Comments (9)
jdblischak
commented on September 26, 2024
2
I also installed the preview version of RStudio 1.4. It works with conda-forge R, so this is more evidence that there is something strange specifically with RStudio 1.3.
| OS | R (conda-forge) | RStudio | Status |
|---|---|---|---|
| Ubuntu 18.04.4 LTS | R 3.6.3 | 1.4.1081 | ✔️ |
| Ubuntu 18.04.4 LTS | R 4.0.3 | 1.4.1081 | ✔️ |
I also wanted to test RStudio 1.2, but the download link is currently broken.
from r-base-feedstock.
jdblischak
commented on September 26, 2024
@martin-jeremy Thanks for the bug report. We expect that the r-base from conda-forge should work with RStudio. Here are some more questions to help us troubleshoot the issue:
- What version of RStudio did you install? Are you using RStudio Desktop or Server? Does it work if you install an older version of RStudio, e.g. 1.1?
- Is there a Docker container we can use to reproduce the issue?
I did some searching, and this error message seems to be a long-standing issue. There doesn't appear to be an easy fix. The common theme seems to be that RStudio gets confused when R is installed via a package manager like conda or spack.
rstudio/rstudio#4904
spack/spack#19051
ContinuumIO/anaconda-issues#4421
from r-base-feedstock.
abalter
commented on September 26, 2024
I'm having the same problem.
I'm using Ubuntu 20.04 in WSL2 on Windows.
(base) balter@ORLT1072346:~/rstudio-diagnostics$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.1 LTS
Release: 20.04
Codename: focal
RStudio Desktop installed from rstudio-1.3.1056-amd64.deb
RStudio Diagnostics Report
==========================
WARNING: This report may contain sensitive security information and / or
personally identifiable information. Please audit the below and redact any
sensitive information before submitting your diagnostics report.
Generated: Fri Dec 4 12:59:24 2020
RStudio Version
--------------------------------------------------
1.3.1056
Session Information
--------------------------------------------------
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS/LAPACK: /home/balter/conda/lib/libopenblasp-r0.3.10.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3
System Information
--------------------------------------------------
sysname : Linux
release : 4.19.128-microsoft-standard
version : #1 SMP Tue Jun 23 12:58:10 UTC 2020
nodename : ORLT1072346
machine : x86_64
login : unknown
user : balter
effective_user : balter
Platform Information
--------------------------------------------------
OS.type : unix
file.sep : /
dynlib.ext : .so
GUI : X11
endian : little
pkgType : source
path.sep : :
r_arch :
Environment Variables
--------------------------------------------------
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_CE_M :
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ADDR2LINE : /home/balter/conda/bin/x86_64-conda-linux-gnu-addr2line
AR : /home/balter/conda/bin/x86_64-conda-linux-gnu-ar
AS : /home/balter/conda/bin/x86_64-conda-linux-gnu-as
BUILD : x86_64-conda-linux-gnu
build_alias : x86_64-conda-linux-gnu
CC : /home/balter/conda/bin/x86_64-conda-linux-gnu-cc
CC_FOR_BUILD : /home/balter/conda/bin/x86_64-conda-linux-gnu-cc
CFLAGS : -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/balter/conda/include
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CONDA_PREFIX : /home/balter/conda
CONDA_PROMPT_MODIFIER : (base)
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CPP : /home/balter/conda/bin/x86_64-conda-linux-gnu-cpp
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CXX : /home/balter/conda/bin/x86_64-conda-linux-gnu-c++
CXX_FOR_BUILD : /home/balter/conda/bin/x86_64-conda-linux-gnu-c++
CXXFILT : /home/balter/conda/bin/x86_64-conda-linux-gnu-c++filt
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F95 : /home/balter/conda/bin/x86_64-conda-linux-gnu-f95
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GSETTINGS_SCHEMA_DIR_CONDA_BACKUP :
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HOME : /home/balter
HOST : *** redacted ***
host_alias : *** redacted ***
HOSTTYPE : x86_64
LANG : C.UTF-8
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LESSCLOSE : /usr/bin/lesspipe %s %s
LESSOPEN : | /usr/bin/lesspipe %s
LIBGL_ALWAYS_INDIRECT : 0
LN_S : ln -s
LOGNAME : *** redacted ***
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MAKE : make
MOTD_SHOWN : update-motd
NAME : ORLT1072346
NM : /home/balter/conda/bin/x86_64-conda-linux-gnu-nm
NVM_DIR : /home/balter/.nvm
OBJCOPY : /home/balter/conda/bin/x86_64-conda-linux-gnu-objcopy
OBJDUMP : /home/balter/conda/bin/x86_64-conda-linux-gnu-objdump
PAGER : less
PATH : /home/balter/utilities/amd_templates/setup:/home/balter/utilities/project-utilities:/home/balter/utilities/analysis-utilities:/home/balter/utilities/amd_templates/setup:/home/balter/utilities/project-utilities:/home/balter/utilities/analysis-utilities:/home/balter/conda/bin:/home/balter/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Users/EACRIA~1/DOCUME~1/MobaXterm/slash/bin:/mnt/c/WINDOWS:/mnt/c/WINDOWS/system32:/mnt/c/Program Files (x86)/Common Files/Oracle/Java/javapath:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/ProgramData/chocolatey/bin:/mnt/c/tools/lxrunoffline:/mnt/c/Program Files/Git/cmd:/mnt/c/Users/eacriadmin/miniconda3:/mnt/c/Users/eacriadmin/miniconda3/Library/mingw-w64/bin:/mnt/c/Users/eacriadmin/miniconda3/Library/bin:/mnt/c/Users/eacriadmin/miniconda3/Scripts:/mnt/c/Users/eacriadmin/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/eacriadmin/AppData/Local/Programs/Microsoft VS Code/bin:/mnt/c/WINDOWS/sysnative:/snap/bin:/usr/lib/rstudio/bin/postback
PWD : /home/balter
R_BROWSER :
R_BZIPCMD : /home/balter/conda/bin/bzip2
R_DOC_DIR : /home/balter/conda/lib/R/doc
R_GZIPCMD : gzip
R_HOME : /home/balter/conda/lib/R
R_INCLUDE_DIR : /home/balter/conda/lib/R/include
R_LIBS_SITE :
R_LIBS_USER : ~/R/x86_64-conda-linux-gnu-library/4.0
R_PAPERSIZE : a4
R_PDFVIEWER :
R_PLATFORM : x86_64-conda-linux-gnu
R_PRINTCMD :
R_RD4PDF : times,hyper
R_SESSION_TMPDIR : /tmp/RtmpIy90MX
R_SHARE_DIR : /home/balter/conda/lib/R/share
R_STRIP_SHARED_LIB : x86_64-conda-linux-gnu-strip --strip-unneeded
R_STRIP_STATIC_LIB : x86_64-conda-linux-gnu-strip --strip-debug
R_SYSTEM_ABI : linux,gcc,gxx,gfortran,gfortran
R_TEXI2DVICMD : texi2dvi
R_UNZIPCMD :
R_ZIPCMD :
RANLIB : /home/balter/conda/bin/x86_64-conda-linux-gnu-ranlib
READELF : /home/balter/conda/bin/x86_64-conda-linux-gnu-readelf
RMARKDOWN_MATHJAX_PATH : /usr/lib/rstudio/resources/mathjax-27
RS_PPM_FD_READ : 10
RS_PPM_FD_WRITE : 11
RS_RPOSTBACK_PATH : /usr/lib/rstudio/bin/rpostback
RS_SHARED_SECRET : *** redacted ***
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RSTUDIO_CONSOLE_COLOR : 256
RSTUDIO_CONSOLE_WIDTH : 80
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RSTUDIO_SESSION_PORT : 10897
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RSTUDIO_WINUTILS : bin/winutils
SCREENDIR : /home/balter/.screen
SED : /home/balter/conda/bin/sed
SHELL : /bin/bash
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SSH_CLIENT : 127.0.0.1 34948 22007
SSH_CONNECTION : 127.0.0.1 34948 127.0.0.1 22007
SSH_TTY : /dev/pts/5
STRINGS : /home/balter/conda/bin/x86_64-conda-linux-gnu-strings
STRIP : /home/balter/conda/bin/x86_64-conda-linux-gnu-strip
TAR : tar
TERM : xterm-256color
USER : balter
WSL_DISTRO_NAME : Ubuntu-20.04
WSL_INTEROP : /run/WSL/30644_interop
WSLENV :
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R Version
--------------------------------------------------
platform : x86_64-conda-linux-gnu
arch : x86_64
os : linux-gnu
system : x86_64, linux-gnu
status :
major : 4
minor : 0.3
year : 2020
month : 10
day : 10
svn rev : 79318
language : R
version.string : R version 4.0.3 (2020-10-10)
nickname : Bunny-Wunnies Freak Out
R Home
--------------------------------------------------
/home/balter/conda/lib/R
R Search Path
--------------------------------------------------
.GlobalEnv
tools:rstudio
package:stats
package:graphics
package:grDevices
package:utils
package:datasets
package:methods
Autoloads
package:base
R Library Paths
--------------------------------------------------
/home/balter/conda/lib/R/library
Loaded Packages
--------------------------------------------------
base : /home/balter/conda/lib/R/library/base
compiler : /home/balter/conda/lib/R/library/compiler
datasets : /home/balter/conda/lib/R/library/datasets
graphics : /home/balter/conda/lib/R/library/graphics
grDevices : /home/balter/conda/lib/R/library/grDevices
methods : /home/balter/conda/lib/R/library/methods
stats : /home/balter/conda/lib/R/library/stats
tools : /home/balter/conda/lib/R/library/tools
utils : /home/balter/conda/lib/R/library/utils
Installed Packages
--------------------------------------------------
Package LibPath Version
1 askpass /home/balter/conda/lib/R/library 1.1
2 assertthat /home/balter/conda/lib/R/library 0.2.1
3 backports /home/balter/conda/lib/R/library 1.2.0
4 base /home/balter/conda/lib/R/library 4.0.3
5 base64enc /home/balter/conda/lib/R/library 0.1-3
6 beeswarm /home/balter/conda/lib/R/library 0.2.3
7 bigrquery /home/balter/conda/lib/R/library 1.3.2
8 bit /home/balter/conda/lib/R/library 4.0.4
9 bit64 /home/balter/conda/lib/R/library 4.0.5
10 blob /home/balter/conda/lib/R/library 1.2.1
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13 broom /home/balter/conda/lib/R/library 0.7.2
14 callr /home/balter/conda/lib/R/library 3.5.1
15 caret /home/balter/conda/lib/R/library 6.0-86
16 cellranger /home/balter/conda/lib/R/library 1.1.0
17 class /home/balter/conda/lib/R/library 7.3-17
18 cli /home/balter/conda/lib/R/library 2.2.0
19 clipr /home/balter/conda/lib/R/library 0.7.1
20 cluster /home/balter/conda/lib/R/library 2.1.0
21 codetools /home/balter/conda/lib/R/library 0.2-18
22 colorspace /home/balter/conda/lib/R/library 2.0-0
23 commonmark /home/balter/conda/lib/R/library 1.7
24 compiler /home/balter/conda/lib/R/library 4.0.3
25 cpp11 /home/balter/conda/lib/R/library 0.2.4
26 crayon /home/balter/conda/lib/R/library 1.3.4
27 crosstalk /home/balter/conda/lib/R/library 1.1.0.1
28 crul /home/balter/conda/lib/R/library 1.0.0
29 curl /home/balter/conda/lib/R/library 4.3
30 data.table /home/balter/conda/lib/R/library 1.13.2
31 datasets /home/balter/conda/lib/R/library 4.0.3
32 DBI /home/balter/conda/lib/R/library 1.1.0
33 dbplyr /home/balter/conda/lib/R/library 2.0.0
34 desc /home/balter/conda/lib/R/library 1.2.0
35 diffobj /home/balter/conda/lib/R/library 0.3.2
36 digest /home/balter/conda/lib/R/library 0.6.27
37 dplyr /home/balter/conda/lib/R/library 1.0.2
38 DT /home/balter/conda/lib/R/library 0.16
39 ellipsis /home/balter/conda/lib/R/library 0.3.1
40 evaluate /home/balter/conda/lib/R/library 0.14
41 fansi /home/balter/conda/lib/R/library 0.4.1
42 farver /home/balter/conda/lib/R/library 2.0.3
43 fastmap /home/balter/conda/lib/R/library 1.0.1
44 forcats /home/balter/conda/lib/R/library 0.5.0
45 foreach /home/balter/conda/lib/R/library 1.5.1
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48 fs /home/balter/conda/lib/R/library 1.5.0
49 gargle /home/balter/conda/lib/R/library 0.5.0
50 generics /home/balter/conda/lib/R/library 0.1.0
51 ggbeeswarm /home/balter/conda/lib/R/library 0.6.0
52 ggplot2 /home/balter/conda/lib/R/library 3.3.2
53 ggsignif /home/balter/conda/lib/R/library 0.6.0
54 gistr /home/balter/conda/lib/R/library 0.9.0
55 glmnet /home/balter/conda/lib/R/library 4.0-2
56 glue /home/balter/conda/lib/R/library 1.4.2
57 gower /home/balter/conda/lib/R/library 0.2.2
58 graphics /home/balter/conda/lib/R/library 4.0.3
59 grDevices /home/balter/conda/lib/R/library 4.0.3
60 grid /home/balter/conda/lib/R/library 4.0.3
61 gridExtra /home/balter/conda/lib/R/library 2.3
62 gtable /home/balter/conda/lib/R/library 0.3.0
63 haven /home/balter/conda/lib/R/library 2.3.1
64 hexbin /home/balter/conda/lib/R/library 1.28.1
65 highr /home/balter/conda/lib/R/library 0.8
66 hms /home/balter/conda/lib/R/library 0.5.3
67 htmltools /home/balter/conda/lib/R/library 0.5.0
68 htmlwidgets /home/balter/conda/lib/R/library 1.5.2
69 httpcode /home/balter/conda/lib/R/library 0.3.0
70 httpuv /home/balter/conda/lib/R/library 1.5.4
71 httr /home/balter/conda/lib/R/library 1.4.2
72 ipred /home/balter/conda/lib/R/library 0.9-9
73 IRdisplay /home/balter/conda/lib/R/library 0.7.0
74 IRkernel /home/balter/conda/lib/R/library 1.1.1
75 isoband /home/balter/conda/lib/R/library 0.2.2
76 iterators /home/balter/conda/lib/R/library 1.0.13
77 jsonlite /home/balter/conda/lib/R/library 1.7.1
78 kableExtra /home/balter/conda/lib/R/library 1.3.1
79 KernSmooth /home/balter/conda/lib/R/library 2.23-18
80 knitr /home/balter/conda/lib/R/library 1.30
81 labeling /home/balter/conda/lib/R/library 0.4.2
82 later /home/balter/conda/lib/R/library 1.1.0.1
83 lattice /home/balter/conda/lib/R/library 0.20-41
84 lava /home/balter/conda/lib/R/library 1.6.8.1
85 lazyeval /home/balter/conda/lib/R/library 0.2.2
86 lifecycle /home/balter/conda/lib/R/library 0.2.0
87 lubridate /home/balter/conda/lib/R/library 1.7.9.2
88 magrittr /home/balter/conda/lib/R/library 2.0.1
89 maps /home/balter/conda/lib/R/library 3.3.0
90 markdown /home/balter/conda/lib/R/library 1.1
91 MASS /home/balter/conda/lib/R/library 7.3-53
92 Matrix /home/balter/conda/lib/R/library 1.2-18
93 memoise /home/balter/conda/lib/R/library 1.1.0
94 methods /home/balter/conda/lib/R/library 4.0.3
95 mgcv /home/balter/conda/lib/R/library 1.8-33
96 mime /home/balter/conda/lib/R/library 0.9
97 ModelMetrics /home/balter/conda/lib/R/library 1.2.2.2
98 modelr /home/balter/conda/lib/R/library 0.1.8
99 munsell /home/balter/conda/lib/R/library 0.5.0
100 nlme /home/balter/conda/lib/R/library 3.1-150
101 nnet /home/balter/conda/lib/R/library 7.3-14
102 numDeriv /home/balter/conda/lib/R/library 2016.8-1.1
103 openssl /home/balter/conda/lib/R/library 1.4.3
104 openxlsx /home/balter/conda/lib/R/library 4.2.3
105 parallel /home/balter/conda/lib/R/library 4.0.3
106 pbdZMQ /home/balter/conda/lib/R/library 0.3-3.1
107 pillar /home/balter/conda/lib/R/library 1.4.7
108 pkgbuild /home/balter/conda/lib/R/library 1.1.0
109 pkgconfig /home/balter/conda/lib/R/library 2.0.3
110 pkgload /home/balter/conda/lib/R/library 1.1.0
111 plogr /home/balter/conda/lib/R/library 0.2.0
112 plyr /home/balter/conda/lib/R/library 1.8.6
113 praise /home/balter/conda/lib/R/library 1.0.0
114 prettyunits /home/balter/conda/lib/R/library 1.1.1
115 pROC /home/balter/conda/lib/R/library 1.16.2
116 processx /home/balter/conda/lib/R/library 3.4.4
117 prodlim /home/balter/conda/lib/R/library 2019.11.13
118 progress /home/balter/conda/lib/R/library 1.2.2
119 promises /home/balter/conda/lib/R/library 1.1.1
120 pryr /home/balter/conda/lib/R/library 0.1.4
121 ps /home/balter/conda/lib/R/library 1.4.0
122 purrr /home/balter/conda/lib/R/library 0.3.4
123 quantmod /home/balter/conda/lib/R/library 0.4.17
124 R6 /home/balter/conda/lib/R/library 2.5.0
125 randomForest /home/balter/conda/lib/R/library 4.6-14
126 rapidjsonr /home/balter/conda/lib/R/library 1.2.0
127 rappdirs /home/balter/conda/lib/R/library 0.3.1
128 rbokeh /home/balter/conda/lib/R/library 0.5.1
129 RColorBrewer /home/balter/conda/lib/R/library 1.1-2
130 Rcpp /home/balter/conda/lib/R/library 1.0.5
131 readr /home/balter/conda/lib/R/library 1.4.0
132 readxl /home/balter/conda/lib/R/library 1.3.1
133 recipes /home/balter/conda/lib/R/library 0.1.15
134 rematch /home/balter/conda/lib/R/library 1.0.1
135 rematch2 /home/balter/conda/lib/R/library 2.1.2
136 repr /home/balter/conda/lib/R/library 1.1.0
137 reprex /home/balter/conda/lib/R/library 0.3.0
138 reshape2 /home/balter/conda/lib/R/library 1.4.4
139 reticulate /home/balter/conda/lib/R/library 1.18
140 rlang /home/balter/conda/lib/R/library 0.4.8
141 rmarkdown /home/balter/conda/lib/R/library 2.5
142 rpart /home/balter/conda/lib/R/library 4.1-15
143 rprojroot /home/balter/conda/lib/R/library 2.0.2
144 RSQLite /home/balter/conda/lib/R/library 2.2.1
145 rstudioapi /home/balter/conda/lib/R/library 0.13
146 rvest /home/balter/conda/lib/R/library 0.3.6
147 scales /home/balter/conda/lib/R/library 1.1.1
148 selectr /home/balter/conda/lib/R/library 0.4-2
149 shape /home/balter/conda/lib/R/library 1.4.5
150 shiny /home/balter/conda/lib/R/library 1.5.0
151 sourcetools /home/balter/conda/lib/R/library 0.1.7
152 spatial /home/balter/conda/lib/R/library 7.3-12
153 splines /home/balter/conda/lib/R/library 4.0.3
154 SQUAREM /home/balter/conda/lib/R/library 2020.5
155 stats /home/balter/conda/lib/R/library 4.0.3
156 stats4 /home/balter/conda/lib/R/library 4.0.3
157 stringi /home/balter/conda/lib/R/library 1.5.3
158 stringr /home/balter/conda/lib/R/library 1.4.0
159 survival /home/balter/conda/lib/R/library 3.2-7
160 sys /home/balter/conda/lib/R/library 3.4
161 tcltk /home/balter/conda/lib/R/library 4.0.3
162 testthat /home/balter/conda/lib/R/library 3.0.0
163 tibble /home/balter/conda/lib/R/library 3.0.4
164 tidyr /home/balter/conda/lib/R/library 1.1.2
165 tidyselect /home/balter/conda/lib/R/library 1.1.0
166 tidyverse /home/balter/conda/lib/R/library 1.3.0
167 timeDate /home/balter/conda/lib/R/library 3043.102
168 tinytex /home/balter/conda/lib/R/library 0.27
169 tools /home/balter/conda/lib/R/library 4.0.3
170 triebeard /home/balter/conda/lib/R/library 0.3.0
171 TTR /home/balter/conda/lib/R/library 0.24.2
172 urltools /home/balter/conda/lib/R/library 1.7.3
173 utf8 /home/balter/conda/lib/R/library 1.1.4
174 utils /home/balter/conda/lib/R/library 4.0.3
175 uuid /home/balter/conda/lib/R/library 0.1-4
176 vctrs /home/balter/conda/lib/R/library 0.3.5
177 vipor /home/balter/conda/lib/R/library 0.4.5
178 viridisLite /home/balter/conda/lib/R/library 0.3.0
179 waldo /home/balter/conda/lib/R/library 0.2.3
180 webshot /home/balter/conda/lib/R/library 0.5.2
181 whisker /home/balter/conda/lib/R/library 0.4
182 withr /home/balter/conda/lib/R/library 2.3.0
183 xfun /home/balter/conda/lib/R/library 0.19
184 xml2 /home/balter/conda/lib/R/library 1.3.2
185 xtable /home/balter/conda/lib/R/library 1.8-4
186 xts /home/balter/conda/lib/R/library 0.12.1
187 yaml /home/balter/conda/lib/R/library 2.2.1
188 zeallot /home/balter/conda/lib/R/library 0.1.0
189 zip /home/balter/conda/lib/R/library 2.1.1
190 zoo /home/balter/conda/lib/R/library 1.8-8
R System Profile: /home/balter/conda/lib/R/library/base/R/Rprofile
--------------------------------------------------
### This is the system Rprofile file. It is always run on startup.
### Additional commands can be placed in site or user Rprofile files
### (see ?Rprofile).
### Copyright (C) 1995-2020 The R Core Team
### Notice that it is a bad idea to use this file as a template for
### personal startup files, since things will be executed twice and in
### the wrong environment (user profiles are run in .GlobalEnv).
.GlobalEnv <- globalenv()
attach(NULL, name = "Autoloads")
.AutoloadEnv <- as.environment(2)
assign(".Autoloaded", NULL, envir = .AutoloadEnv)
T <- TRUE
F <- FALSE
R.version <- structure(R.Version(), class = "simple.list")
version <- R.version # for S compatibility
## for backwards compatibility only
R.version.string <- R.version$version.string
## NOTA BENE: options() for non-base package functionality are in places like
## --------- ../utils/R/zzz.R
options(keep.source = interactive())
options(warn = 0)
# options(repos = c(CRAN="@CRAN@"))
# options(BIOC = "http://www.bioconductor.org")
## setting from an env variable added in 4.0.2
local({to <- as.integer(Sys.getenv("R_DEFAULT_INTERNET_TIMEOUT", 60))
if (is.na(to) || to <= 0) to <- 60L
options(timeout = to)
})
options(encoding = "native.enc")
options(show.error.messages = TRUE)
## keep in sync with PrintDefaults() in ../../main/print.c :
options(scipen = 0)
options(max.print = 99999)# max. #{entries} in internal printMatrix()
options(add.smooth = TRUE)# currently only used in 'plot.lm'
if(isFALSE(as.logical(Sys.getenv("_R_OPTIONS_STRINGS_AS_FACTORS_",
"FALSE")))) {
options(stringsAsFactors = FALSE)
} else {
options(stringsAsFactors = TRUE)
}
if(!interactive() && is.null(getOption("showErrorCalls")))
options(showErrorCalls = TRUE)
local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
if(identical(dp, "")) ## it fact methods is done first
dp <- c("datasets", "utils", "grDevices", "graphics",
"stats", "methods")
else if(identical(dp, "NULL")) dp <- character(0)
else dp <- strsplit(dp, ",")[[1]]
dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp) # strip whitespace
options(defaultPackages = dp)
})
## Expand R_LIBS_* environment variables.
Sys.setenv(R_LIBS_SITE =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))
Sys.setenv(R_LIBS_USER =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_USER")))
local({
if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_CPU")))
setSessionTimeLimit(cpu = tl)
if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_ELAPSED")))
setSessionTimeLimit(elapsed = tl)
})
.First.sys <- function()
{
for(pkg in getOption("defaultPackages")) {
res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE)
if(!res)
warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)),
call. = FALSE, domain = NA)
}
}
## called at C level in the startup process prior to .First.sys
.OptRequireMethods <- function()
{
pkg <- "methods" # done this way to avoid R CMD check warning
if(pkg %in% getOption("defaultPackages"))
if(!require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE))
warning('package "methods" in options("defaultPackages") was not found',
call. = FALSE)
}
if(nzchar(Sys.getenv("R_BATCH"))) {
.Last.sys <- function()
{
cat("> proc.time()\n")
print(proc.time())
}
## avoid passing on to spawned R processes
## A system has been reported without Sys.unsetenv, so try this
try(Sys.setenv(R_BATCH=""))
}
local({
if(nzchar(rv <- Sys.getenv("_R_RNG_VERSION_")))
suppressWarnings(RNGversion(rv))
})
###-*- R -*- Unix Specific ----
.Library <- file.path(R.home(), "library")
.Library.site <- Sys.getenv("R_LIBS_SITE")
.Library.site <- if(!nchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strsplit(.Library.site, ":"))
.Library.site <- .Library.site[file.exists(.Library.site)]
invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ":")),
unlist(strsplit(Sys.getenv("R_LIBS_USER"), ":")
))))
local({
popath <- Sys.getenv("R_TRANSLATIONS", "")
if(!nzchar(popath)) {
paths <- file.path(.libPaths(), "translations", "DESCRIPTION")
popath <- dirname(paths[file.exists(paths)][1])
}
bindtextdomain("R", popath)
bindtextdomain("R-base", popath)
assign(".popath", popath, .BaseNamespaceEnv)
})
local({
## we distinguish between R_PAPERSIZE as set by the user and by configure
papersize <- Sys.getenv("R_PAPERSIZE_USER")
if(!nchar(papersize)) {
lcpaper <- Sys.getlocale("LC_PAPER") # might be null: OK as nchar is 0
papersize <- if(nchar(lcpaper))
if(length(grep("(_US|_CA)", lcpaper))) "letter" else "a4"
else Sys.getenv("R_PAPERSIZE")
}
options(papersize = papersize,
printcmd = Sys.getenv("R_PRINTCMD"),
dvipscmd = Sys.getenv("DVIPS", "dvips"),
texi2dvi = Sys.getenv("R_TEXI2DVICMD"),
browser = Sys.getenv("R_BROWSER"),
pager = file.path(R.home(), "bin", "pager"),
pdfviewer = Sys.getenv("R_PDFVIEWER"),
useFancyQuotes = TRUE)
})
## non standard settings for the R.app GUI of the macOS port
if(.Platform$GUI == "AQUA") {
## this is set to let RAqua use both X11 device and X11/TclTk
if (Sys.getenv("DISPLAY") == "")
Sys.setenv("DISPLAY" = ":0")
## this is to allow gfortran compiler to work
Sys.setenv("PATH" = paste(Sys.getenv("PATH"),":/usr/local/bin",sep = ""))
}## end "Aqua"
## de-dupe the environment on macOS (bug in Yosemite which affects things like PATH)
if (grepl("^darwin", R.version$os)) local({
## we have to de-dupe one at a time and re-check since the bug affects how
## environment modifications propagate
while(length(dupes <- names(Sys.getenv())[table(names(Sys.getenv())) > 1])) {
env <- dupes[1]
value <- Sys.getenv(env)
Sys.unsetenv(env) ## removes the dupes, good
.Internal(Sys.setenv(env, value)) ## wrapper requries named vector, a pain, hence internal
}
})
local({
tests_startup <- Sys.getenv("R_TESTS")
if(nzchar(tests_startup)) source(tests_startup)
})
R Site Profile: /home/balter/conda/lib/R/etc/Rprofile.site
--------------------------------------------------
(File does not exist)
R User Profile: /home/balter/.Rprofile
--------------------------------------------------
(File does not exist)
R Site Environ: /home/balter/conda/lib/R/etc/Renviron.site
--------------------------------------------------
(File does not exist)
R User Environ: /home/balter/.Renviron
--------------------------------------------------
(File does not exist)
R Temporary Directory
--------------------------------------------------
/tmp/RtmpIy90MX
Files in R Temporary Directory
--------------------------------------------------
rs-graphics-b0a800de-ecd4-4928-a796-7086922c1806
Log file: /home/balter/.rstudio-desktop/log/rdesktop.log
--------------------------------------------------
(Not Found)
Log file: /home/balter/.rstudio-desktop/log/rsession-balter.log
--------------------------------------------------
04 Dec 2020 20:56:02 [rsession-balter] ERROR r error 4 (R code execution error) [errormsg: Error in tools::startDynamicHelp() : internet routines cannot be loaded
]; OCCURRED AT rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:171; LOGGED FROM: rstudio::core::Error rstudio::session::modules::help::initialize() src/cpp/session/modules/SessionHelp.cpp:1029
User prefs: /home/balter/.config/rstudio/rstudio-prefs.json
--------------------------------------------------
{
"panes": {
"quadrants": [
"Source",
"TabSet2",
"TabSet1",
"Console"
],
"tabSet1": [
"Environment",
"History",
"Files",
"Plots",
"Connections",
"Packages",
"Help",
"Build",
"VCS",
"Tutorial",
"Presentation"
],
"tabSet2": [
"Viewer"
],
"console_left_on_top": false,
"console_right_on_top": false
},
"pdf_previewer": "none",
"posix_terminal_shell": "bash",
"console_double_click_select": true,
"help_font_size_points": 9,
"full_project_path_in_window_title": true,
"remove_history_duplicates": true,
"show_doc_outline_rmd": true,
"show_rmd_render_command": true
}
System prefs: /etc/rstudio/rstudio-prefs.json
--------------------------------------------------
(Not Found)
User state: /home/balter/.local/share/rstudio/rstudio-desktop.json
--------------------------------------------------
{
"context_id": "EAEA9570",
"error_handler_type": "traceback"
}
from r-base-feedstock.
martin-jeremy
commented on September 26, 2024
@martin-jeremy Thanks for the bug report. We expect that the r-base from conda-forge should work with RStudio. Here are some more questions to help us troubleshoot the issue:
1. What version of RStudio did you install? Are you using RStudio Desktop or Server? Does it work if you install an older version of RStudio, e.g. 1.1? 2. Is there a Docker container we can use to reproduce the issue?I did some searching, and this error message seems to be a long-standing issue. There doesn't appear to be an easy fix. The common theme seems to be that RStudio gets confused when R is installed via a package manager like conda or spack.
rstudio/rstudio#4904
spack/spack#19051
ContinuumIO/anaconda-issues#4421
Thank's for your return. I have find these link but it didn't look likes there is a good solution to my problem;
I use RStudio Desktop v1.3.1093 Apricot Nasturtium from the .deb file on rstudio website. I can't try with RStudio 1.1 because lot of dependencies are deprecated.
I also tried to install rstudioapi from the conda-forge, thinking it will be a possible way to fix it but it won't.
I don't have a docker file to reproduce it, but I have this issue with Ubuntu 20.04 and Pop OS! 20.04 and colleagues with Ubuntu 18.04
from r-base-feedstock.
martin-jeremy
commented on September 26, 2024
Well, I think I have found how to fix my problem !
It looks like as rstudio didn't load all the libraries in the conda environment. For instance if I run :
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATHI can use normally rstudio, but if I won't, I have :
Error in tools::startDynamicHelp() :
internet routines cannot be loaded
So, what I have done is to write two little script env_vars.sh in $CONDA_PREFIX/etc/conda/activate.d/ and in $CONDA_PREFIX/etc/conda/deactivate.d/ :
$CONDA_PREFIX/etc/conda/activate.d/env_vars.sh :
#!/usr/bin/env sh
# store old LD_LIBRARY_PATH:
if [ ! -z ${LD_LIBRARY_PATH+x} ]; then
OLD_LD_LIBRARY_PATH="$LD_LIBRARY_PATH"
fi
# export Conda env libs
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$D_LIBRARY_PATH$CONDA_PREFIX/etc/conda/deactivate.d/env_vars.sh :
#!/usr/bin/env sh
# unset library path
unset LD_LIBRARY_PATH
# restore old library path
if [ ! -z ${OLD_LD_LIBRARY_PATH+x} ]; then
export LD_LIBRARY_PATH=$OLD_LD_LIBRARY_PATH
fi
unset OLD_LD_LIBRARY_PATHThat I don't know is why this fix my problem, because if I run a diagnostic report of RStudio from my Fedora 31 Desktop, where RStudio and Conda R run correctly, I can see this line :
LD_LIBRARY_PATH : /home/USER/bin/conda/envs/idh/lib/R/lib:
And with my laptop, I have the same line but with :
LD_LIBRARY_PATH : /home/USER/bin/conda/envs/idh/lib/R/lib: it doesn't runs correctly and with
LD_LIBRARY_PATH : /home/USER/bin/conda/envs/idh/lib:/home/USER/bin/conda/envs/idh/lib/R/lib: it runs correctly.
Also, if anyone can tell me, how can I automated the creation of these two env_vars script when I do a conda create -n CONDA_ENV , it will be very helpful.
Thank's a lot for your help
from r-base-feedstock.
jdblischak
commented on September 26, 2024
So, what I have done is to write to little script env_vars.sh in $CONDA_PREFIX/etc/conda/activate.d/ and in $CONDA_PREFIX/etc/conda/deactivate.d/ :
@martin-jeremy Good job finding a workaround! I'm glad you have it working for now.
Since one month, I can't run RStudio with my conda environment activated.
Similar to you, I rely on being able to use the RStudio executable installed from the .deb with R installed from conda-forge. This always used to work, so something clearly changed. While your workaround fixes the issue, this is not a great long-term solution. Most conda users aren't familiar with activation scripts (and shouldn't have to be). Also, I like to avoid directly fiddling with LD_LIBRARY_PATH if at all possible. It almost always causes unforeseen headaches.
Based on some testing I did, I think the issue is with RStudio. Everything works fine with RStudio 1.1, but I get the same error as you with RStudio 1.3.
| OS | R (conda-forge) | RStudio | Status |
|---|---|---|---|
| Ubuntu 18.04.4 LTS | R 3.6.3 | 1.1.383 | ✔️ |
| Ubuntu 18.04.4 LTS | R 4.0.3 | 1.1.383 | ✔️ |
| Ubuntu 18.04.4 LTS | R 3.6.3 | 1.3.1093 | ❌ |
| Ubuntu 18.04.4 LTS | R 4.0.3 | 1.3.1093 | ❌ |
from r-base-feedstock.
abalter
commented on September 26, 2024
@jdblischak Bingo! You did it!
from r-base-feedstock.
martin-jeremy
commented on September 26, 2024
I also installed the preview version of RStudio 1.4. It works with conda-forge R, so this is more evidence that there is something strange specifically with RStudio 1.3.
OS R (conda-forge) RStudio Status
Ubuntu 18.04.4 LTS R 3.6.3 1.4.1081 ✔️
Ubuntu 18.04.4 LTS R 4.0.3 1.4.1081 ✔️I also wanted to test RStudio 1.2, but the download link is currently broken.
This is cleaner than my solution ^^ and yes, it fix the problem, I close the issue and I give the link for my colleagues ! Thank's a lot for yours tests !
from r-base-feedstock.
jdblischak
commented on September 26, 2024
The download links for RStudio 1.2 were fixed, and I confirmed that 1.2 also works with conda-installed R.
| OS | R (conda-forge) | RStudio | Status |
|---|---|---|---|
| Ubuntu 18.04.4 LTS | R 3.6.3 | 1.2.5042 | ✔️ |
| Ubuntu 18.04.4 LTS | R 4.0.3 | 1.2.5042 | ✔️ |
from r-base-feedstock.
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