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conda-forge / r-base-feedstock

A conda-smithy repository for r-base.
BSD 3-Clause "New" or "Revised" License
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Incompatibility between R and RStudio on Debian Systems #146

Closed martin-jeremy closed 3 years ago

martin-jeremy commented 3 years ago

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 ```
jdblischak commented 3 years ago

@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.

https://github.com/rstudio/rstudio/issues/4904 https://github.com/spack/spack/issues/19051 https://github.com/ContinuumIO/anaconda-issues/issues/4421

abalter commented 3 years ago

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
--------------------------------------------------
_                                 : /usr/bin/rstudio
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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
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BUILD                             : x86_64-conda-linux-gnu
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CC_FOR_BUILD                      : /home/balter/conda/bin/x86_64-conda-linux-gnu-cc
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LESSOPEN                          : | /usr/bin/lesspipe %s
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MOTD_SHOWN                        : update-motd
NAME                              : ORLT1072346
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PWD                               : /home/balter
R_BROWSER                         : 
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RS_SHARED_SECRET                  : *** redacted ***
RSTUDIO                           : 1
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RSTUDIO_CONSOLE_WIDTH             : 80
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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                            : 
XDG_DATA_DIRS                     : /usr/local/share:/usr/share:/var/lib/snapd/desktop

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
11          boot /home/balter/conda/lib/R/library     1.3-25
12          brio /home/balter/conda/lib/R/library      1.1.0
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
46       foreign /home/balter/conda/lib/R/library     0.8-80
47       formatR /home/balter/conda/lib/R/library        1.7
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"
}
martin-jeremy commented 3 years ago

@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

martin-jeremy commented 3 years ago

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_PATH

I 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_PATH

That 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

jdblischak commented 3 years ago

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 :heavy_check_mark:
Ubuntu 18.04.4 LTS R 4.0.3 1.1.383 :heavy_check_mark:
Ubuntu 18.04.4 LTS R 3.6.3 1.3.1093 :x:
Ubuntu 18.04.4 LTS R 4.0.3 1.3.1093 :x:
jdblischak commented 3 years ago

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 :heavy_check_mark:
Ubuntu 18.04.4 LTS R 4.0.3 1.4.1081 :heavy_check_mark:

I also wanted to test RStudio 1.2, but the download link is currently broken.

abalter commented 3 years ago

@jdblischak Bingo! You did it!

martin-jeremy commented 3 years ago

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 !

jdblischak commented 3 years ago

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 :heavy_check_mark:
Ubuntu 18.04.4 LTS R 4.0.3 1.2.5042 :heavy_check_mark: