yifanyang/miniforge3/envs/r4=/usr/local/src/conda-prefix  -c file17c1e6c5c9ec.cpp -o file17c1e6c5c9ec.o
file17c1e6c5c9ec.cpp:6:30: error: no member named 'Rlog1p' in namespace 'std'; did you mean simply 'Rlog1p'?
double e330(double x){return std::log1p(x);}
                             ^~~~~~~~~~
                             Rlog1p
/Users/yifanyang/miniforge3/envs/r4/lib/R/include/Rmath.h:74:9: note: 'Rlog1p' declared here
double  Rlog1p(double);
        ^
1 error generated.

Possible Solutions

ISSUE1/ISSUE2

a. ___kmpc_for_static_fini is related to openMP, hence for the current environment, --disable-openmp might work;

b. There is no reason to use OpenBLAS since some benchmarks illustrate that vecLib outperforms OpenBLAS alike. Besides, I came across the sameFFLAG errors when compiling R --with-BLAS-shlib.

I recompiled R with the following options (without X, and veclib should be replaced by -framework Accelerate):

./configure --enable-R-shlib --with-x=no --with-blas=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Versions/A/libBLAS.tbd --disable-openmp

Both issues vanish.

Issue with prcomp yielding wrong results

Issue:
r-base 3.5.1=1008 or later, prcomp yields wrong results.

pca-test.zip

The following code

mat <- readRDS("pca-test.rds")
pca_res <- prcomp(t(mat))
pca_res$x[, c("PC1", "PC2")]

yields (r-base 3.5.1=h08e1455_1008):

                  PC1         PC2
RD1-RD1    -153.73114   -287.6794
R9-R9       964.82819  -1262.4030
R10-R10     614.66393   -562.6454
RD2-RD2    1178.01419   -204.4405
RD3-RD3  -30033.83454  13510.5386
R11-R11   20674.64154 -15557.0076
RD4-RD4     802.96772  -4416.1874
R12-R12  -17401.18650  11483.0780
CD1-CD1      33.08999    686.5682
R13-R13     244.18843  -1469.0925
CD2-CD2     -43.04547   -316.5862
CD3-CD3    -556.21340    801.2634
RD5-RD5    3146.69929  -3992.1866
R14-R14   21590.16889  -9317.4246
C4-C4     23831.05987 -10874.4983
RD6-RD6   -1387.88353  -3306.7689
C5-C5     28128.73808  13590.9572
RD7-RD7   28853.29923 -86335.1008
RD8-RD8 -105437.42858   5964.5896
C6-C6     -6764.47756  51738.5563

however, it should yield

                PC1        PC2
RD1-RD1 -215736.201 -100893.89
R9-R9    166233.730  -82179.68
R10-R10   82191.587  -56091.08
RD2-RD2 -238182.268 -144915.18
RD3-RD3  -96705.664  217674.02
R11-R11   48225.206   64622.52
RD4-RD4  109692.808  250054.55
R12-R12  267496.360  105345.14
CD1-CD1  -82556.976 -219191.07
R13-R13  132561.434  120980.12
CD2-CD2   81396.817   35450.26
CD3-CD3    1953.878 -169643.81
RD5-RD5  131811.902  204761.21
R14-R14  133771.667  -67880.41
C4-C4     27481.237 -155492.69
RD6-RD6 -176154.906   15660.61
C5-C5     68511.627 -128803.60
RD7-RD7 -374452.334  254410.69
RD8-RD8 -146208.592   34880.71
C6-C6     78668.688 -178748.41

which is the case for earlier build of r-base 3.5.1 and also for r-base 3.6.0!

Hence, something good: with r-base 3.6.0 all is fine. However, I think it won't hurt to have this as kind of an integration test. It must have been something with one of the dependencies (maybe openblas?) while r-base 3.5.1=1008 was built.

Pending changes to defaults r-base packages

The r-base packages in the r channel and in https://repo.continuum.io/pkgs/r will be patched in the coming days to make room for the addition of MRO packages to the channel. The central problem is that we need to provide exclusivity between the r-base package and an mro-base package; they cannot be installed into the same environment, due to overlapping paths.

We've considered many technical solutions to this problem, including changes to conda, and we've arrived at the solution that requires us to patch metadata of the r-base package. Specifically, we have to add one additional dependency--a package that allows us to enforce the exclusivity.

Specifically, we're adding an additional package to the r channel with the following meta.yaml

package:
  name: _r-mutex
  version: 1.0.0

build:
  string: anacondar_1
  number: 1
  track_features:
    - anacondar

about:
  license: BSD
  summary: A mutex package to ensure environment exclusivity between Anaconda R and MRO.

(There's a similar _r-mutex package that we're using for mro, just with a different build string.)

All r-base packages will now include, or be patched to include

"_r-mutex 1.* anacondar_1"

in the depends list.

Without this step, users will often end up with both r-base and mro-base installed in the same environment.

For the r channel, I'm working on a script that will just download the package, patch the metadata, and then re-upload the package in place. We're doing this with the understanding that it will change the md5 of the package, and so it could raise alarms for people mirroring repositories. It's the least bad of all the alternatives we have right now though.

If the conda-forge community wants to use my script, I'll be happy to share it.

If instead the community wants to take the route of just rebuilding the packages, it'll be necessary to remove the main tag on anaconda.org from any r-base packages without "_r-mutex 1.* anacondar_1" in the dependency list.

We'll likely be releasing the MRO packages in the r and https://repo.continuum.io/pkgs/r defaults channel early next week.

Missing fonts in R?

Issue:
Hi Colleagues.
A week or two ago we got some help from @ocefpaf to make a MUCH more streamlined docker file to support both R and python. THe image works wonderfully EXCEPT R is having a hard time finding fonts in the image. All of our plots now look like this:

Screen Shot 2019-07-09 at 7 17 37 PM

the boxes should be text but are unfortunately missing characters (i think)? I've placed a link to our docker image below.

Can you tell me if there is some way to help R find fonts when it's installed via conda-forge. Again this worked when the install was not conda-forge but the image it much faster via conda-forge if we can get the fonts to work!

Many thanks for any suggestions and please say the word if this is not posted in the correct place. i'm posting here at a simple plot() call can't find the fonts which seems like a base r issue rather than a specific package (i could be wrong!!).


Environment (conda list):

https://github.com/earthlab/r-python-eds-lessons-env/blob/master/Dockerfile

$ conda list


Details about conda and system ( conda info ):
$ conda info

Package Apache 2.0 license file

The Apache 2.0 license is the only major license used by many CRAN packages not included in the r-base package, which makes it harder to provide proper license_file entries in dependant R packages. Providing it along with the other licenses in lib/R/share/licenses would be great.

Cannot install packages using r351_1000

Issue:

After having extremely frustrating issues with conda and https, I removed and reinstalled conda today. I installed r351_1000 and am now unable to run install.packages within an R environment. I keep getting the error:

Warning: unable to access index for repository https://ftp.osuosl.org/pub/cran/src/contrib:
  internet routines cannot be loaded
Warning messages:
1: In download.file(url, destfile = f, quiet = TRUE) :
  unable to load shared object '/home/dfiler/tools/miniconda3/lib/R/modules//internet.so':
  libssl.so.1.0.0: cannot open shared object file: No such file or directory
2: package ‘tcpl’ is not available (for R version 3.5.1) 

Note: I get the same error trying multiple CRAN packages. I AM able to install packages using conda install r-*.

Here is my ldpaths file and my openssl info:

(base) [dfiler@ht4 etc]$ which openssl
~/tools/miniconda3/bin/openssl

(base) [dfiler@ht4 etc]$ ldd ~/tools/miniconda3/bin/openssl 
linux-vdso.so.1 =>  (0x00007fff85cb3000)
libssl.so.1.1 => /home/dfiler/tools/miniconda3/bin/../lib/libssl.so.1.1 (0x00002acb01058000)
libcrypto.so.1.1 => /home/dfiler/tools/miniconda3/bin/../lib/libcrypto.so.1.1 (0x00002acb010ee000)
libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00002acb01409000)
libc.so.6 => /usr/lib64/libc.so.6 (0x00002acb01625000)
libdl.so.2 => /usr/lib64/libdl.so.2 (0x00002acb019e9000)
/lib64/ld-linux-x86-64.so.2 (0x0000560c13f73000)

(base) [dfiler@ht4 etc]$ cat ldpaths 
# https://github.com/conda/conda/issues/1679:
#  Internally R_system() calls system() which
# uses /bin/sh to launch various programs. If
# /bin/sh is called with LD_LIBRARY_PATH that
# loads condas shared libraries things break.
#  It may be that not setting LD_LIBRARY_PATH
# causes other things to break, in which case
# R_system() will need to be modified so that
# it calls execve() with an environment which
# has these modifications to LD_LIBRARY_PATH
# removed which may be tricky to orchestrate
if [ "$(uname -s)" = "Linux" ]; then
return 0
fi
: ${JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.151-1.b12.el7_4.x86_64/jre}
: ${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server}
if test -n "/home/dfiler/tools/miniconda3/lib"; then
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib:/home/dfiler/tools/miniconda3/lib}
else
  : ${R_LD_LIBRARY_PATH=${R_HOME}/lib}
fi
if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"
fi
## This is DYLD_FALLBACK_LIBRARY_PATH on Darwin (macOS) and
## LD_LIBRARY_PATH elsewhere.
## However, on macOS >=10.11 (if SIP is enabled, the default), the
## environment value will not be passed to a script such as R.sh, so
## would not seen here.
if test -z "${LD_LIBRARY_PATH}"; then
LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
else
  LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}"
fi
export LD_LIBRARY_PATH

Environment (conda list):
$ conda list
# packages in environment at /home/dfiler/tools/miniconda3:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1  
asn1crypto                0.24.0                   py37_0  
bcftools                  1.9                  h47928c2_1    bioconda
binutils_impl_linux-64    2.31.1               h6176602_1    conda-forge
binutils_linux-64         2.31.1               h6176602_3    conda-forge
bioconductor-annotationdbi 1.44.0                   r351_0    bioconda
bioconductor-biobase      2.42.0           r351h14c3975_0    bioconda
bioconductor-biocgenerics 0.28.0                   r351_1    bioconda
bioconductor-biocparallel 1.16.2           r351h1c2f66e_1    bioconda
bioconductor-biomart      2.38.0                   r351_0    bioconda
bioconductor-biostrings   2.50.1           r351h14c3975_0    bioconda
bioconductor-bsgenome     1.50.0                   r351_0    bioconda
bioconductor-delayedarray 0.8.0            r351h14c3975_0    bioconda
bioconductor-genomeinfodb 1.18.1                   r351_0    bioconda
bioconductor-genomeinfodbdata 1.2.0                    r351_0    bioconda
bioconductor-genomicalignments 1.18.0           r351h14c3975_0    bioconda
bioconductor-genomicfeatures 1.34.1                   r351_0    bioconda
bioconductor-genomicranges 1.34.0           r351h14c3975_0    bioconda
bioconductor-iranges      2.16.0           r351h14c3975_0    bioconda
bioconductor-rsamtools    1.34.0           r351hf484d3e_0    bioconda
bioconductor-rtracklayer  1.42.1           r351h14c3975_0    bioconda
bioconductor-s4vectors    0.20.1           r351h14c3975_0    bioconda
bioconductor-summarizedexperiment 1.12.0                   r351_0    bioconda
bioconductor-variantannotation 1.28.3           r351h14c3975_0    bioconda
bioconductor-xvector      0.22.0           r351h14c3975_0    bioconda
bioconductor-zlibbioc     1.28.0           r351h14c3975_0    bioconda
bwidget                   1.9.11                        1  
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.14.12              h8948797_3  
certifi                   2018.11.29            py37_1000    conda-forge
cffi                      1.11.5           py37he75722e_1  
chardet                   3.0.4                    py37_1  
conda                     4.6.4                    py37_0    conda-forge
conda-env                 2.6.0                         1  
cryptography              2.5              py37h1ba5d50_0  
curl                      7.63.0            hbc83047_1000  
fontconfig                2.13.0               h9420a91_0  
freetype                  2.9.1             h94bbf69_1005    conda-forge
fribidi                   1.0.5             h14c3975_1000    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_3    conda-forge
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_1    conda-forge
gfortran_linux-64         7.3.0                h553295d_3    conda-forge
glib                      2.56.2            had28632_1001    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gsl                       2.4                  h14c3975_4  
gxx_impl_linux-64         7.3.0                hdf63c60_1    conda-forge
gxx_linux-64              7.3.0                h553295d_3    conda-forge
harfbuzz                  1.9.0             he243708_1001    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.8                      py37_0  
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.16.1               h173b8e3_7  
libcurl                   7.63.0            h20c2e04_1000  
libdeflate                1.0                  h14c3975_1    bioconda
libedit                   3.1.20170329         h6b74fdf_2  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 8.2.0                hdf63c60_1  
libgfortran-ng            7.3.0                hdf63c60_0  
libiconv                  1.15              h14c3975_1004    conda-forge
libpng                    1.6.36            h84994c4_1000    conda-forge
libssh2                   1.8.0                         1    conda-forge
libstdcxx-ng              8.2.0                hdf63c60_1  
libtiff                   4.0.10            h648cc4a_1001    conda-forge
libuuid                   1.0.3                         1    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
make                      4.2.1             h14c3975_2004    conda-forge
ncurses                   6.1                  he6710b0_1  
openssl                   1.1.1a            h14c3975_1000    conda-forge
pango                     1.42.4               h049681c_0  
pcre                      8.42                 h439df22_0  
pip                       18.1                     py37_0  
pixman                    0.34.0            h14c3975_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
pycosat                   0.6.3            py37h14c3975_0  
pycparser                 2.19                     py37_0  
pyopenssl                 18.0.0                   py37_0  
pysocks                   1.6.8                    py37_0  
python                    3.7.2                h0371630_0  
r                         3.5.1                 r351_1000    conda-forge
r-assertthat              0.2.0           r351h6115d3f_1001    conda-forge
r-base                    3.5.1                h1e0a451_2  
r-bh                      1.69.0_1         r351h6115d3f_0    conda-forge
r-bit                     1.1_12          r351h14c3975_1002    conda-forge
r-bit64                   0.9_7           r351h96ca727_1000    conda-forge
r-bitops                  1.0_6           r351h96ca727_1002    conda-forge
r-blob                    1.1.1                 r351_1001    conda-forge
r-boot                    1.3_20                r351_1000    conda-forge
r-class                   7.3_15          r351h96ca727_1000    conda-forge
r-cluster                 2.0.7_1         r351ha65eedd_1000    conda-forge
r-codetools               0.2_16          r351h6115d3f_1000    conda-forge
r-crayon                  1.3.4           r351h6115d3f_1001    conda-forge
r-curl                    3.3              r351h96ca727_0    conda-forge
r-data.table              1.11.6           r351hc070d10_0    bioconda
r-dbi                     1.0.0           r351h6115d3f_1001    conda-forge
r-digest                  0.6.18          r351h96ca727_1000    conda-forge
r-foreign                 0.8_71          r351h96ca727_1002    conda-forge
r-formatr                 1.5             r351h6115d3f_1001    conda-forge
r-futile.logger           1.4.3           r351h6115d3f_1001    conda-forge
r-futile.options          1.0.1           r351h6115d3f_1000    conda-forge
r-glue                    1.3.0           r351h14c3975_1002    conda-forge
r-hms                     0.4.2           r351h6115d3f_1000    conda-forge
r-httr                    1.4.0           r351h6115d3f_1000    conda-forge
r-jsonlite                1.6             r351h96ca727_1000    conda-forge
r-kernsmooth              2.23_15         r351ha65eedd_1002    conda-forge
r-lambda.r                1.2.3           r351h6115d3f_1000    conda-forge
r-lattice                 0.20_38         r351h96ca727_1000    conda-forge
r-magrittr                1.5             r351h6115d3f_1001    conda-forge
r-mass                    7.3_51.1        r351h96ca727_1000    conda-forge
r-matrix                  1.2_15          r351h96ca727_1000    conda-forge
r-matrixstats             0.54.0          r351h96ca727_1000    conda-forge
r-memoise                 1.1.0           r351h6115d3f_1001    conda-forge
r-mgcv                    1.8_26          r351h96ca727_1000    conda-forge
r-mime                    0.6             r351h96ca727_1000    conda-forge
r-nlme                    3.1_137         r351ha65eedd_1000    conda-forge
r-nnet                    7.3_12          r351h96ca727_1002    conda-forge
r-openssl                 1.0.2            r351h96ca727_1  
r-pkgconfig               2.0.2           r351h6115d3f_1001    conda-forge
r-plogr                   0.2.0           r351h6115d3f_1001    conda-forge
r-prettyunits             1.0.2           r351h6115d3f_1001    conda-forge
r-progress                1.2.0           r351h6115d3f_1002    conda-forge
r-r6                      2.3.0           r351h6115d3f_1000    conda-forge
r-rcpp                    1.0.0           r351h29659fb_1000    conda-forge
r-rcurl                   1.95_4.11       r351h96ca727_1003    conda-forge
r-recommended             3.5.1                 r351_1001    conda-forge
r-rlang                   0.3.1            r351h96ca727_0    conda-forge
r-rpart                   4.1_13          r351h96ca727_1002    conda-forge
r-rsqlite                 2.1.1           r351h29659fb_1000    conda-forge
r-snow                    0.4_3           r351h6115d3f_1000    conda-forge
r-spatial                 7.3_11          r351h96ca727_1002    conda-forge
r-stringi                 1.2.4           r351h29659fb_1001    conda-forge
r-stringr                 1.3.1           r351h6115d3f_1001    conda-forge
r-survival                2.43_3          r351h96ca727_1000    conda-forge
r-xml                     3.98_1.16       r351h96ca727_1000    conda-forge
readline                  7.0                  h7b6447c_5  
requests                  2.21.0                   py37_0  
ruamel_yaml               0.15.46          py37h14c3975_0  
samtools                  1.9                  h91753b0_5    bioconda
setuptools                40.6.3                   py37_0  
six                       1.12.0                   py37_0  
sqlite                    3.26.0               h7b6447c_0  
tk                        8.6.8                hbc83047_0  
tktable                   2.10                 h14c3975_0  
urllib3                   1.24.1                   py37_0  
wget                      1.19.5               h20c2e04_0  
wheel                     0.32.3                   py37_0  
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.2             h14c3975_1007    conda-forge
xz                        5.2.4                h14c3975_4  
yaml                      0.1.7                had09818_2  
zlib                      1.2.11               h7b6447c_3  


Details about conda and system ( conda info ):
$ conda info
     active environment : base
    active env location : /home/dfiler/tools/miniconda3
            shell level : 1
       user config file : /home/dfiler/.condarc
 populated config files : /home/dfiler/.condarc
          conda version : 4.6.4
    conda-build version : not installed
         python version : 3.7.2.final.0
       base environment : /home/dfiler/tools/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/dfiler/tools/miniconda3/pkgs
                          /home/dfiler/.conda/pkgs
       envs directories : /home/dfiler/tools/miniconda3/envs
                          /home/dfiler/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.4 requests/2.21.0 CPython/3.7.2 Linux/3.10.0-693.5.2.el7.x86_64 centos/7.4.1708 glibc/2.17
                UID:GID : 4757:2000
             netrc file : None
           offline mode : False

Details about conda configuration ( conda config --show ):
(base) [dfiler@ht4 etc]$ conda config --show
add_anaconda_token: True
add_pip_as_python_dependency: True
aggressive_update_packages:
  - ca-certificates
  - certifi
  - openssl
allow_conda_downgrades: False
allow_cycles: True
allow_non_channel_urls: False
allow_softlinks: False
always_copy: False
always_softlink: False
always_yes: None
anaconda_upload: None
auto_activate_base: True
auto_update_conda: True
bld_path: 
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: flexible
channels:
  - bioconda
  - conda-forge
  - defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
conda_build: {}
create_default_packages: []
croot: /home/dfiler/tools/miniconda3/conda-bld
custom_channels:
  pkgs/main: https://repo.anaconda.com
  pkgs/free: https://repo.anaconda.com
  pkgs/r: https://repo.anaconda.com
  pkgs/pro: https://repo.anaconda.com
custom_multichannels:
  defaults: 
    - https://repo.anaconda.com/pkgs/main
    - https://repo.anaconda.com/pkgs/free
    - https://repo.anaconda.com/pkgs/r
  local: 
debug: False
default_channels:
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/free
  - https://repo.anaconda.com/pkgs/r
default_python: 3.7
deps_modifier: not_set
disallowed_packages: []
download_only: False
dry_run: False
enable_private_envs: False
env_prompt: ({default_env}) 
envs_dirs:
  - /home/dfiler/tools/miniconda3/envs
  - /home/dfiler/.conda/envs
error_upload_url: https://conda.io/conda-post/unexpected-error
extra_safety_checks: False
force: False
force_32bit: False
force_reinstall: False
force_remove: False
ignore_pinned: False
json: False
local_repodata_ttl: 1
migrated_channel_aliases: []
migrated_custom_channels: {}
non_admin_enabled: True
notify_outdated_conda: True
offline: False
override_channels_enabled: True
path_conflict: clobber
pinned_packages: []
pip_interop_enabled: False
pkgs_dirs:
  - /home/dfiler/tools/miniconda3/pkgs
  - /home/dfiler/.conda/pkgs
proxy_servers: {}
prune: False
quiet: False
remote_connect_timeout_secs: 9.15
remote_max_retries: 3
remote_read_timeout_secs: 60.0
report_errors: None
rollback_enabled: True
root_prefix: /home/dfiler/tools/miniconda3
safety_checks: warn
sat_solver: pycosat
shortcuts: True
show_channel_urls: None
solver_ignore_timestamps: False
ssl_verify: True
subdir: linux-64
subdirs:
  - linux-64
  - noarch
target_prefix_override: 
track_features: []
update_modifier: update_specs
use_index_cache: False
use_local: False
verbosity: 0
whitelist_channels: []

Vanilla install pulls in pkgs/r/r with different version

Using conda install -c conda-forge r=3.6 in a fresh environment installs r & r-base from different channels:

  r                  pkgs/r/linux-64::r-3.6.0-r36_0
  r-base             conda-forge/linux-64::r-base-3.6.1-h8900bf8_2

(for completeness: conda install -c conda-forge r=3.6.1 fails with PackagesNotFoundError and conda install -c conda-forge r pulls everything for r=3.5.1 from conda-forge)

I'm guessing that https://github.com/conda-forge/r-feedstock needs to be rerendered?

BTW, there's more R-packages being pulled from pkgs/{r,main}:

  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
  r                  pkgs/r/linux-64::r-3.6.0-r36_0
  r-base             conda-forge/linux-64::r-base-3.6.1-h8900bf8_2
  r-boot             pkgs/r/noarch::r-boot-1.3_20-r36h6115d3f_0
  r-class            pkgs/r/linux-64::r-class-7.3_15-r36h96ca727_0
  r-cluster          pkgs/r/linux-64::r-cluster-2.0.8-r36ha65eedd_0
  r-codetools        pkgs/r/noarch::r-codetools-0.2_16-r36h6115d3f_0
  r-foreign          pkgs/main/linux-64::r-foreign-0.8_71-r36h96ca727_0
  r-kernsmooth       pkgs/r/linux-64::r-kernsmooth-2.23_15-r36ha65eedd_4
  r-lattice          conda-forge/linux-64::r-lattice-0.20_38-r36hcdcec82_1001
  r-mass             pkgs/r/linux-64::r-mass-7.3_51.3-r36h96ca727_0
  r-matrix           pkgs/r/linux-64::r-matrix-1.2_17-r36h96ca727_0
  r-mgcv             pkgs/r/linux-64::r-mgcv-1.8_28-r36h96ca727_0
  r-nlme             pkgs/main/linux-64::r-nlme-3.1_139-r36ha65eedd_0
  r-nnet             pkgs/main/linux-64::r-nnet-7.3_12-r36h96ca727_0
  r-recommended      pkgs/r/linux-64::r-recommended-3.6.0-r36_0
  r-rpart            pkgs/r/linux-64::r-rpart-4.1_15-r36h96ca727_0
  r-spatial          pkgs/main/linux-64::r-spatial-7.3_11-r36h96ca727_4
  r-survival         pkgs/r/linux-64::r-survival-2.44_1.1-r36h96ca727_0
  sed                conda-forge/linux-64::sed-4.7-h1bed415_1000

Environment (conda list):
$ conda list
# packages in environment at /opt/conda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main
asn1crypto                0.24.0                py37_1003    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
certifi                   2019.6.16                py37_0    conda-forge
cffi                      1.12.3           py37h8022711_0    conda-forge
chardet                   3.0.4                 py37_1003    conda-forge
conda                     4.7.5                    py37_0    conda-forge
conda-package-handling    1.3.11                   py37_0    conda-forge
cryptography              2.7              py37h72c5cf5_0    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.8                   py37_1000    conda-forge
libarchive                3.3.3             hb44662c_1005    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.1.0                hdf63c60_0
libiconv                  1.15              h516909a_1005    conda-forge
libstdcxx-ng              9.1.0                hdf63c60_0
libxml2                   2.9.9                h13577e0_1    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
lzo                       2.10              h14c3975_1000    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openssl                   1.1.1c               h516909a_0    conda-forge
pip                       19.1.1                   py37_0    conda-forge
pycosat                   0.6.3           py37h14c3975_1001    conda-forge
pycparser                 2.19                     py37_1    conda-forge
pyopenssl                 19.0.0                   py37_0    conda-forge
pysocks                   1.7.0                    py37_0    conda-forge
python                    3.7.3                h33d41f4_1    conda-forge
python-libarchive-c       2.8                   py37_1004    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
requests                  2.22.0                   py37_1    conda-forge
ruamel_yaml               0.15.71         py37h14c3975_1000    conda-forge
setuptools                41.0.1                   py37_0    conda-forge
six                       1.12.0                py37_1000    conda-forge
sqlite                    3.29.0               hcee41ef_0    conda-forge
tk                        8.6.9             hed695b0_1002    conda-forge
tqdm                      4.32.2                     py_0    conda-forge
urllib3                   1.25.3                   py37_0    conda-forge
wheel                     0.33.4                   py37_0    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
yaml                      0.1.7             h14c3975_1001    conda-forge
zlib                      1.2.11            h516909a_1005    conda-forge
zstd                      1.4.0                h3b9ef0a_0    conda-forge

Details about conda and system ( conda info ):
$ conda info

     active environment : base
    active env location : /opt/conda
            shell level : 1
       user config file : /root/.condarc
 populated config files : /root/.condarc
          conda version : 4.7.5
    conda-build version : not installed
         python version : 3.7.3.final.0
       virtual packages :
       base environment : /opt/conda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda/pkgs
                          /root/.conda/pkgs
       envs directories : /opt/conda/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.22.0 CPython/3.7.3 Linux/4.15.0-51-generic ubuntu/18.04.2 glibc/2.27
                UID:GID : 0:0
             netrc file : None
           offline mode : False

Incompatibility between R and RStudio on Debian Systems

Issue:
Since one month, I can't run RStudio with my conda environment activated. For some project, I could cheat using Conda rstudio package and R 3.6.1, but for others projects, I need R > 4 and the conda rstudio is incompatible R > 3.6.1.

When my conda env is activated, and I run RStudio, it return an error :

Error in tools::startDynamicHelp() : 
    internet routines cannot be loaded

Then, I can't install any libraries, I can't use package which need to interact with localhost (neo4r) or with internet (STRINGdb).

When I run R in terminal, I don't have this issue, it's only when I start Rstudio with my environment.

Also, this issue occures on debian system (Ubuntu, PopOS, Debian), but no with Fedora system... I don't understand this behaviours. Any suggestion to solve it ?


Environment (conda list):
$ conda list
# packages in environment at /home/jeremy/Applications/Miniconda3/envs/modelisation:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
binutils_impl_linux-64    2.35.1               h17ad2fc_0    conda-forge
binutils_linux-64         2.35                hc3fd857_29    conda-forge
bwidget                   1.9.14               ha770c72_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h36c2ea0_0    conda-forge
ca-certificates           2020.11.8            ha878542_0    conda-forge
cairo                     1.16.0            h9f066cc_1006    conda-forge
curl                      7.71.1               he644dc0_8    conda-forge
fontconfig                2.13.1            h7e3eb15_1002    conda-forge
freetype                  2.10.4               h7ca028e_0    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gcc_impl_linux-64         9.3.0               h28f5a38_17    conda-forge
gcc_linux-64              9.3.0               h7247604_29    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
gfortran_impl_linux-64    9.3.0               h2bb4189_17    conda-forge
gfortran_linux-64         9.3.0               ha1c937c_29    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gsl                       2.6                  hf94e986_0    conda-forge
gxx_impl_linux-64         9.3.0               h53cdd4c_17    conda-forge
gxx_linux-64              9.3.0               h0d07fa4_29    conda-forge
harfbuzz                  2.7.2                ha5b49bf_1    conda-forge
icu                       67.1                 he1b5a44_0    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
kernel-headers_linux-64   2.6.32              h77966d4_13    conda-forge
krb5                      1.17.2               h926e7f8_0    conda-forge
ld_impl_linux-64          2.35.1               hed1e6ac_0    conda-forge
libblas                   3.9.0                3_openblas    conda-forge
libcblas                  3.9.0                3_openblas    conda-forge
libcurl                   7.71.1               hcdd3856_8    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  h58526e2_1    conda-forge
libgcc-devel_linux-64     9.3.0               hfd08b2a_17    conda-forge
libgcc-ng                 9.3.0               h5dbcf3e_17    conda-forge
libgfortran-ng            9.3.0               he4bcb1c_17    conda-forge
libgfortran5              9.3.0               he4bcb1c_17    conda-forge
libglib                   2.66.3               h1f3bc88_1    conda-forge
libgomp                   9.3.0               h5dbcf3e_17    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0                3_openblas    conda-forge
libnghttp2                1.41.0               h8cfc5f6_2    conda-forge
libopenblas               0.3.12          pthreads_h4812303_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-devel_linux-64  9.3.0               h4084dd6_17    conda-forge
libstdcxx-ng              9.3.0               h2ae2ef3_17    conda-forge
libtiff                   4.1.0                h4f3a223_6    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp-base              1.1.0                h36c2ea0_3    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.10               h68273f3_2    conda-forge
lz4-c                     1.9.2                he1b5a44_3    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openssl                   1.1.1h               h516909a_0    conda-forge
pango                     1.42.4               h69149e4_5    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
pcre2                     10.35                h032f7d1_2    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
r-base                    4.0.3                ha43b4e8_2    conda-forge
r-desolve                 1.28              r40h580db52_2    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
sysroot_linux-64          2.12                h77966d4_13    conda-forge
tk                        8.6.10               hed695b0_1    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.12               h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.5                h6597ccf_2    conda-forge

Details about conda and system ( conda info ):
$ conda info
     active environment : modelisation
    active env location : /home/jeremy/Applications/Miniconda3/envs/modelisation
            shell level : 1
       user config file : /home/jeremy/.condarc
 populated config files : /home/jeremy/.condarc
          conda version : 4.9.0
    conda-build version : not installed
         python version : 3.7.8.final.0
       virtual packages : __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/jeremy/Applications/Miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/jeremy/Applications/Miniconda3/pkgs
                          /home/jeremy/.conda/pkgs
       envs directories : /home/jeremy/Applications/Miniconda3/envs
                          /home/jeremy/.conda/envs
               platform : linux-64
             user-agent : conda/4.9.0 requests/2.24.0 CPython/3.7.8 Linux/5.8.0-7625-generic pop/20.04 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

R-base is not building with zlib 1.2.11

I can confirm that pinning to zlib 1.2.8 still works.

Here is the error:

checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... no
configure: error: zlib library and headers are required
checking whether zlib support suffices... Traceback (most recent call last):

See for the full log: https://circleci.com/gh/conda-forge/r-base-feedstock/3

xref: https://github.com/conda-forge/zlib-feedstock/pull/12/commits

lib/R/etc/ldpaths: No such file or directory

Issue:

I get the following error when using some conda R environment with galaxy or snakemake in HPC infrastructure:

R
$CONDA_PREFIX/lib/R/bin/R: line 238: $CONDA_PREFIX/lib/R/etc/ldpaths: No such file or directory

After tracking the issue, it appears that activating the conda environment with R runs the command R CMD javareconf that updates the file $CONDA_ENV/lib/R/etc/ldpaths.

I get this issue in two different cluster infrastructures:

  • The first one is a galaxy VM (CentOS 6) submitting jobs to computation nodes (CentOS 6) with SGE 6.2u4.
  • The second one a cluster node (CentOS 7) submitting jobs to computation nodes (CentOS 7) with SGE 8.1.9.

In both case, conda envs are stored on NFSv3 or BeeGFS shares mounted on computation nodes.

Concurrent activations like it can append during a galaxy school or with some snakemake wokflows with network latency lead to two cases:

  • the most common: $CONDA_PREFIX/lib/R/etc/ldpaths doesn't exists during a short gap of time and another activation appends during this gap producing this error for some jobs.
  • the less common: something when wrong during the previous case (an error, user CTRL+C, interblocking processes, ...) and the $CONDA_PREFIX/lib/R/etc/ldpaths doesn't exists anymore. One way to solve the issue is to reinstall the r-base package.

IMHO, I think a way to solve this issue is to replace the file only when needed, not at each environment activation.

Regards

Philippe


Environment (conda list):
$ conda list
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1  
bwidget                   1.9.11                        1  
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.10.15           ha4d7672_0    conda-forge
cairo                     1.14.12              h276e583_5    conda-forge
curl                      7.63.0               h74213dd_0    conda-forge
expat                     2.2.5                hfc679d8_2    conda-forge
fontconfig                2.13.1               h65d0f4c_0    conda-forge
freetype                  2.9.1                h6debe1e_4    conda-forge
gettext                   0.19.8.1             h5e8e0c9_1    conda-forge
glib                      2.56.2               h464dc38_0    conda-forge
graphite2                 1.3.12               hfc679d8_1    conda-forge
gsl                       2.2.1                h0c605f7_3  
harfbuzz                  1.9.0                hee26f79_1    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
krb5                      1.16.2               hbb41f41_0    conda-forge
libcurl                   7.63.0               hbdb9355_0    conda-forge
libedit                   3.1.20170329         haf1bffa_1    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3    conda-forge
libgfortran               3.0.0                         1    conda-forge
libiconv                  1.15                 h470a237_3    conda-forge
libpng                    1.6.35               ha92aebf_2    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3    conda-forge
libtiff                   4.0.9                he6b73bb_2    conda-forge
libuuid                   2.32.1               h470a237_2    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_5    conda-forge
make                      4.2.1             h470a237_1003    conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
openssl                   1.0.2p               h470a237_1    conda-forge
pango                     1.40.14              he752989_2    conda-forge
pcre                      8.41                 hfc679d8_3    conda-forge
pixman                    0.34.0               h470a237_3    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
r                         3.5.1                 r351_1000    conda-forge
r-assertthat              0.2.0           r351h6115d3f_1001    conda-forge
r-backports               1.1.3            r351hc070d10_0    conda-forge
r-base                    3.5.1                h391c2eb_4    conda-forge
r-boot                    1.3_20                r351_1000    conda-forge
r-callr                   3.1.1           r351h6115d3f_1000    conda-forge
r-class                   7.3_15           r351hc070d10_0    conda-forge
r-cli                     1.0.1           r351h6115d3f_1000    conda-forge
r-clipr                   0.4.1           r351h6115d3f_1001    conda-forge
r-clisymbols              1.2.0           r351h6115d3f_1001    conda-forge
r-cluster                 2.0.7_1          r351h364d78e_0    conda-forge
r-codetools               0.2_16          r351h6115d3f_1000    conda-forge
r-crayon                  1.3.4           r351h6115d3f_1001    conda-forge
r-curl                    3.2              r351hc070d10_2    conda-forge
r-desc                    1.2.0           r351h6115d3f_1001    conda-forge
r-devtools                2.0.1           r351h6115d3f_1000    conda-forge
r-digest                  0.6.18           r351hc070d10_0    conda-forge
r-foreign                 0.8_71           r351hc070d10_2    conda-forge
r-fs                      1.2.6            r351h9d2a408_0    conda-forge
r-gh                      1.0.1           r351h6115d3f_1001    conda-forge
r-git2r                   0.23.0           r351h1b3b946_0    conda-forge
r-glue                    1.3.0            r351h470a237_2    conda-forge
r-httr                    1.4.0           r351h6115d3f_1000    conda-forge
r-ini                     0.3.1           r351h6115d3f_1001    conda-forge
r-jsonlite                1.6              r351hc070d10_0    conda-forge
r-kernsmooth              2.23_15          r351h364d78e_2    conda-forge
r-lattice                 0.20_38          r351hc070d10_0    conda-forge
r-magrittr                1.5             r351h6115d3f_1001    conda-forge
r-mass                    7.3_51.1         r351hc070d10_0    conda-forge
r-matrix                  1.2_15           r351hc070d10_0    conda-forge
r-memoise                 1.1.0           r351h6115d3f_1001    conda-forge
r-mgcv                    1.8_26           r351hc070d10_0    conda-forge
r-mime                    0.6              r351hc070d10_0    conda-forge
r-nlme                    3.1_137          r351h364d78e_0    conda-forge
r-nnet                    7.3_12           r351hc070d10_2    conda-forge
r-openssl                 1.1              r351h9f97512_0    conda-forge
r-pkgbuild                1.0.2           r351h6115d3f_1001    conda-forge
r-pkgload                 1.0.2            r351h9d2a408_0    conda-forge
r-prettyunits             1.0.2           r351h6115d3f_1001    conda-forge
r-processx                3.2.1            r351hc070d10_0    conda-forge
r-ps                      1.3.0            r351hc070d10_0    conda-forge
r-r6                      2.3.0           r351h6115d3f_1000    conda-forge
r-rcmdcheck               1.3.2           r351h6115d3f_1000    conda-forge
r-rcpp                    1.0.0            r351h9d2a408_0    conda-forge
r-recommended             3.5.1                 r351_1001    conda-forge
r-remotes                 2.0.2           r351h6115d3f_1000    conda-forge
r-rlang                   0.3.0.1          r351h470a237_0    conda-forge
r-rpart                   4.1_13           r351hc070d10_2    conda-forge
r-rprojroot               1.3_2           r351h6115d3f_1001    conda-forge
r-rstudioapi              0.8             r351h6115d3f_1001    conda-forge
r-sessioninfo             1.1.1           r351h6115d3f_1000    conda-forge
r-spatial                 7.3_11           r351hc070d10_2    conda-forge
r-survival                2.43_3           r351hc070d10_0    conda-forge
r-usethis                 1.4.0           r351h6115d3f_1000    conda-forge
r-whisker                 0.3_2           r351h6115d3f_1001    conda-forge
r-withr                   2.1.2           r351h6115d3f_1000    conda-forge
r-xml                     3.98_1.16        r351hc070d10_0    conda-forge
r-xopen                   1.0.0           r351h6115d3f_1000    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
tk                        8.6.8                ha92aebf_0    conda-forge
tktable                   2.10                 h14c3975_0  
udunits2                  2.2.25               hd30922c_1  
xorg-kbproto              1.0.7                h470a237_2    conda-forge
xorg-libice               1.0.9                h470a237_4    conda-forge
xorg-libsm                1.2.2                h8c8a85c_6    conda-forge
xorg-libx11               1.6.6                h470a237_0    conda-forge
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xorg-libxext              1.3.3                h470a237_4    conda-forge
xorg-libxrender           0.9.10               h470a237_2    conda-forge
xorg-libxt                1.1.5                h470a237_2    conda-forge
xorg-renderproto          0.11.1               h470a237_2    conda-forge
xorg-xextproto            7.3.0                h470a237_2    conda-forge
xorg-xproto               7.0.31               h470a237_7    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ):
$ conda info
     active environment : None
       user config file : $HOME/.condarc
 populated config files : $HOME/.condarc
          conda version : 4.5.12
    conda-build version : 3.17.5
         python version : 3.7.1.final.0
       base environment : $HOME/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : $HOME/miniconda3/pkgs
                           $HOME/.conda/pkgs
       envs directories : $HOME/miniconda3/envs
                          / $HOME/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.12 requests/2.21.0 CPython/3.7.1 Linux/3.10.0-862.14.4.el7.x86_64 centos/7 glibc/2.17
                UID:GID : XXXXXXX:YYYYYYY
             netrc file : None
           offline mode : False

Coordinating r-base updates

There are lots of changes to be made to the r-base recipe. We need to decide which changes we make simultaneously and which we do in independent stages:

For me, the highest priority are the first two items. I propose we migrate to conda-build 3 and update to R 3.5.1 together as the next big change.

Re-arranging the Windows R layout to be the same as Unix is still a work-in-progress, and would involve updating the R package recipes to properly find the license files shipped with r-base. Thus I think this change should wait until after the big update to 3.5.1.

If we want to allow users to install Microsoft R Open from the defaults channel while also having access to non-R packages from conda-forge, we need to add r-mutex 1.* anacondar_1 as a run dependency. I don't use Microsoft R Open, and don't fully understand the consequences of adding this dependency, so we'll need someone willing to take charge on this.

conda-forge has dropped support for win-32 builds, and the r-base recipes has multiple patches for win-32, so at some point we should remove these if they are no longer relevant.

To get a sense of the changes that have taken place on the defaults r-base (it's currently at 3.5.0), check out PR #45.

.libPaths() can conflict with user/system installed R/RStudio

Hello,

I think I've finally found the issue and the right place to post it, but apologies if I'm mistaken.

It appears that when you have R installed from conda-forge and a system R (say RStudio), the conda installed R will include the user-package directory used by the system R in it's search path (.libPaths()).

This means if you have an R package installed with conda in your environment and the same package installed in RStudio, your conda environment will use the RStudio package (from your user directory) instead of the conda package. If there were any built extensions in that package (which usually there are) you'll end up with a cryptic segfault or memory not mapped error as the conda R is not binary compatible with the system R.

The reason the user-directory is included in .libPaths() is because of this section of the Renviron file.

If you install r-base and then comment out that section in ~/.conda/envs/<whatever>/lib/R/etc/Renviron the issue with .libPaths() disappears and your library() calls will only ever see your conda environment's packages, which I believe is kind of the entire point of conda.

I think this repo is where one would provide a patch file to drop that section of the Renviron file to make R installations isolated under conda. Assuming I'm not missing something important, would it make sense to provide a PR to fix this for everyone?

Cross referencing this issue: qiime2/q2-dada2#68 (where we have been trying to figure this out for a while).

Windows Makeconf issues

When building OpenMx on windows, the build fails because the default Makeconf that R ships with windows has CXX14 set to empty, but it always takes presence over use-level config. See conda-forge/r-openmx-feedstock#22 . I imagine this would be a problem with other packages that use CXX14 or CXX17?

Should we fix it here (make a patch for src/gnuwin32/fixed/etc/Makeconf), or is this something to take up with the R folks?

conda build Windows Error: m2w64_c_win-64 and R packages

I am attempting to install a newer version of the sf R package than is currently available via conda install (as the current version using conda install causes a significant set of dependency conflicts against other packages I already have installed).

To do so, I have tried to first run conda skeleton cran sf to create the sf meta yaml, which is listed below. Then, I attempt to build the new skeleton using conda build r-sf --debug. This causes the following error (with full debug at the end):

conda.exceptions.ResolvePackageNotFound:
  - m2w64_cxx_win-64
  - m2w64_c_win-64

In a naive attempt to try to resolve this, I tried conda installing all of the conda packages prefixed by m2w*, including the m2w64 toolkit, but it still returns the same error message.

Is there something that I need to do to enable conda build to find the compilers listed and/or to install the compilers beyond installing all of the m2w* packages, or is this a bug with conda build for R packages on windows? I have been able to install a number of R packages using conda install without running into any similar issue.


Environment (conda list):
$ conda list
# Name                    Version                   Build  Channel
_py-xgboost-mutex         2.0                       cpu_0
_r-mutex                  1.0.0               anacondar_1    r
attrs                     19.1.0                   py37_1
backcall                  0.1.0                    py37_0
blas                      1.0                         mkl
bleach                    3.1.0                    py37_0
ca-certificates           2019.8.28                     0
certifi                   2019.9.11                py37_0
colorama                  0.4.1                    py37_0
decorator                 4.4.0                    py37_1
defusedxml                0.6.0                      py_0
entrypoints               0.3                      py37_0
font-ttf-dejavu-sans-mono 2.37                 h6964260_0
font-ttf-inconsolata      2.001                hcb22688_0
font-ttf-source-code-pro  2.030                h7457263_0
font-ttf-ubuntu           0.83                 h8b1ccd4_0
fonts-anaconda            1                    h8fa9717_0
freetype                  2.9.1                ha9979f8_1
icc_rt                    2019.0.0             h0cc432a_1
icu                       58.2                 ha66f8fd_1
intel-openmp              2019.4                      245
ipykernel                 5.1.2            py37h39e3cac_0
ipython                   7.8.0            py37h39e3cac_0
ipython_genutils          0.2.0                    py37_0
jedi                      0.15.1                   py37_0
jinja2                    2.10.1                   py37_0
joblib                    0.13.2                   py37_0
jpeg                      9b                   hb83a4c4_2
json5                     0.8.5                      py_0
jsonschema                3.0.2                    py37_0
jupyter_client            5.3.3                      py_0
jupyter_core              4.5.0                      py_0
jupyterlab                1.0.2            py37hf63ae98_0
jupyterlab_server         1.0.6                      py_0
libpng                    1.6.37               h2a8f88b_0
libsodium                 1.0.16               h9d3ae62_0
libxgboost                0.90                          0
m2-bash                   4.3.042                       5
m2-coreutils              8.25                        102
m2-findutils              4.6.0                         2
m2-gcc-libs               5.3.0                         4
m2-gmp                    6.1.0                         3
m2-heimdal                1.5.3                        10
m2-heimdal-libs           1.5.3                        10
m2-icu                    56.1                          2
m2-libcrypt               1.3                           2
m2-libdb                  5.3.28                        3
m2-libedit                3.1                    20150326
m2-libiconv               1.14                          3
m2-libintl                0.19.7                        4
m2-libopenssl             1.0.2.g                       2
m2-libreadline            6.3.008                       8
m2-libsqlite              3.10.0.0                      2
m2-msys2-runtime          2.5.0.17080.65c939c               3
m2-ncurses                6.0.20160220                  2
m2-openssh                7.1p2                         2
m2-openssl                1.0.2.g                       2
m2-zlib                   1.2.8                         4
m2w64-binutils            2.25.1                        5
m2w64-bwidget             1.9.10                        2
m2w64-bzip2               1.0.6                         6
m2w64-c-ares              1.11.0                        2
m2w64-ca-certificates     20150426                    104
m2w64-crt-git             5.0.0.4636.2595836               2
m2w64-curl                7.48.0                        2
m2w64-diffutils           3.3.2                         2
m2w64-dlfcn               1.1.1                h1e6a91a_1
m2w64-dsdp                5.8                           1
m2w64-expat               2.1.1                         2
m2w64-fftw                3.3.4                         6
m2w64-flac                1.3.1                         3
m2w64-gcc                 5.3.0                         6
m2w64-gcc-ada             5.3.0                         6
m2w64-gcc-fortran         5.3.0                         6
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gcc-objc            5.3.0                         6
m2w64-gettext             0.19.7                        2
m2w64-glpk                4.61                          1
m2w64-gmp                 6.1.0                         2
m2w64-gnutls              3.4.11                        2
m2w64-grep                2.24                          2
m2w64-gsl                 2.1                           2
m2w64-headers-git         5.0.0.4636.c0ad18a               2
m2w64-icu                 58.2                 heb44b8b_2
m2w64-isl                 0.16.1                        2
m2w64-jansson             2.7                           3
m2w64-libffi              3.2.1                         4
m2w64-libiconv            1.14                          6
m2w64-libidn              1.32                          4
m2w64-libjpeg-turbo       1.4.2                         3
m2w64-libmangle-git       5.0.0.4509.2e5a9a2               2
m2w64-libmetalink         0.1.3                         2
m2w64-libogg              1.3.2                         3
m2w64-libpng              1.6.21                        2
m2w64-libsndfile          1.0.26                        2
m2w64-libsodium           1.0.10                        2
m2w64-libssh2             1.7.0                         2
m2w64-libsystre           1.0.1                         3
m2w64-libtasn1            4.7                           2
m2w64-libtiff             4.0.6                         2
m2w64-libtre-git          122.c2f5d13                   5
m2w64-libvorbis           1.3.5                         2
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
m2w64-libxml2             2.9.3                         4
m2w64-make                4.1.2351.a80a8b8               2
m2w64-metis               5.1.0                         1
m2w64-mpc                 1.0.3                         3
m2w64-mpfr                3.1.4                         4
m2w64-nettle              3.1.1                         4
m2w64-nghttp2             1.9.2                         2
m2w64-nlopt               2.4.2                         3
m2w64-ntldd-git           15.e7622f6                    3
m2w64-openblas            0.2.19                        1
m2w64-openssl             1.0.2.g                       2
m2w64-p11-kit             0.23.2                        3
m2w64-pcre                8.38                          2
m2w64-pkg-config          0.29.1                        2
m2w64-rtmpdump-git        499.a107cef                   4
m2w64-speex               1.2rc2                        3
m2w64-speexdsp            1.2rc3                        3
m2w64-suitesparse         4.5.5                         1
m2w64-tcl                 8.6.5                         3
m2w64-tk                  8.6.5                         3
m2w64-tktable             2.10                          5
m2w64-toolchain           5.3.0                         7
m2w64-toolchain_win-64    2.4.0                         0
m2w64-tools-git           5.0.0.4592.90b8472               2
m2w64-udunits2            2.2.25                        1
m2w64-windows-default-manifest 6.4                           3
m2w64-wineditline         2.101                         5
m2w64-winpthreads-git     5.0.0.4634.697f757               2
m2w64-xz                  5.2.2                         2
m2w64-zeromq              4.1.4                         2
m2w64-zlib                1.2.8                        10
markupsafe                1.1.1            py37he774522_0
mistune                   0.8.4            py37he774522_0
mkl                       2019.4                      245
mkl-service               2.3.0            py37hb782905_0
mkl_fft                   1.0.14           py37h14836fe_0
mkl_random                1.1.0            py37h675688f_0
msys2-conda-epoch         20160418                      1
nbconvert                 5.6.0                    py37_1
nbformat                  4.4.0                    py37_0
notebook                  6.0.1                    py37_0
numpy                     1.16.5           py37h19fb1c0_0
numpy-base                1.16.5           py37hc3f5095_0
openjdk                   8.0.152              h7382acf_1
openssl                   1.0.2t           vc14h62dcd97_0
pandoc                    2.2.3.2                       0
pandocfilters             1.4.2                    py37_1
parso                     0.5.1                      py_0
pickleshare               0.7.5                    py37_0
pip                       19.2.3                   py37_0
plotly                    4.1.1                      py_0
prometheus_client         0.7.1                      py_0
prompt_toolkit            2.0.9                    py37_0
py-xgboost                0.90                     py37_0
pygments                  2.4.2                      py_0
pyrsistent                0.15.4           py37he774522_0
python                    3.7.1                h33f27b4_4
python-dateutil           2.8.0                    py37_0
pywin32                   223              py37hfa6e2cd_1
pywinpty                  0.5.5                 py37_1000
pyzmq                     18.1.0           py37ha925a31_0
qt                        5.6.2           vc14h6f8c307_12
r-askpass                 1.0                       r36_0    r
r-assertable              0.2.5             r36h6115d3f_0    r
r-assertthat              0.2.1             r36h6115d3f_0    r
r-backports               1.1.4             r36h6115d3f_0    r
r-base                    3.6.1                h8a96d1b_0    r
r-base64enc               0.1_3             r36h6115d3f_4    r
r-bh                      1.69.0_1          r36h6115d3f_0    r
r-bit                     1.1_14            r36h6115d3f_0    r
r-bit64                   0.9_7             r36h6115d3f_0    r
r-bitops                  1.0_6             r36h6115d3f_4    r
r-blob                    1.1.1             r36h6115d3f_0    r
r-boot                    1.3_20            r36h6115d3f_0    r
r-broom                   0.5.2             r36h6115d3f_0    r
r-callr                   3.2.0             r36h6115d3f_0    r
r-caret                   6.0_83            r36h6115d3f_0    r
r-catools                 1.17.1.2          r36h6115d3f_0    r
r-cellranger              1.1.0             r36h6115d3f_0    r
r-class                   7.3_15            r36h6115d3f_0    r
r-cli                     1.1.0             r36h6115d3f_0    r
r-clipr                   0.6.0             r36h6115d3f_0    r
r-cluster                 2.0.8             r36h6115d3f_0    r
r-codetools               0.2_16            r36h6115d3f_0    r
r-colorspace              1.4_1             r36h6115d3f_0    r
r-config                  0.3               r36h6115d3f_0    r
r-crayon                  1.3.4             r36h6115d3f_0    r
r-crosstalk               1.0.0             r36h6115d3f_0    r
r-curl                    3.3               r36h6115d3f_0    r
r-data.table              1.12.2            r36h6115d3f_0    r
r-dbi                     1.0.0             r36h6115d3f_0    r
r-dbplyr                  1.4.0             r36h6115d3f_0    r
r-dichromat               2.0_0             r36h6115d3f_4    r
r-digest                  0.6.18            r36h6115d3f_0    r
r-dplyr                   0.8.0.1           r36h6115d3f_0    r
r-dt                      0.5               r36h6115d3f_0    r
r-ellipsis                0.1.0             r36h6115d3f_0    r
r-essentials              3.6.0                     r36_0    r
r-evaluate                0.13              r36h6115d3f_0    r
r-fansi                   0.4.0             r36h6115d3f_0    r
r-forcats                 0.4.0             r36h6115d3f_0    r
r-foreach                 1.4.4             r36h6115d3f_0    r
r-foreign                 0.8_71            r36h6115d3f_0    r
r-forge                   0.2.0             r36h6115d3f_0    r
r-formatr                 1.6               r36h6115d3f_0    r
r-fs                      1.2.7             r36h6115d3f_0    r
r-generics                0.0.2             r36h6115d3f_0    r
r-ggplot2                 3.1.1             r36h6115d3f_0    r
r-glmnet                  2.0_16            r36h6115d3f_0    r
r-glue                    1.3.1             r36h6115d3f_0    r
r-gower                   0.2.0             r36h6115d3f_0    r
r-gridextra               2.3               r36h6115d3f_0    r
r-gtable                  0.3.0             r36h6115d3f_0    r
r-haven                   2.1.0             r36h6115d3f_0    r
r-hexbin                  1.27.2            r36h6115d3f_0    r
r-highr                   0.8               r36h6115d3f_0    r
r-hms                     0.4.2             r36h6115d3f_0    r
r-htmltools               0.3.6             r36h6115d3f_0    r
r-htmlwidgets             1.3               r36h6115d3f_0    r
r-httpuv                  1.5.1             r36h6115d3f_0    r
r-httr                    1.4.0             r36h6115d3f_0    r
r-ipred                   0.9_8             r36h6115d3f_0    r
r-irdisplay               0.7.0             r36h6115d3f_0    r
r-irkernel                0.8.15                    r36_0    r
r-iterators               1.0.10            r36h6115d3f_0    r
r-jsonlite                1.6               r36h6115d3f_0    r
r-kernsmooth              2.23_15           r36h6115d3f_4    r
r-knitr                   1.22              r36h6115d3f_0    r
r-labeling                0.3               r36h6115d3f_4    r
r-later                   0.8.0             r36h6115d3f_0    r
r-lattice                 0.20_38           r36h6115d3f_0    r
r-lava                    1.6.5             r36h6115d3f_0    r
r-lazyeval                0.2.2             r36h6115d3f_0    r
r-leaflet                 2.0.2             r36h6115d3f_0    r
r-lubridate               1.7.4             r36h6115d3f_0    r
r-magrittr                1.5               r36h6115d3f_4    r
r-maps                    3.3.0             r36h6115d3f_0    r
r-markdown                0.9               r36h6115d3f_0    r
r-mass                    7.3_51.3          r36h6115d3f_0    r
r-matrix                  1.2_17            r36h6115d3f_0    r
r-mgcv                    1.8_28            r36h6115d3f_0    r
r-mime                    0.6               r36h6115d3f_0    r
r-miniui                  0.1.1.1           r36h6115d3f_0    r
r-modelmetrics            1.2.2             r36h6115d3f_0    r
r-modelr                  0.1.4             r36h6115d3f_0    r
r-mongolite               2.0.1             r36h6115d3f_0    r
r-munsell                 0.5.0             r36h6115d3f_0    r
r-nlme                    3.1_139           r36h6115d3f_0    r
r-nnet                    7.3_12            r36h6115d3f_0    r
r-numderiv                2016.8_1          r36h6115d3f_0    r
r-odbc                    1.1.5                     r36_0    r
r-openssl                 1.3               r36h6115d3f_0    r
r-openxlsx                4.1.0             r36h6115d3f_0    r
r-packrat                 0.5.0             r36h6115d3f_0    r
r-pbdzmq                  0.3_3             r36h6115d3f_0    r
r-pillar                  1.3.1             r36h6115d3f_0    r
r-pkgconfig               2.0.2             r36h6115d3f_0    r
r-pki                     0.1_5.1           r36h6115d3f_1    r
r-plogr                   0.2.0             r36h6115d3f_0    r
r-plotly                  4.9.0             r36h6115d3f_0    r
r-plyr                    1.8.4             r36h6115d3f_0    r
r-png                     0.1_7             r36h6115d3f_0    r
r-prettyunits             1.0.2             r36h6115d3f_0    r
r-processx                3.3.0             r36h6115d3f_0    r
r-prodlim                 2018.04.18        r36h6115d3f_0    r
r-profvis                 0.3.5             r36h6115d3f_0    r
r-progress                1.2.0             r36h6115d3f_0    r
r-promises                1.0.1             r36h6115d3f_0    r
r-ps                      1.3.0             r36h6115d3f_0    r
r-purrr                   0.3.2             r36h6115d3f_0    r
r-quantmod                0.4_14            r36h6115d3f_0    r
r-r2d3                    0.2.3             r36h6115d3f_0    r
r-r6                      2.4.0             r36h6115d3f_0    r
r-randomforest            4.6_14            r36h6115d3f_0    r
r-rappdirs                0.3.1             r36h6115d3f_0    r
r-raster                  2.8_19            r36h6115d3f_0    r
r-rbokeh                  0.6.3                     r36_0    r
r-rcolorbrewer            1.1_2             r36h6115d3f_0    r
r-rcpp                    1.0.1             r36h6115d3f_0    r
r-rcpproll                0.3.0             r36h6115d3f_0    r
r-rcurl                   1.95_4.12         r36h6115d3f_0    r
r-readr                   1.3.1             r36h6115d3f_0    r
r-readxl                  1.3.1             r36h6115d3f_0    r
r-recipes                 0.1.5             r36h6115d3f_0    r
r-recommended             3.6.0                     r36_0    r
r-rematch                 1.0.1             r36h6115d3f_0    r
r-repr                    0.19.2            r36h6115d3f_0    r
r-reprex                  0.2.1             r36h6115d3f_0    r
r-reshape2                1.4.3             r36h6115d3f_0    r
r-rjava                   0.9_11            r36h6115d3f_0    r
r-rjdbc                   0.2_7.1           r36h6115d3f_0    r
r-rjsonio                 1.3_1.1           r36h6115d3f_0    r
r-rlang                   0.3.4             r36h6115d3f_0    r
r-rmarkdown               1.12              r36h6115d3f_0    r
r-rpart                   4.1_15            r36h6115d3f_0    r
r-rprojroot               1.3_2             r36h6115d3f_0    r
r-rsconnect               0.8.13            r36h6115d3f_0    r
r-rstudioapi              0.10              r36h6115d3f_0    r
r-rvest                   0.3.3             r36h6115d3f_0    r
r-scales                  1.0.0             r36h6115d3f_0    r
r-selectr                 0.4_1             r36h6115d3f_0    r
r-shiny                   1.3.2             r36h6115d3f_0    r
r-shinythemes             1.1.2             r36h6115d3f_0    r
r-sourcetools             0.1.7             r36h6115d3f_0    r
r-sp                      1.3_1             r36h6115d3f_0    r
r-sparklyr                1.0.0             r36h6115d3f_0    r
r-spatial                 7.3_11            r36h6115d3f_4    r
r-squarem                 2017.10_1         r36h6115d3f_0    r
r-stringi                 1.4.3             r36h6115d3f_0    r
r-stringr                 1.4.0             r36h6115d3f_0    r
r-survival                2.44_1.1          r36h6115d3f_0    r
r-sys                     3.2               r36h6115d3f_0    r
r-tibble                  2.1.1             r36h6115d3f_0    r
r-tidyr                   0.8.3             r36h6115d3f_0    r
r-tidyselect              0.2.5             r36h6115d3f_0    r
r-tidyverse               1.2.1             r36h6115d3f_0    r
r-timedate                3043.102          r36h6115d3f_0    r
r-tinytex                 0.12              r36h6115d3f_0    r
r-ttr                     0.23_4            r36h6115d3f_0    r
r-utf8                    1.1.4             r36h6115d3f_0    r
r-uuid                    0.1_2             r36h6115d3f_4    r
r-viridis                 0.5.1             r36h6115d3f_0    r
r-viridislite             0.3.0             r36h6115d3f_0    r
r-whisker                 0.3_2             r36h6115d3f_4    r
r-withr                   2.1.2             r36h6115d3f_0    r
r-xfun                    0.6               r36h6115d3f_0    r
r-xgboost                 0.90.0.2          r36h796a38f_0    r
r-xml2                    1.2.0             r36h6115d3f_0    r
r-xtable                  1.8_4             r36h6115d3f_0    r
r-xts                     0.11_2            r36h6115d3f_0    r
r-yaml                    2.2.0             r36h6115d3f_0    r
r-zip                     2.0.1             r36h6115d3f_0    r
r-zoo                     1.8_5             r36h6115d3f_0    r
retrying                  1.3.3                    py37_2
rstudio                   1.1.456          vc14h1ad3211_1  [vc14]  r
rtools                    3.4.0                         0    r
scikit-learn              0.21.3           py37h6288b17_0
scipy                     1.3.1            py37h29ff71c_0
send2trash                1.5.0                    py37_0
setuptools                41.2.0                   py37_0
six                       1.12.0                   py37_0
sqlite                    3.29.0               he774522_0
terminado                 0.8.2                    py37_0
testpath                  0.4.2                    py37_0
tornado                   6.0.3            py37he774522_0
traitlets                 4.3.2                    py37_0
vc                        14.1                 h0510ff6_4
vs2015_runtime            14.16.27012          hf0eaf9b_0
wcwidth                   0.1.7                    py37_0
webencodings              0.5.1                    py37_1
wheel                     0.33.6                   py37_0
wincertstore              0.2                      py37_0
winpty                    0.4.3                         4
zeromq                    4.3.1                h33f27b4_3
zlib                      1.2.11               h62dcd97_3

Details about conda and system ( conda info ):
$ conda info
     active environment : Grant Default
    active env location : C:\Users\grantng\AppData\Local\Continuum\anaconda3\envs\Grant Default
            shell level : 1
       user config file : C:\Users\grantng\.condarc
 populated config files : C:\Users\grantng\.condarc
          conda version : 4.7.12
    conda-build version : 3.18.8
         python version : 3.7.3.final.0
       virtual packages :
       base environment : C:\Users\grantng\AppData\Local\Continuum\anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\grantng\AppData\Local\Continuum\anaconda3\pkgs
                          C:\Users\grantng\.conda\pkgs
                          C:\Users\grantng\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\grantng\AppData\Local\Continuum\anaconda3\envs
                          C:\Users\grantng\.conda\envs
                          C:\Users\grantng\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.3 Windows/10 Windows/10.0.16299
          administrator : False
             netrc file : None
           offline mode : False

meta.yaml:
{% set version = '0.8-0' %}

{% set posix = 'm2-' if win else '' %}
{% set native = 'm2w64-' if win else '' %}

package:
  name: r-sf
  version: {{ version|replace("-", "_") }}

source:
  url:
    - {{ cran_mirror }}/src/contrib/sf_{{ version }}.tar.gz
    - {{ cran_mirror }}/src/contrib/Archive/sf/sf_{{ version }}.tar.gz
  sha256: 8ee354f70b073bce124f2c138ebd2748936f890a7b4c380075c189cf36c0be15

build:
  merge_build_host: True  # [win]
  # If this is a new build for the same version, increment the build number.
  number: 0

  # This is required to make R link correctly on Linux.
  rpaths:
    - lib/R/lib/
    - lib/

# Suggests: blob, covr, dplyr (>= 0.8-3), ggplot2, knitr, lwgeom (>= 0.1-5), maps, maptools, mapview, microbenchmark, odbc, pillar, pool, raster, rgdal, rgeos, rlang, rmarkdown, RPostgres (>= 1.1.0), RPostgreSQL, RSQLite, sp (>= 1.2-4), spatstat, stars (>= 0.2-0), testthat, tibble (>= 1.4.1), tidyr (>= 1.0-0), tmap (>= 2.0), vctrs
requirements:
  build:
    - {{ compiler('c') }}              # [not win]
    - {{ compiler('m2w64_c') }}        # [win]
    - {{ compiler('cxx') }}            # [not win]
    - {{ compiler('m2w64_cxx') }}      # [win]
    - {{posix}}filesystem        # [win]
    - {{posix}}sed               # [win]
    - {{posix}}grep              # [win]
    - {{posix}}autoconf
    - {{posix}}automake          # [not win]
    - {{posix}}automake-wrapper  # [win]
    - {{posix}}pkg-config
    - {{posix}}make
    - {{posix}}coreutils         # [win]
    - {{posix}}zip               # [win]

  host:
    - r-base
    - r-dbi >=0.8
    - r-rcpp >=0.12.18
    - r-classint >=0.4_1
    - r-magrittr
    - r-units >=0.6_0

  run:
    - r-base
    - {{native}}gcc-libs         # [win]
    - r-dbi >=0.8
    - r-rcpp >=0.12.18
    - r-classint >=0.4_1
    - r-magrittr
    - r-units >=0.6_0

test:
  commands:
    # You can put additional test commands to be run here.
    - $R -e "library('sf')"           # [not win]
    - "\"%R%\" -e \"library('sf')\""  # [win]

  # You can also put a file called run_test.py, run_test.sh, or run_test.bat
  # in the recipe that will be run at test time.

  # requires:
    # Put any additional test requirements here.

about:
  home: https://github.com/r-spatial/sf/, https://r-spatial.github.io/sf/
  license: GPL-2 | MIT + file LICENSE
  summary: Support for simple features, a standardized way to encode spatial vector data. Binds
    to 'GDAL' for reading and writing data, to 'GEOS' for geometrical operations, and
    to 'PROJ' for projection conversions and datum transformations.
  license_family: GPL2

# The original CRAN metadata for this package was:

# Package: sf
# Version: 0.8-0
# Title: Simple Features for R
# Authors@R:  c(person(given = "Edzer", family = "Pebesma", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0001-8049-7069")), person(given = "Roger", family = "Bivand", role = "ctb", comment = c(ORCID = "0000-0003-2392-6140")), person(given = "Etienne", family = "Racine", role = "ctb"), person(given = "Michael", family = "Sumner", role = "ctb"), person(given = "Ian", family = "Cook", role = "ctb"), person(given = "Tim", family = "Keitt", role = "ctb"), person(given = "Robin", family = "Lovelace", role = "ctb"), person(given = "Hadley", family = "Wickham", role = "ctb"), person(given = "Jeroen", family = "Ooms", role = "ctb", comment = c(ORCID = "0000-0002-4035-0289")), person(given = "Kirill", family = "Muller", role = "ctb"), person(given = "Thomas Lin", family = "Pedersen", role = "ctb"), person(given = "Dan", family = "Baston", role = "ctb"))
# Description: Support for simple features, a standardized way to encode spatial vector data. Binds to 'GDAL' for reading and writing data, to 'GEOS' for geometrical operations, and to 'PROJ' for projection conversions and datum transformations.
# License: GPL-2 | MIT + file LICENSE
# URL: https://github.com/r-spatial/sf/, https://r-spatial.github.io/sf/
# BugReports: https://github.com/r-spatial/sf/issues/
# Depends: methods, R (>= 3.3.0)
# Imports: classInt (>= 0.4-1), DBI (>= 0.8), graphics, grDevices, grid, magrittr, Rcpp (>= 0.12.18), stats, tools, units (>= 0.6-0), utils
# Suggests: blob, covr, dplyr (>= 0.8-3), ggplot2, knitr, lwgeom (>= 0.1-5), maps, maptools, mapview, microbenchmark, odbc, pillar, pool, raster, rgdal, rgeos, rlang, rmarkdown, RPostgres (>= 1.1.0), RPostgreSQL, RSQLite, sp (>= 1.2-4), spatstat, stars (>= 0.2-0), testthat, tibble (>= 1.4.1), tidyr (>= 1.0-0), tmap (>= 2.0), vctrs
# LinkingTo: Rcpp
# VignetteBuilder: knitr
# Encoding: UTF-8
# RoxygenNote: 6.1.1
# SystemRequirements: C++11, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0)
# Collate: 'RcppExports.R' 'init.R' 'crs.R' 'bbox.R' 'read.R' 'db.R' 'sfc.R' 'sfg.R' 'sf.R' 'bind.R' 'wkb.R' 'wkt.R' 'plot.R' 'geom.R' 'transform.R' 'sp.R' 'grid.R' 'arith.R' 'tidyverse.R' 'cast_sfg.R' 'cast_sfc.R' 'graticule.R' 'datasets.R' 'aggregate.R' 'agr.R' 'maps.R' 'join.R' 'sample.R' 'valid.R' 'collection_extract.R' 'jitter.R' 'sgbp.R' 'spatstat.R' 'stars.R' 'crop.R' 'gdal_utils.R' 'nearest.R' 'normalize.R' 'deprecated.R'
# NeedsCompilation: yes
# Packaged: 2019-09-16 20:18:14 UTC; edzer
# Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>), Etienne Racine [ctb], Michael Sumner [ctb], Ian Cook [ctb], Tim Keitt [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Kirill Muller [ctb], Thomas Lin Pedersen [ctb], Dan Baston [ctb]
# Maintainer: Edzer Pebesma <[email protected]>
# Repository: CRAN
# Date/Publication: 2019-09-17 04:40:03 UTC

# See
# https://docs.conda.io/projects/conda-build for
# more information about meta.yaml

Error message for conda build r-sf --debug
(Grant Default) C:\Users\grantng>conda build r-sf --debug
No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for r-sf
INFO:conda_build.metadata:Attempting to finalize metadata for r-sf
DEBUG:conda_build.index:found subdirs {'win-64', 'noarch'}
Building repodata for C:\Users\grantng\AppData\Local\Continuum\anaconda3\conda-bld\noarch
INFO:conda_build.index:Building repodata for C:\Users\grantng\AppData\Local\Continuum\anaconda3\conda-bld\noarch
DEBUG:conda.core.package_cache_data:package cache directory 'C:\Users\grantng\AppData\Local\Continuum\anaconda3\pkgs' writable: True
Building repodata for C:\Users\grantng\AppData\Local\Continuum\anaconda3\conda-bld\win-64
INFO:conda_build.index:Building repodata for C:\Users\grantng\AppData\Local\Continuum\anaconda3\conda-bld\win-64
DEBUG:conda.core.solve:solving prefix C:\Users\grantng\AppData\Local\Temp\_7se4fxzxXX0W82PWGW
  specs_to_remove: frozenset()
  specs_to_add: frozenset({MatchSpec("m2-filesystem"), MatchSpec("m2w64_cxx_win-64"), MatchSpec("m2-autoconf"), MatchSpec("m2-grep"), MatchSpec("m2-coreutils"), MatchSpec("m2w64_c_win-64"), MatchSpec("m2-automake-wrapper"), MatchSpec("m2-sed"), MatchSpec("m2-pkg-config"), MatchSpec("m2-zip"), MatchSpec("m2-make")})
  prune: False
DEBUG conda.core.solve:solve_final_state(223): solving prefix C:\Users\grantng\AppData\Local\Temp\_7se4fxzxXX0W82PWGW
  specs_to_remove: frozenset()
  specs_to_add: frozenset({MatchSpec("m2-filesystem"), MatchSpec("m2w64_cxx_win-64"), MatchSpec("m2-autoconf"), MatchSpec("m2-grep"), MatchSpec("m2-coreutils"), MatchSpec("m2w64_c_win-64"), MatchSpec("m2-automake-wrapper"), MatchSpec("m2-sed"), MatchSpec("m2-pkg-config"), MatchSpec("m2-zip"), MatchSpec("m2-make")})
  prune: False
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... DEBUG:conda.resolve:Retrieving packages for:
  - m2-autoconf
  - m2-automake-wrapper
  - m2-coreutils
  - m2-filesystem
  - m2-grep
  - m2-make
  - m2-pkg-config
  - m2-sed
  - m2-zip
  - m2w64_c_win-64
  - m2w64_cxx_win-64
DEBUG conda.resolve:get_reduced_index(542): Retrieving packages for:
  - m2-autoconf
  - m2-automake-wrapper
  - m2-coreutils
  - m2-filesystem
  - m2-grep
  - m2-make
  - m2-pkg-config
  - m2-sed
  - m2-zip
  - m2w64_c_win-64
  - m2w64_cxx_win-64
failed

Leaving build/test directories:
  Work:
 C:\Users\grantng\AppData\Local\Continuum\anaconda3\conda-bld\work
  Test:
 C:\Users\grantng\AppData\Local\Continuum\anaconda3\conda-bld\test_tmp
Leaving build/test environments:
  Test:
source activate  C:\Users\grantng\AppData\Local\Continuum\anaconda3\conda-bld\_test_env
  Build:
source activate  C:\Users\grantng\AppData\Local\Continuum\anaconda3\conda-bld\_build_env


Traceback (most recent call last):
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\environ.py", line 756, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\common\io.py", line 88, in decorated
    return f(*args, **kwds)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\plan.py", line 474, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\solve.py", line 117, in solve_for_transaction
    should_retry_solve)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\solve.py", line 158, in solve_for_diff
    force_remove, should_retry_solve)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\solve.py", line 275, in solve_final_state
    ssc = self._add_specs(ssc)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\solve.py", line 555, in _add_specs
    explicit_pool = ssc.r._get_package_pool(self.specs_to_add)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\resolve.py", line 523, in _get_package_pool
    pool = self.get_reduced_index(specs)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\common\io.py", line 88, in decorated
    return f(*args, **kwds)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\resolve.py", line 544, in get_reduced_index
    explicit_specs, features = self.verify_specs(explicit_specs)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\resolve.py", line 280, in verify_specs
    raise ResolvePackageNotFound(bad_deps)
conda.exceptions.ResolvePackageNotFound:
  - m2w64_cxx_win-64
  - m2w64_c_win-64

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\Scripts\conda-build-script.py", line 10, in <module>
    sys.exit(main())
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 445, in main
    execute(sys.argv[1:])
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 436, in execute
    verify=args.verify, variants=args.variants)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\api.py", line 209, in build
    notest=notest, need_source_download=need_source_download, variants=variants)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\build.py", line 2324, in build_tree
    notest=notest,
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\build.py", line 1333, in build
    output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)])
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\render.py", line 747, in expand_outputs
    for (output_dict, m) in _m.copy().get_output_metadata_set(permit_unsatisfiable_variants=False):
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\metadata.py", line 2047, in get_output_metadata_set
    bypass_env_check=bypass_env_check)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\metadata.py", line 721, in finalize_outputs_pass
    permit_unsatisfiable_variants=permit_unsatisfiable_variants)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\render.py", line 528, in finalize_metadata
    exclude_pattern)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\render.py", line 391, in add_upstream_pins
    permit_unsatisfiable_variants, exclude_pattern)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\render.py", line 379, in _read_upstream_pin_files
    permit_unsatisfiable_variants=permit_unsatisfiable_variants)
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\render.py", line 154, in get_env_dependencies
    channel_urls=tuple(m.config.channel_urls))
  File "C:\Users\grantng\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_build\environ.py", line 758, in get_install_actions
    raise DependencyNeedsBuildingError(exc, subdir=subdir)
conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform win-64: {'m2w64_c_win-64', 'm2w64_cxx_win-64'}

Default shared library extension is wrong(?) on OSX

In the R 3.5.1 build, .Platform$dynlib.ext was set to .so, which worked because the shared libraries we ship tend to end in .so, regardless of the platform. Under the R 3.6.1 build, this got changed to the (presumably default) .dylib. That is then breaking things such as this PR: conda-forge/r-catboost-feedstock#26

My guess is that this had previously been changed in one of the many patches.

R 3.3.1 version

Would it be possible to also get a R 3.3.1 version with a higher build number than in the r channel? This old in in the R channel has problems with plotting and breaks a lot of things.

@johanneskoester @lecorguille

r-base-3.2.2 does not pin to readline 6

Hi,

I have a problem with my bioconda packages for R that should build against r-base 3.2.2. The readline version 7.0 is pulled in instead of 6.2, against which r-base 3.2.2 is apparently build. See here for some example output from the bioconda build system.

Is r-base 3.2.2 discontinued? If not, how can I add the version pin to this repo -- it apparently starts at a 3.3 version!?

segfault with r-base=3.5.1

Issue:
I have to install r-base=3.5.1 (because it's compatible with r-rjags), but after I install it on my Mac (High Sierra), I enter R from terminal and right after I load any library it crashes like this

caught segfault...
> library(devtools)

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 4: asNamespace(ns)
 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
 6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 7: asNamespace(ns)
 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
 9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
14: library(devtools)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

If I remove r-base=3.5.1 and substitute it by r-base=3.6.0, it all goes back to normal except that r-rjags gets removed.

So, how can I install r-base=3.5.1 with conda? (and finally install r-rjags)


Environment (conda list):
$ conda list
# packages in environment at /Users/lapotok/.pyenv/versions/miniconda3-4.3.30:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1  
appnope                   0.1.0            py36hf537a9a_0  
argtable2                 2.13                          0    etetoolkit
arpack                    3.6.3             h06d5271_1004    conda-forge
asn1crypto                0.22.0           py36hb705621_1  
attrs                     19.1.0                   py36_1  
backcall                  0.1.0                    py36_0  
beautifulsoup4            4.7.1                    pypi_0    pypi
biopython                 1.72             py36h6440ff4_0  
blas                      2.7                    openblas    conda-forge
bleach                    3.1.0                    py36_0  
bs4                       0.0.1                    pypi_0    pypi
bwidget                   1.9.11                        1  
bzip2                     1.0.6                h1de35cc_5  
ca-certificates           2019.5.15                     0  
cairo                     1.14.12              hc4e6be7_4  
cctools                   895                  h7512d6f_0    conda-forge
certifi                   2019.6.16                py36_0  
cffi                      1.10.0           py36h880867e_1  
chardet                   3.0.4            py36h96c241c_1  
clang                     4.0.1                h662ec87_0  
clang_osx-64              4.0.1               h1ce6c1d_16  
clangxx                   4.0.1                hc9b4283_0  
clangxx_osx-64            4.0.1               h22b1bf0_16  
clustalo                  1.2.4                h8fd5eaf_0    etetoolkit
compiler-rt               4.0.1                h5487866_0    conda-forge
conda                     4.6.14                   py36_0  
conda-env                 2.6.0                         1  
cryptography              2.7              py36h212c5bf_0    conda-forge
curl                      7.64.1               ha441bb4_0  
cycler                    0.10.0           py36hfc81398_0  
cyrus-sasl                2.1.26               hb48c43a_4  
dbus                      1.13.6               h90a0687_0  
decorator                 4.4.0                    py36_1  
defusedxml                0.5.0                    py36_1  
dialigntx                 1.0.2                h9803431_0    etetoolkit
entrypoints               0.3                      py36_0  
ete3                      3.1.1              pyhf5214e1_0    etetoolkit
ete_toolchain             3.0.0                h73706c9_0    etetoolkit
expat                     2.2.6                h0a44026_0  
fastcache                 1.1.0            py36h1de35cc_0  
faster-than-requests      0.1                      pypi_0    pypi
fasttree                  2.1                  hda580f3_0    etetoolkit
ffmpeg                    4.0                  h01ea3c9_0  
fftw                      3.3.8           nompi_h5c49c53_1105    conda-forge
font-ttf-dejavu-sans-mono 2.37                 h6964260_0  
font-ttf-inconsolata      2.001                hcb22688_0  
font-ttf-source-code-pro  2.030                h7457263_0  
font-ttf-ubuntu           0.83                 h8b1ccd4_0  
fontconfig                2.13.1            h1027ab8_1000    conda-forge
fonts-anaconda            1                    h8fa9717_0  
freetype                  2.9.1                hb4e5f40_0  
fribidi                   1.0.5             h1de35cc_1000    conda-forge
gettext                   0.19.8.1             h15daf44_3  
gevent                    1.3a1                    py36_0    conda-forge
gfortran_osx-64           4.8.5                h22b1bf0_8    conda-forge
glib                      2.56.2               hd9629dc_0  
gmp                       6.1.2             h0a44026_1000    conda-forge
gmpy2                     2.0.8            py36h6ef4df4_2  
graphite2                 1.3.13            h2098e52_1000    conda-forge
greenlet                  0.4.15           py36h01d97ff_0    conda-forge
grequests                 0.3.0                      py_1    conda-forge
gsl                       2.4                  h1de35cc_4  
harfbuzz                  1.8.8                hb8d4a28_0  
icu                       58.2                 h4b95b61_1  
idna                      2.6              py36h8628d0a_1  
intel-openmp              2019.3                      199  
ipykernel                 5.1.0            py36h39e3cac_0  
ipython                   7.4.0            py36h39e3cac_0  
ipython_genutils          0.2.0            py36h241746c_0  
ipywidgets                7.4.2                    py36_0  
iqtree                    1.5.5                h8fdce63_0    etetoolkit
jedi                      0.13.3                   py36_0  
jinja2                    2.10                     py36_0  
jpeg                      9c                h1de35cc_1001    conda-forge
jsonschema                3.0.1                    py36_0  
jupyter                   1.0.0                    py36_7  
jupyter_client            5.2.4                    py36_0  
jupyter_console           6.0.0                    py36_0  
jupyter_contrib_core      0.3.3                      py_2    conda-forge
jupyter_contrib_nbextensions 0.5.1                    py36_0    conda-forge
jupyter_core              4.4.0                    py36_0  
jupyter_highlight_selected_word 0.2.0                 py36_1000    conda-forge
jupyter_latex_envs        1.4.4                 py36_1000    conda-forge
jupyter_nbextensions_configurator 0.4.1                    py36_0    conda-forge
jupyterlab                0.35.4                   py36_0    conda-forge
jupyterlab_server         0.2.0                      py_0    conda-forge
kalign                    2.03                 hf9ccdb1_0    etetoolkit
kiwisolver                1.0.1            py36h0a44026_0  
krb5                      1.16.3            hcfa6398_1001    conda-forge
lapack                    3.6.1                ha44fe06_2    conda-forge
ld64                      274.2                h7c2db76_0    conda-forge
libblas                   3.8.0                7_openblas    conda-forge
libcblas                  3.8.0                7_openblas    conda-forge
libcurl                   7.64.1               h051b688_0  
libcxx                    4.0.1                h579ed51_0  
libcxxabi                 4.0.1                hebd6815_0  
libdb                     6.1.26            h0a44026_2000    conda-forge
libedit                   3.1.20181209         hb402a30_0  
libffi                    3.2.1                hd939716_3  
libgcc                    4.8.5               hdbeacc1_10  
libgfortran               3.0.1                h93005f0_2  
libiconv                  1.15                 hdd342a3_7  
liblapack                 3.8.0                7_openblas    conda-forge
liblapacke                3.8.0                7_openblas    conda-forge
libntlm                   1.4               h1de35cc_1001    conda-forge
libopenblas               0.2.20               hdc02c5d_7  
libopus                   1.3                  h1de35cc_0  
libosxunwind              0.0.5             h04f5b5a_1000    conda-forge
libpng                    1.6.37               ha441bb4_0  
libsodium                 1.0.16               h3efe00b_0  
libssh2                   1.8.2                ha12b0ac_0  
libtiff                   4.0.10               hcb84e12_2  
libvpx                    1.7.0                h378b8a2_0  
libxml2                   2.9.9                hab757c2_0  
libxslt                   1.1.33               h33a18ac_0  
llvm                      4.0.1                hc748206_0    conda-forge
llvm-lto-tapi             4.0.1                h6701bc3_0    conda-forge
llvm-openmp               4.0.1                hcfea43d_1  
lxml                      4.3.2            py36hef8c89e_0  
mafft                     6.861                h419a82f_0    etetoolkit
make                      4.2.1             h1de35cc_2004    conda-forge
markupsafe                1.1.1            py36h1de35cc_0  
matplotlib                3.0.3            py36h54f8f79_0  
metis                     5.1.0             h0a44026_1003    conda-forge
mistune                   0.8.4            py36h1de35cc_0  
mkl                       2019.3                      199  
mkl_fft                   1.0.13           py36h01d97ff_1    conda-forge
mkl_random                1.0.4            py36h051e8ed_0    conda-forge
mpc                       1.1.0                h6ef4df4_1  
mpfr                      4.0.2                h0a95893_0    conda-forge
mpmath                    1.1.0                    py36_0  
muscle                    3.8.31               hcb68c7d_0    etetoolkit
nbconvert                 5.4.1                    py36_3  
nbformat                  4.4.0            py36h827af21_0  
nbtutor                   1.0.4                 py36_1003    conda-forge
ncurses                   6.1                  h0a44026_1  
nodejs                    11.11.0              h0a44026_0    conda-forge
notebook                  5.0.0                    py36_0  
numpy                     1.16.4           py36h6b0580a_0    conda-forge
numpy-base                1.14.3           py36h9797aa9_0  
olefile                   0.46                     py36_0  
openblas                  0.3.5             h436c29b_1001    conda-forge
openjdk                   8.0.152              h393ad39_1  
openlibm                  0.5.4             h1de35cc_1000    conda-forge
openspecfun               0.5.3             h12d9a10_1000    conda-forge
openssl                   1.1.1c               h1de35cc_1  
paml                      4.8                  hace986f_0    etetoolkit
pandas                    0.24.2           py36h0a44026_0  
pandoc                    2.2.3.2                       0  
pandocfilters             1.4.2                    py36_1  
pango                     1.42.4               h060686c_0  
parso                     0.3.4                    py36_0  
pcre                      8.43                 h0a44026_0  
pcre2                     10.23                         2    conda-forge
pexpect                   4.6.0                    py36_0  
phylobayes                4.1c                 hf7d3357_0    etetoolkit
phyml                     20160115.patched      h98c79a7_0    etetoolkit
pickleshare               0.7.5                    py36_0  
pillow                    5.4.1            py36hb68e598_0  
pip                       19.0.3                   py36_0  
pixman                    0.34.0            h1de35cc_1003    conda-forge
pmodeltest                1.4              py36h1cf33f0_0    etetoolkit
prometheus_client         0.6.0                    py36_0  
prompt_toolkit            2.0.9                    py36_0  
ptyprocess                0.6.0                    py36_0  
pycosat                   0.6.3            py36h1de35cc_0  
pycparser                 2.18             py36h724b2fc_1  
pygments                  2.3.1                    py36_0  
pyopenssl                 17.2.0           py36h5d7bf08_0  
pyparsing                 2.3.1                    py36_0  
pyqt                      5.9.2            py36h655552a_2  
pyrsistent                0.14.11          py36h1de35cc_0  
pysocks                   1.6.7            py36hfa33cec_1  
python                    3.6.8                haf84260_0  
python-dateutil           2.8.0                    py36_0  
python.app                2                py36h54569d5_7  
pytz                      2018.9                   py36_0  
pyyaml                    5.1              py36h1de35cc_0    conda-forge
pyzmq                     18.0.1           py36h4cc6ddd_0    conda-forge
qt                        5.9.7                h468cd18_1  
qtconsole                 4.4.3                    py36_0  
raxml                     8.2.11               hab3343f_0    etetoolkit
readline                  7.0                  h1de35cc_5  
requests                  2.18.4           py36h4516966_1  
ruamel_yaml               0.11.14          py36h9d7ade0_2  
scipy                     1.3.0            py36hab3da7d_0    conda-forge
send2trash                1.5.0                    py36_0  
setuptools                36.5.0           py36h2134326_0  
singledispatch            3.4.0.3          py36hf20db9d_0  
sip                       4.19.8           py36h0a44026_0  
six                       1.11.0           py36h0e22d5e_1  
slr                       1.4.3                h3de9e2b_0    etetoolkit
soupsieve                 1.9                      pypi_0    pypi
sqlite                    3.27.2               ha441bb4_0  
suitesparse               4.5.6             h7019593_1202    conda-forge
sympy                     1.4                      py36_0  
t_coffee                  11.00                h5f19bac_0    etetoolkit
tbb                       2019.7               h770b8ee_0    conda-forge
terminado                 0.8.1                    py36_1  
testpath                  0.4.2                    py36_0  
tk                        8.6.9             h2573ce8_1002    conda-forge
tktable                   2.10                 h1de35cc_0  
tornado                   6.0.2            py36h1de35cc_0  
traitlets                 4.3.2            py36h65bd3ce_0  
trimal                    1.4                  h2778685_0    etetoolkit
tzlocal                   1.5.1                      py_0    conda-forge
unixodbc                  2.3.7                h1de35cc_0  
urllib3                   1.22             py36h68b9469_0  
viennarna                 2.4.11           py36hd9629dc_2    bioconda
wcwidth                   0.1.7            py36h8c6ec74_0  
webencodings              0.5.1                    py36_1  
wheel                     0.29.0           py36h3597b6d_1  
widgetsnbextension        3.4.2                    py36_0  
xz                        5.2.4                h1de35cc_4  
yaml                      0.1.7                hff548bb_1  
zeromq                    4.2.5                h0a44026_1  
zlib                      1.2.11               h60db283_1  
zstd                      1.3.7                h5bba6e5_0  


Details about conda and system ( conda info ):
$ conda info

     active environment : None
       user config file : /Users/lapotok/.condarc
 populated config files : /Users/lapotok/.condarc
          conda version : 4.6.14
    conda-build version : not installed
         python version : 3.6.8.final.0
       base environment : /Users/lapotok/.pyenv/versions/miniconda3-4.3.30  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/bioconda/osx-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/lapotok/.pyenv/versions/miniconda3-4.3.30/pkgs
                          /Users/lapotok/.conda/pkgs
       envs directories : /Users/lapotok/.pyenv/versions/miniconda3-4.3.30/envs
                          /Users/lapotok/.conda/envs
               platform : osx-64
             user-agent : conda/4.6.14 requests/2.18.4 CPython/3.6.8 Darwin/17.7.0 OSX/10.13.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Can not install r-base=4.0.2 in fresh Anaconda 2020.07 environment

Issue:

R installation hangs and later fails on fresh Anaconda environment:

./anaconda3/bin/conda install -c conda-forge --strict-channel-priority r-base=4.0.2

Environment (conda list):
$ conda list

# packages in environment at /home/user/anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py38_0  
_libgcc_mutex             0.1                        main  
alabaster                 0.7.12                     py_0  
anaconda                  2020.07                  py38_0  
anaconda-client           1.7.2                    py38_0  
anaconda-navigator        1.9.12                   py38_0  
anaconda-project          0.8.4                      py_0  
argh                      0.26.2                   py38_0  
asn1crypto                1.3.0                    py38_0  
astroid                   2.4.2                    py38_0  
astropy                   4.0.1.post1      py38h7b6447c_1  
atomicwrites              1.4.0                      py_0  
attrs                     19.3.0                     py_0  
autopep8                  1.5.3                      py_0  
babel                     2.8.0                      py_0  
backcall                  0.2.0                      py_0  
backports                 1.0                        py_2  
backports.functools_lru_cache 1.6.1                      py_0  
backports.shutil_get_terminal_size 1.0.0                    py38_2  
backports.tempfile        1.0                        py_1  
backports.weakref         1.0.post1                  py_1  
beautifulsoup4            4.9.1                    py38_0  
bitarray                  1.4.0            py38h7b6447c_0  
bkcharts                  0.2                      py38_0  
blas                      1.0                         mkl  
bleach                    3.1.5                      py_0  
blosc                     1.19.0               hd408876_0  
bokeh                     2.1.1                    py38_0  
boto                      2.49.0                   py38_0  
bottleneck                1.3.2            py38heb32a55_1  
brotlipy                  0.7.0           py38h7b6447c_1000  
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2020.6.24                     0  
cairo                     1.14.12              h8948797_3  
certifi                   2020.6.20                py38_0  
cffi                      1.14.0           py38he30daa8_1  
chardet                   3.0.4                 py38_1003  
click                     7.1.2                      py_0  
cloudpickle               1.5.0                      py_0  
clyent                    1.2.2                    py38_1  
colorama                  0.4.3                      py_0  
conda                     4.8.3                    py38_0  
conda-build               3.18.11                  py38_0  
conda-env                 2.6.0                         1  
conda-package-handling    1.6.1            py38h7b6447c_0  
conda-verify              3.4.2                      py_1  
contextlib2               0.6.0.post1                py_0  
cryptography              2.9.2            py38h1ba5d50_0  
curl                      7.71.1               hbc83047_1  
cycler                    0.10.0                   py38_0  
cython                    0.29.21          py38he6710b0_0  
cytoolz                   0.10.1           py38h7b6447c_0  
dask                      2.20.0                     py_0  
dask-core                 2.20.0                     py_0  
dbus                      1.13.16              hb2f20db_0  
decorator                 4.4.2                      py_0  
defusedxml                0.6.0                      py_0  
diff-match-patch          20200713                   py_0  
distributed               2.20.0                   py38_0  
docutils                  0.16                     py38_1  
entrypoints               0.3                      py38_0  
et_xmlfile                1.0.1                   py_1001  
expat                     2.2.9                he6710b0_2  
fastcache                 1.1.0            py38h7b6447c_0  
filelock                  3.0.12                     py_0  
flake8                    3.8.3                      py_0  
flask                     1.1.2                      py_0  
fontconfig                2.13.0               h9420a91_0  
freetype                  2.10.2               h5ab3b9f_0  
fribidi                   1.0.9                h7b6447c_0  
fsspec                    0.7.4                      py_0  
future                    0.18.2                   py38_1  
get_terminal_size         1.0.0                haa9412d_0  
gevent                    20.6.2           py38h7b6447c_0  
glib                      2.65.0               h3eb4bd4_0  
glob2                     0.7                        py_0  
gmp                       6.1.2                h6c8ec71_1  
gmpy2                     2.0.8            py38hd5f6e3b_3  
graphite2                 1.3.14               h23475e2_0  
greenlet                  0.4.16           py38h7b6447c_0  
gst-plugins-base          1.14.0               hbbd80ab_1  
gstreamer                 1.14.0               hb31296c_0  
h5py                      2.10.0           py38h7918eee_0  
harfbuzz                  2.4.0                hca77d97_1  
hdf5                      1.10.4               hb1b8bf9_0  
heapdict                  1.0.1                      py_0  
html5lib                  1.1                        py_0  
icu                       58.2                 he6710b0_3  
idna                      2.10                       py_0  
imageio                   2.9.0                      py_0  
imagesize                 1.2.0                      py_0  
importlib-metadata        1.7.0                    py38_0  
importlib_metadata        1.7.0                         0  
intel-openmp              2020.1                      217  
intervaltree              3.0.2                      py_1  
ipykernel                 5.3.2            py38h5ca1d4c_0  
ipython                   7.16.1           py38h5ca1d4c_0  
ipython_genutils          0.2.0                    py38_0  
ipywidgets                7.5.1                      py_0  
isort                     4.3.21                   py38_0  
itsdangerous              1.1.0                      py_0  
jbig                      2.1                  hdba287a_0  
jdcal                     1.4.1                      py_0  
jedi                      0.17.1                   py38_0  
jeepney                   0.4.3                      py_0  
jinja2                    2.11.2                     py_0  
joblib                    0.16.0                     py_0  
jpeg                      9b                   h024ee3a_2  
json5                     0.9.5                      py_0  
jsonschema                3.2.0                    py38_0  
jupyter                   1.0.0                    py38_7  
jupyter_client            6.1.6                      py_0  
jupyter_console           6.1.0                      py_0  
jupyter_core              4.6.3                    py38_0  
jupyterlab                2.1.5                      py_0  
jupyterlab_server         1.2.0                      py_0  
keyring                   21.2.1                   py38_0  
kiwisolver                1.2.0            py38hfd86e86_0  
krb5                      1.18.2               h173b8e3_0  
lazy-object-proxy         1.4.3            py38h7b6447c_0  
lcms2                     2.11                 h396b838_0  
ld_impl_linux-64          2.33.1               h53a641e_7  
libarchive                3.4.2                h62408e4_0  
libcurl                   7.71.1               h20c2e04_1  
libedit                   3.1.20191231         h14c3975_1  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_0  
liblief                   0.10.1               he6710b0_0  
libllvm9                  9.0.1                h4a3c616_1  
libpng                    1.6.37               hbc83047_0  
libsodium                 1.0.18               h7b6447c_0  
libspatialindex           1.9.3                he6710b0_0  
libssh2                   1.9.0                h1ba5d50_1  
libstdcxx-ng              9.1.0                hdf63c60_0  
libtiff                   4.1.0                h2733197_1  
libtool                   2.4.6                h7b6447c_5  
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.14                 h7b6447c_0  
libxml2                   2.9.10               he19cac6_1  
libxslt                   1.1.34               hc22bd24_0  
llvmlite                  0.33.0           py38hc6ec683_1  
locket                    0.2.0                    py38_1  
lxml                      4.5.2            py38hefd8a0e_0  
lz4-c                     1.9.2                he6710b0_0  
lzo                       2.10                 h7b6447c_2  
markupsafe                1.1.1            py38h7b6447c_0  
matplotlib                3.2.2                         0  
matplotlib-base           3.2.2            py38hef1b27d_0  
mccabe                    0.6.1                    py38_1  
mistune                   0.8.4           py38h7b6447c_1000  
mkl                       2020.1                      217  
mkl-service               2.3.0            py38he904b0f_0  
mkl_fft                   1.1.0            py38h23d657b_0  
mkl_random                1.1.1            py38h0573a6f_0  
mock                      4.0.2                      py_0  
more-itertools            8.4.0                      py_0  
mpc                       1.1.0                h10f8cd9_1  
mpfr                      4.0.2                hb69a4c5_1  
mpmath                    1.1.0                    py38_0  
msgpack-python            1.0.0            py38hfd86e86_1  
multipledispatch          0.6.0                    py38_0  
navigator-updater         0.2.1                    py38_0  
nbconvert                 5.6.1                    py38_0  
nbformat                  5.0.7                      py_0  
ncurses                   6.2                  he6710b0_1  
networkx                  2.4                        py_1  
nltk                      3.5                        py_0  
nose                      1.3.7                    py38_2  
notebook                  6.0.3                    py38_0  
numba                     0.50.1           py38h0573a6f_1  
numexpr                   2.7.1            py38h423224d_0  
numpy                     1.18.5           py38ha1c710e_0  
numpy-base                1.18.5           py38hde5b4d6_0  
numpydoc                  1.1.0                      py_0  
olefile                   0.46                       py_0  
openpyxl                  3.0.4                      py_0  
openssl                   1.1.1g               h7b6447c_0  
packaging                 20.4                       py_0  
pandas                    1.0.5            py38h0573a6f_0  
pandoc                    2.10                          0  
pandocfilters             1.4.2                    py38_1  
pango                     1.45.3               hd140c19_0  
parso                     0.7.0                      py_0  
partd                     1.1.0                      py_0  
patchelf                  0.11                 he6710b0_0  
path                      13.1.0                   py38_0  
path.py                   12.4.0                        0  
pathlib2                  2.3.5                    py38_0  
pathtools                 0.1.2                      py_1  
patsy                     0.5.1                    py38_0  
pcre                      8.44                 he6710b0_0  
pep8                      1.7.1                    py38_0  
pexpect                   4.8.0                    py38_0  
pickleshare               0.7.5                 py38_1000  
pillow                    7.2.0            py38hb39fc2d_0  
pip                       20.1.1                   py38_1  
pixman                    0.40.0               h7b6447c_0  
pkginfo                   1.5.0.1                  py38_0  
pluggy                    0.13.1                   py38_0  
ply                       3.11                     py38_0  
prometheus_client         0.8.0                      py_0  
prompt-toolkit            3.0.5                      py_0  
prompt_toolkit            3.0.5                         0  
psutil                    5.7.0            py38h7b6447c_0  
ptyprocess                0.6.0                    py38_0  
py                        1.9.0                      py_0  
py-lief                   0.10.1           py38h403a769_0  
pycodestyle               2.6.0                      py_0  
pycosat                   0.6.3            py38h7b6447c_1  
pycparser                 2.20                       py_2  
pycurl                    7.43.0.5         py38h1ba5d50_0  
pydocstyle                5.0.2                      py_0  
pyflakes                  2.2.0                      py_0  
pygments                  2.6.1                      py_0  
pylint                    2.5.3                    py38_0  
pyodbc                    4.0.30           py38he6710b0_0  
pyopenssl                 19.1.0                     py_1  
pyparsing                 2.4.7                      py_0  
pyqt                      5.9.2            py38h05f1152_4  
pyrsistent                0.16.0           py38h7b6447c_0  
pysocks                   1.7.1                    py38_0  
pytables                  3.6.1            py38h9fd0a39_0  
pytest                    5.4.3                    py38_0  
python                    3.8.3                hcff3b4d_2  
python-dateutil           2.8.1                      py_0  
python-jsonrpc-server     0.3.4                      py_1  
python-language-server    0.34.1                   py38_0  
python-libarchive-c       2.9                        py_0  
pytz                      2020.1                     py_0  
pywavelets                1.1.1            py38h7b6447c_0  
pyxdg                     0.26                       py_0  
pyyaml                    5.3.1            py38h7b6447c_1  
pyzmq                     19.0.1           py38he6710b0_1  
qdarkstyle                2.8.1                      py_0  
qt                        5.9.7                h5867ecd_1  
qtawesome                 0.7.2                      py_0  
qtconsole                 4.7.5                      py_0  
qtpy                      1.9.0                      py_0  
readline                  8.0                  h7b6447c_0  
regex                     2020.6.8         py38h7b6447c_0  
requests                  2.24.0                     py_0  
ripgrep                   11.0.2               he32d670_0  
rope                      0.17.0                     py_0  
rtree                     0.9.4                    py38_1  
ruamel_yaml               0.15.87          py38h7b6447c_1  
scikit-image              0.16.2           py38h0573a6f_0  
scikit-learn              0.23.1           py38h423224d_0  
scipy                     1.5.0            py38h0b6359f_0  
seaborn                   0.10.1                     py_0  
secretstorage             3.1.2                    py38_0  
send2trash                1.5.0                    py38_0  
setuptools                49.2.0                   py38_0  
simplegeneric             0.8.1                    py38_2  
singledispatch            3.4.0.3                  py38_0  
sip                       4.19.13          py38he6710b0_0  
six                       1.15.0                     py_0  
snappy                    1.1.8                he6710b0_0  
snowballstemmer           2.0.0                      py_0  
sortedcollections         1.2.1                      py_0  
sortedcontainers          2.2.2                      py_0  
soupsieve                 2.0.1                      py_0  
sphinx                    3.1.2                      py_0  
sphinxcontrib             1.0                      py38_1  
sphinxcontrib-applehelp   1.0.2                      py_0  
sphinxcontrib-devhelp     1.0.2                      py_0  
sphinxcontrib-htmlhelp    1.0.3                      py_0  
sphinxcontrib-jsmath      1.0.1                      py_0  
sphinxcontrib-qthelp      1.0.3                      py_0  
sphinxcontrib-serializinghtml 1.1.4                      py_0  
sphinxcontrib-websupport  1.2.3                      py_0  
spyder                    4.1.4                    py38_0  
spyder-kernels            1.9.2                    py38_0  
sqlalchemy                1.3.18           py38h7b6447c_0  
sqlite                    3.32.3               h62c20be_0  
statsmodels               0.11.1           py38h7b6447c_0  
sympy                     1.6.1                    py38_0  
tbb                       2020.0               hfd86e86_0  
tblib                     1.6.0                      py_0  
terminado                 0.8.3                    py38_0  
testpath                  0.4.4                      py_0  
threadpoolctl             2.1.0              pyh5ca1d4c_0  
tk                        8.6.10               hbc83047_0  
toml                      0.10.1                     py_0  
toolz                     0.10.0                     py_0  
tornado                   6.0.4            py38h7b6447c_1  
tqdm                      4.47.0                     py_0  
traitlets                 4.3.3                    py38_0  
typing_extensions         3.7.4.2                    py_0  
ujson                     1.35             py38h7b6447c_0  
unicodecsv                0.14.1                   py38_0  
unixodbc                  2.3.7                h14c3975_0  
urllib3                   1.25.9                     py_0  
watchdog                  0.10.3                   py38_0  
wcwidth                   0.2.5                      py_0  
webencodings              0.5.1                    py38_1  
werkzeug                  1.0.1                      py_0  
wheel                     0.34.2                   py38_0  
widgetsnbextension        3.5.1                    py38_0  
wrapt                     1.11.2           py38h7b6447c_0  
wurlitzer                 2.0.1                    py38_0  
xlrd                      1.2.0                      py_0  
xlsxwriter                1.2.9                      py_0  
xlwt                      1.3.0                    py38_0  
xmltodict                 0.12.0                     py_0  
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h7b6447c_0  
yapf                      0.30.0                     py_0  
zeromq                    4.3.2                he6710b0_2  
zict                      2.0.0                      py_0  
zipp                      3.1.0                      py_0  
zlib                      1.2.11               h7b6447c_3  
zope                      1.0                      py38_1  
zope.event                4.4                      py38_0  
zope.interface            4.7.1            py38h7b6447c_0  
zstd                      1.4.5                h0b5b093_0

Details about conda and system ( conda info ):
$ conda info

     active environment : base
    active env location : /home/user/anaconda3
            shell level : 1
       user config file : /home/user/.condarc
 populated config files : 
          conda version : 4.8.3
    conda-build version : 3.18.11
         python version : 3.8.3.final.0
       virtual packages : __glibc=2.28
       base environment : /home/user/anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/user/anaconda3/pkgs
                          /home/user/.conda/pkgs
       envs directories : /home/user/anaconda3/envs
                          /home/user/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.3 requests/2.24.0 CPython/3.8.3 Linux/4.19.0-10-cloud-amd64 debian/10 glibc/2.28
                UID:GID : 1009:1010
             netrc file : None
           offline mode : False

Hard-coded path to sed causes package installation failure

Issue: Installing RcppParallel in r-base=3.6.1 fails due to hard-coded path in R. No r-cppparallel package is available yet for R 3.6.1

* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** using staged installation
/cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12/lib/R/bin/R: line 211: /home/conda/feedstock_root/build_artifacts/r-base_1562703117796/_build_env/bin/sed: No such file or directory
/cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12/lib/R/bin/R: line 211: /home/conda/feedstock_root/build_artifacts/r-base_1562703117796/_build_env/bin/sed: No such file or directory
Fatal error: cannot open file '': No such file or directory
ERROR: configuration failed for package ‘RcppParallel’
* removing ‘/cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12/lib/R/library/RcppParall

Modifying R to point to a real sed version resolves the issue:

sed -i 's|^SED=.*|SED=/bin/sed|' $(which R)
sed -i 's|^SED=.*|SED=/bin/sed|'  $(dirname $(which R))/../lib/R/bin/R

(dada2-1.12) ningal:~ $ R

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('RcppParallel')
......[snip].....
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppParallel)


Environment (conda list):
# packages in environment at /cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main
_r-mutex                  1.0.1               anacondar_1    conda-forge
binutils_impl_linux-64    2.31.1               h6176602_1
binutils_linux-64         2.31.1               h6176602_7
bwidget                   1.9.11                        1
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
cairo                     1.16.0            h18b612c_1001    conda-forge
curl                      7.64.1               hf8cf82a_0    conda-forge
fontconfig                2.13.1            he4413a7_1000    conda-forge
freetype                  2.10.0               he983fc9_0    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_7    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_1
gfortran_linux-64         7.3.0                h553295d_7
glib                      2.58.3            h6f030ca_1001    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gsl                       2.5                  h294904e_0    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1    conda-forge
gxx_linux-64              7.3.0                h553295d_7    conda-forge
harfbuzz                  2.4.0                h37c48d4_1    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.16.3            h05b26f9_1001    conda-forge
libblas                   3.8.0               10_openblas    conda-forge
libcblas                  3.8.0               10_openblas    conda-forge
libcurl                   7.64.1               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.1.0                hdf63c60_0
libgfortran-ng            7.3.0                hdf63c60_0
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0               10_openblas    conda-forge
libopenblas               0.3.6                h6e990d7_4    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.1.0                hdf63c60_0
libtiff                   4.0.10            h57b8799_1003    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.9                h13577e0_1    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
make                      4.2.1             h14c3975_2004    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openblas                  0.3.6                h6e990d7_4    conda-forge
openssl                   1.1.1c               h516909a_0    conda-forge
pango                     1.40.14           he7ab937_1005    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
r-base                    3.6.1                h8900bf8_1    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
tk                        8.6.9             hed695b0_1002    conda-forge
tktable                   2.10                 h14c3975_0
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h516909a_1004    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge
zstd                      1.4.0                h3b9ef0a_0    conda-forge


Details about conda and system ( conda info ):
     active environment : dada2-1.12
    active env location : /cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12
            shell level : 2
       user config file : /homes/jabbott/.condarc
 populated config files : /homes/jabbott/.condarc
          conda version : 4.7.5
    conda-build version : 3.18.7
         python version : 3.7.3.final.0
       virtual packages :
       base environment : /cluster/gjb_lab/jabbott/miniconda3  (writable)
           channel URLs : https://dag.compbio.dundee.ac.uk/conda_dev/linux-64
                          https://dag.compbio.dundee.ac.uk/conda_dev/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /cluster/gjb_lab/jabbott/miniconda3/pkgs
                          /homes/jabbott/.conda/pkgs
       envs directories : /cluster/gjb_lab/jabbott/miniconda3/envs
                          /homes/jabbott/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.22.0 CPython/3.7.3 Linux/2.6.32-754.el6.x86_64 centos/6.10 glibc/2.12
                UID:GID : 14463:8000
             netrc file : None
           offline mode : False

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