conda-forge / r-changeforest-feedstock

A conda-smithy repository for r-changeforest.

About r-changeforest-feedstock

Feedstock license: BSD-3-Clause

Home: https://github.com/mlondschien/changeforest

Package license: BSD-3-Clause

Summary: Classifier based non-parametric change point detection

Development: https://github.com/mlondschien/changeforest

Change point detection aims to identify structural breaks in the probability distribution of a time series. Existing methods either assume a parametric model for within-segment distributions or are based on ranks or distances and thus fail in scenarios with a reasonably large dimensionality.

changeforest implements a classifier-based algorithm that consistently estimates change points without any parametric assumptions, even in high-dimensional scenarios. It uses the out-of-bag probability predictions of a random forest to construct a classifier log-likelihood ratio that gets optimized using a computationally feasible two-step method.

See [1] for details.

[1] M. Londschien, P. Bühlmann, and S. Kovács (2023). "Random Forests for Change Point Detection" Journal of Machine Learning Research

Current build status

Azure

Variant Status linux_64_r_base4.2 linux_64_r_base4.3 osx_64_r_base4.2 osx_64_r_base4.3 osx_arm64_r_base4.2 osx_arm64_r_base4.3

Current release info

Name	Downloads	Version	Platforms

Installing r-changeforest

Installing r-changeforest 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, r-changeforest can be installed with conda:

conda install r-changeforest

or with mamba:

mamba install r-changeforest

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

conda search r-changeforest --channel conda-forge

or with mamba:

mamba search r-changeforest --channel conda-forge

Alternatively, mamba repoquery may provide more information:

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

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

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

About conda-forge

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-changeforest-feedstock

If you would like to improve the r-changeforest 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-changeforest-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

• @conda-forge/r
• @mlondschien

r-changeforest-feedstock's Issues

@conda-forge-admin, please add user @conda-forge/r

Additional comment:

Consider adding the Conda Forge R Team as maintainers.

Linking issue on osx-arm64

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

I received a bug report that installing changeforest with conda results in linkage issues. I was able to reproduce the error on an osx-arm64 (M1 Macbook) machine.

(r-test) ~ $ R

R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20.0.0 (64-bit)

R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
Tippen Sie 'license()' or 'licence()' für Details dazu.

  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.

Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
Tippen Sie 'q()', um R zu verlassen.

[Vorher gesicherter Workspace wiederhergestellt]

> library(changeforest)
Fehler: Laden von Paket oder Namensraum für ‘changeforest’ in dyn.load(file, DLLpath = DLLpath, ...): fehlgeschlagen
 kann shared object '/Users/mlondschien/mambaforge/envs/r-test/lib/R/library/changeforest/libs/changeforest.dylib' nicht laden:
  dlopen(/Users/mlondschien/mambaforge/envs/r-test/lib/R/library/changeforest/libs/changeforest.dylib, 0x0006): symbol not found in flat namespace '_R_init_changeforestr_extendr'
> 

Suprisingly, this used to work when I last tested (~1 year ago). Downgrading did not solve the issue. Could this be an OS compatability issue? I upgraded to OSX 13 (Ventura) since last testing this. Building the package locally (R CMD INSTALL --build changeforest-r) works, as long as I add -F/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/ to the PGK_LIBS flags in the Makevars.

(r-test) ~ $ mamba install r-changeforest=0.6.0

Looking for: ['r-changeforest=0.6.0']

conda-forge/osx-arm64                                       Using cache
conda-forge/noarch                                          Using cache
Transaction

  Prefix: /Users/mlondschien/mambaforge/envs/r-test

  Updating specs:

   - r-changeforest=0.6.0
   - ca-certificates
   - openssl


  Package           Version  Build                 Channel           Size
───────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────

  + libcblas          3.9.0  20_osxarm64_openblas  conda-forge     Cached
  + gsl                 2.7  h6e638da_0            conda-forge     Cached

  Change:
───────────────────────────────────────────────────────────────────────────

  - libllvm17        17.0.6  haab561b_1            conda-forge     Cached
  + libllvm17        17.0.6  hc359061_0            conda-forge       25MB
  - llvm-tools       17.0.6  haab561b_1            conda-forge     Cached
  + llvm-tools       17.0.6  hc359061_0            conda-forge       22MB
  - r-r6              2.5.1  r43hc72bb7e_2         conda-forge     Cached
  + r-r6              2.5.1  r41hc72bb7e_1         conda-forge       92kB

  Downgrade:
───────────────────────────────────────────────────────────────────────────

  - pcre2             10.42  h26f9a81_0            conda-forge     Cached
  + pcre2             10.40  hb34f9b4_0            conda-forge     Cached
  - libxml2          2.12.3  h0d0cfa8_0            conda-forge     Cached
  + libxml2          2.11.6  h0d0cfa8_0            conda-forge      589kB
  - libglib          2.78.3  hb438215_0            conda-forge     Cached
  + libglib          2.78.1  hd9b11f9_0            conda-forge     Cached
  - r-base            4.3.2  h9389748_1            conda-forge     Cached
  + r-base            4.1.3  hc95f692_12           conda-forge       26MB
  - r-changeforest    1.1.2  r43h4614cfb_0         conda-forge     Cached
  + r-changeforest    0.6.0  r41h1ed4d5f_0         conda-forge       88kB

  Summary:

  Install: 2 packages
  Change: 3 packages
  Downgrade: 5 packages

  Total download: 73MB

───────────────────────────────────────────────────────────────────────────


Confirm changes: [Y/n] y
r-r6                                                92.4kB @ 451.0kB/s  0.2s
libxml2                                            588.7kB @   2.7MB/s  0.2s
r-changeforest                                      88.3kB @ 150.3kB/s  0.4s
r-base                                              25.7MB @   7.6MB/s  3.4s
libllvm17                                           24.6MB @   4.8MB/s  5.1s
llvm-tools                                          21.8MB @   3.9MB/s  5.5s

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(r-test) ~ $ R
library
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20.0.0 (64-bit)

R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
Tippen Sie 'license()' or 'licence()' für Details dazu.

  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.

Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
Tippen Sie 'q()', um R zu verlassen.

[Vorher gesicherter Workspace wiederhergestellt]

(changefores> library(changeforest)
Fehler: Laden von Paket oder Namensraum für ‘changeforest’ in dyn.load(file, DLLpath = DLLpath, ...): fehlgeschlagen
 kann shared object '/Users/mlondschien/mambaforge/envs/r-test/lib/R/library/changeforest/libs/changeforest.dylib' nicht laden:
  dlopen(/Users/mlondschien/mambaforge/envs/r-test/lib/R/library/changeforest/libs/changeforest.dylib, 0x0006): symbol not found in flat namespace '_R_init_changeforestr_extendr'
> 

@xhochy, is there anything that immediately comes to mind?

(r-test) ~ $ conda list
# packages in environment at /Users/mlondschien/mambaforge/envs/r-test:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
bwidget                   1.9.14               hce30654_1    conda-forge
bzip2                     1.0.8                h93a5062_5    conda-forge
c-ares                    1.24.0               h93a5062_0    conda-forge
ca-certificates           2023.11.17           hf0a4a13_0    conda-forge
cairo                     1.18.0               hd1e100b_0    conda-forge
cctools_osx-arm64         973.0.1             h998149b_15    conda-forge
clang                     17.0.6               haab561b_1    conda-forge
clang-17                  17.0.6          default_hd209bcb_1    conda-forge
clang_impl_osx-arm64      17.0.6               he47c785_7    conda-forge
clang_osx-arm64           17.0.6               h54d7cd3_7    conda-forge
clangxx                   17.0.6          default_h5c94ee4_1    conda-forge
clangxx_impl_osx-arm64    17.0.6               h50f59cd_7    conda-forge
clangxx_osx-arm64         17.0.6               h54d7cd3_7    conda-forge
compiler-rt               17.0.6               h3808999_1    conda-forge
compiler-rt_osx-arm64     17.0.6               h3808999_1    conda-forge
curl                      8.5.0                h2d989ff_0    conda-forge
expat                     2.5.0                hb7217d7_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_1    conda-forge
fontconfig                2.14.2               h82840c6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               hadb7bae_2    conda-forge
fribidi                   1.0.10               h27ca646_0    conda-forge
gettext                   0.21.1               h0186832_0    conda-forge
gfortran_impl_osx-arm64   12.3.0               hbbb9e1e_1    conda-forge
gfortran_osx-arm64        12.3.0               h57527a5_1    conda-forge
gmp                       6.3.0                h965bd2d_0    conda-forge
graphite2                 1.3.13            h9f76cd9_1001    conda-forge
harfbuzz                  8.3.0                h8f0ba13_0    conda-forge
icu                       73.2                 hc8870d7_0    conda-forge
isl                       0.25                 h9a09cb3_0    conda-forge
krb5                      1.21.2               h92f50d5_0    conda-forge
ld64_osx-arm64            609                 h6a44367_15    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libblas                   3.9.0           20_osxarm64_openblas    conda-forge
libclang-cpp17            17.0.6          default_hd209bcb_1    conda-forge
libcurl                   8.5.0                h2d989ff_0    conda-forge
libcxx                    16.0.6               h4653b0c_0    conda-forge
libdeflate                1.19                 hb547adb_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h93a5062_2    conda-forge
libexpat                  2.5.0                hb7217d7_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_1    conda-forge
libgfortran-devel_osx-arm64 12.3.0               hc62be1c_1    conda-forge
libgfortran5              13.2.0               hf226fd6_1    conda-forge
libglib                   2.78.3               hb438215_0    conda-forge
libiconv                  1.17                 h0d3ecfb_2    conda-forge
libjpeg-turbo             3.0.0                hb547adb_1    conda-forge
liblapack                 3.9.0           20_osxarm64_openblas    conda-forge
libllvm17                 17.0.6               haab561b_1    conda-forge
libnghttp2                1.58.0               ha4dd798_1    conda-forge
libopenblas               0.3.25          openmp_h6c19121_0    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libssh2                   1.11.0               h7a5bd25_0    conda-forge
libtiff                   4.6.0                ha8a6c65_2    conda-forge
libwebp-base              1.3.2                hb547adb_0    conda-forge
libxml2                   2.12.3               h0d0cfa8_0    conda-forge
libzlib                   1.2.13               h53f4e23_5    conda-forge
llvm-openmp               17.0.6               hcd81f8e_0    conda-forge
llvm-tools                17.0.6               haab561b_1    conda-forge
make                      4.3                  he57ea6c_1    conda-forge
mpc                       1.3.1                h91ba8db_0    conda-forge
mpfr                      4.2.1                h9546428_0    conda-forge
ncurses                   6.4                  h463b476_2    conda-forge
openssl                   3.2.0                h0d3ecfb_1    conda-forge
pango                     1.50.14              hcf40dda_2    conda-forge
pcre2                     10.42                h26f9a81_0    conda-forge
pixman                    0.42.2               h13dd4ca_0    conda-forge
r-base                    4.3.2                h9389748_1    conda-forge
r-changeforest            1.1.2             r43h4614cfb_0    conda-forge
r-r6                      2.5.1             r43hc72bb7e_2    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
sigtool                   0.1.3                h44b9a77_0    conda-forge
tapi                      1100.0.11            he4954df_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
tktable                   2.10                 hd996620_5    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
zlib                      1.2.13               h53f4e23_5    conda-forge
zstd                      1.5.5                h4f39d0f_0    conda-forge

(r-test) ~ $ conda info 

     active environment : r-test
    active env location : /Users/mlondschien/mambaforge/envs/r-test
            shell level : 2
       user config file : /Users/mlondschien/.condarc
 populated config files : /Users/mlondschien/mambaforge/.condarc
                          /Users/mlondschien/.config/conda/.condarc
          conda version : 23.5.2
    conda-build version : not installed
         python version : 3.10.12.final.0
       virtual packages : __archspec=1=arm64
                          __osx=13.2.1=0
                          __unix=0=0
       base environment : /Users/mlondschien/mambaforge  (writable)
      conda av data dir : /Users/mlondschien/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/mlondschien/mambaforge/pkgs
                          /Users/mlondschien/.conda/pkgs
       envs directories : /Users/mlondschien/mambaforge/envs
                          /Users/mlondschien/.conda/envs
               platform : osx-arm64
             user-agent : conda/23.5.2 requests/2.31.0 CPython/3.10.12 Darwin/22.3.0 OSX/13.2.1
                UID:GID : 501:20
             netrc file : None
           offline mode : False