How to manually set all required environment variables in RStudio Server Open Source

rstudio
anaconda

#1

I'm running RStudio Server Open Source edition. I use conda as my package manager. In the open source edition there is no provision to select an R executable through the IDE. You need to set it globally in /etc/rstudio/rserver.conf.

I've been playing around with using my .Rprofile to manually set paths for the conda environment I want to use for a specific project. Here is an example:

If I start R in a particular conda environment then all the paths seem to set automatically as required.

(base) balter@conda-test:~/rsenvtest$ source activate r35
(r35) balter@conda-test:~/rsenvtest$ R

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

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.
>
> Sys.getenv()
_CONDA_PYTHON_SYSCONFIGDATA_NAME
                        _sysconfigdata_x86_64_conda_cos6_linux_gnu
ADDR2LINE               /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-addr2line
AR                      /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-ar
AS                      /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-as
CC                      /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-cc
CFLAGS                  -march=nocona -mtune=haswell -ftree-vectorize
                        -fPIC -fstack-protector-strong -fno-plt -O2
                        -pipe
COLUMNS                 198
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME
                        _sysconfigdata_x86_64_conda_cos6_linux_gnu
CONDA_BACKUP_ADDR2LINE
                        /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-addr2line
CONDA_BACKUP_AR         /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-ar
CONDA_BACKUP_AS         /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-as
CONDA_BACKUP_CC         /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-cc
CONDA_BACKUP_CFLAGS     -march=nocona -mtune=haswell -ftree-vectorize
                        -fPIC -fstack-protector-strong -fno-plt -O2
                        -pipe
CONDA_BACKUP_CPP        /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-cpp
CONDA_BACKUP_CPPFLAGS   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2
CONDA_BACKUP_CXX        /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-c++
CONDA_BACKUP_CXXFILT    /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-c++filt
CONDA_BACKUP_CXXFLAGS   -fvisibility-inlines-hidden -std=c++17
                        -fmessage-length=0 -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
CONDA_BACKUP_DEBUG_CFLAGS
                        -march=nocona -mtune=haswell -ftree-vectorize
                        -fPIC -fstack-protector-all -fno-plt -Og -g
                        -Wall -Wextra -fvar-tracking-assignments -pipe
CONDA_BACKUP_DEBUG_CPPFLAGS
                        -D_DEBUG -D_FORTIFY_SOURCE=2 -Og
CONDA_BACKUP_DEBUG_CXXFLAGS
                        -fvisibility-inlines-hidden -std=c++17
                        -fmessage-length=0 -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-all
                        -fno-plt -Og -g -Wall -Wextra
                        -fvar-tracking-assignments -pipe
CONDA_BACKUP_DEBUG_FFLAGS
                        -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe -fopenmp -march=nocona
                        -mtune=haswell -ftree-vectorize -fPIC
                        -fstack-protector-all -fno-plt -Og -g -Wall
                        -Wextra -fcheck=all -fbacktrace -fimplicit-none
                        -fvar-tracking-assignments -pipe
CONDA_BACKUP_DEBUG_FORTRANFLAGS
                        -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe -fopenmp -march=nocona
                        -mtune=haswell -ftree-vectorize -fPIC
                        -fstack-protector-all -fno-plt -Og -g -Wall
                        -Wextra -fcheck=all -fbacktrace -fimplicit-none
                        -fvar-tracking-assignments -pipe
CONDA_BACKUP_ELFEDIT    /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-elfedit
CONDA_BACKUP_F77        /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gfortran
CONDA_BACKUP_F95        /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-f95
CONDA_BACKUP_FC         /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gfortran
CONDA_BACKUP_FFLAGS     -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
CONDA_BACKUP_FORTRANFLAGS
                        -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
CONDA_BACKUP_GCC        /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gcc
CONDA_BACKUP_GCC_AR     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
CONDA_BACKUP_GCC_NM     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
CONDA_BACKUP_GCC_RANLIB
                        /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
CONDA_BACKUP_GFORTRAN   /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gfortran
CONDA_BACKUP_GPROF      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gprof
CONDA_BACKUP_GXX        /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-g++
CONDA_BACKUP_HOST       x86_64-conda_cos6-linux-gnu
CONDA_BACKUP_LD         /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-ld
CONDA_BACKUP_LD_GOLD    /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-ld.gold
CONDA_BACKUP_LDFLAGS    -Wl,-O2 -Wl,--sort-common -Wl,--as-needed
                        -Wl,-z,relro -Wl,-z,now
CONDA_BACKUP_NM         /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-nm
CONDA_BACKUP_OBJCOPY    /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-objcopy
CONDA_BACKUP_OBJDUMP    /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-objdump
CONDA_BACKUP_RANLIB     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-ranlib
CONDA_BACKUP_READELF    /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-readelf
CONDA_BACKUP_SIZE       /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-size
CONDA_BACKUP_STRINGS    /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-strings
CONDA_BACKUP_STRIP      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-strip
CONDA_DEFAULT_ENV       r35
CONDA_EXE               /home/lab/conda/bin/conda
CONDA_PREFIX            /home/lab/conda/envs/r35
CONDA_PREFIX_1          /home/lab/conda
CONDA_PROMPT_MODIFIER   (r35)
CONDA_PYTHON_EXE        /home/lab/conda/bin/python
CONDA_SHLVL             2
CPP                     /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-cpp
CPPFLAGS                -DNDEBUG -D_FORTIFY_SOURCE=2 -O2
CURL_CA_BUNDLE          /home/lab/conda/envs/r35/lib/R/lib/microsoft-r-cacert.pem
CXX                     /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-c++
CXXFILT                 /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-c++filt
CXXFLAGS                -fvisibility-inlines-hidden -std=c++17
                        -fmessage-length=0 -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
DEBUG_CFLAGS            -march=nocona -mtune=haswell -ftree-vectorize
                        -fPIC -fstack-protector-all -fno-plt -Og -g
                        -Wall -Wextra -fvar-tracking-assignments -pipe
DEBUG_CPPFLAGS          -DNDEBUG -D_FORTIFY_SOURCE=2 -O2
DEBUG_CXXFLAGS          -fvisibility-inlines-hidden -std=c++17
                        -fmessage-length=0 -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-all
                        -fno-plt -Og -g -Wall -Wextra
                        -fvar-tracking-assignments -pipe
DEBUG_FFLAGS            -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
DEBUG_FORTRANFLAGS      -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
EDITOR                  vi
ELFEDIT                 /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-elfedit
F77                     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gfortran
F95                     /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-f95
FC                      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gfortran
FFLAGS                  -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
FORTRANFLAGS            -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
GCC                     /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-gcc
GCC_AR                  /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
GCC_NM                  /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
GCC_RANLIB              /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
GFORTRAN                /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-gfortran
GPROF                   /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-gprof
GXX                     /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-g++
HOME                    /home/balter
HOST                    x86_64-conda_cos6-linux-gnu
LANG                    C.UTF-8
LD                      /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-ld
LD_GOLD                 /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-ld.gold
LD_LIBRARY_PATH         /home/lab/conda/envs/r35/lib/R/lib:/builddir/vendor/build/lib
LDFLAGS                 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed
                        -Wl,-z,relro -Wl,-z,now
LESSCLOSE               /usr/bin/lesspipe %s %s
LESSOPEN                | /usr/bin/lesspipe %s
LINES                   57
LN_S                    ln -s
LOGNAME                 balter
LS_COLORS               rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*
.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:
*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01
;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35
:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.m
pg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=0
1;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.m
id=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
MAIL                    /var/mail/balter
MAKE                    make
NM                      /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-nm
OBJCOPY                 /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-objcopy
OBJDUMP                 /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-objdump
OLDPWD                  /home/balter
PAGER                   less
PATH                    /home/lab/conda/envs/r35/bin:/home/lab/conda/envs/r35/bin:/home/lab/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/b
in
PWD                     /home/balter/rsenvtest
R_ARCH
R_BROWSER               open
R_BZIPCMD               bzip2
R_DOC_DIR               /home/lab/conda/envs/r35/lib/R/doc
R_GZIPCMD               gzip
R_HOME                  /home/lab/conda/envs/r35/lib/R
R_INCLUDE_DIR           /home/lab/conda/envs/r35/lib/R/include/
R_LIBS_SITE             /home/lab/conda/envs/r35/lib/R/library/
R_LIBS_USER             /home/balter/R/
R_PAPERSIZE             a4
R_PDFVIEWER             open
R_PLATFORM              x86_64-pc-linux-gnu
R_PRINTCMD
R_RD4PDF                times,inconsolata,hyper
R_SESSION_TMPDIR        /tmp/RtmpMZxAm2
R_SHARE_DIR             /home/lab/conda/envs/r35/lib/R/share
R_SYSTEM_ABI            linux,gcc,gxx,gfortran,?
R_TEXI2DVICMD           texi2dvi
R_UNZIPCMD              unzip
R_ZIPCMD                zip
RANLIB                  /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-ranlib
READELF                 /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-readelf
SED                     /bin/sed
SHELL                   /bin/bash
SHLVL                   1
SIZE                    /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-size
SSH_CLIENT              73.11.33.164 50893 22
SSH_CONNECTION          73.11.33.164 50893 178.128.190.17 22
SSH_TTY                 /dev/pts/1
STRINGS                 /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-strings
STRIP                   /home/lab/conda/envs/r35/bin/x86_64-conda_cos6-linux-gnu-strip
TAR                     tar
TCL_LIBRARY             /home/lab/conda/envs/r35/lib/R/share/tcl8.6/
TERM                    xterm-256color
USER                    balter
XDG_DATA_DIRS           /usr/local/share:/usr/share:/var/lib/snapd/desktop
XDG_RUNTIME_DIR         /run/user/1000
XDG_SESSION_ID          491

And I can install the Bioconductor installer.

>
> source("https://bioconductor.org/biocLite.R")
trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/BiocInstaller_1.30.0.tar.gz'
Content type 'application/x-gzip' length 19149 bytes (18 KB)
==================================================
downloaded 18 KB

/home/balter/rsenvtest
initial path is /home/lab/conda/envs/r35/bin:/home/lab/conda/envs/r35/bin:/home/lab/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PATH: /home/lab/conda/envs/r35/bin:/home/lab/conda/envs/r35/bin:/home/lab/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
/home/lab/conda/envs/r35/bin:/home/lab/conda/envs/r35/bin:/home/lab/conda/envs/r35/bin:/home/lab/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/s
nap/bin
/home/lab/conda/envs/r35/bin/R
* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
* DONE (BiocInstaller)

The downloaded source packages are in
        ‘/tmp/RtmpMZxAm2/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
>

This is my attempt to set all the paths manually in a .Rprofile:

(base) balter@conda-test:~/rsenvtest$ cat .Rprofile
system('pwd')
system('echo "initial path is $PATH"')

env_base = "/home/lab/conda/envs/r35"

PATH = Sys.getenv('PATH')

Sys.setenv("R_LIBS_SITE"=paste0(env_base, "/lib/R/library/"))
Sys.setenv("R_LIBS_USER"="/home/balter/R/")
Sys.setenv("R_INCLUDE_DIR"= paste0(env_base, "/lib/R/include/"))
Sys.setenv("R_SHARE_DIR"=paste0(env_base, "/lib/R/share"))
Sys.setenv("R_HOME"=paste0(env_base, "/lib/R"))
Sys.setenv(PATH=paste0(env_base, "/bin:", PATH))
.libPaths(paste0(env_base, "/lib/R/library/"))

message(paste0("PATH: ",PATH))
system('echo $PATH')
system('which R')

However, this clearly does not handle all issues:

(base) balter@conda-test:~/rsenvtest$ R

R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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.

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.

/home/balter/rsenvtest
initial path is /home/lab/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PATH: /home/lab/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
/home/lab/conda/envs/r35/bin:/home/lab/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
/home/lab/conda/envs/r35/bin/R
> system('which R')
/home/lab/conda/envs/r35/bin/R
> Sys.getenv()
_                       /home/lab/conda/bin/R
_CONDA_PYTHON_SYSCONFIGDATA_NAME
                        _sysconfigdata_x86_64_conda_cos6_linux_gnu
ADDR2LINE               /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-addr2line
AR                      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-ar
AS                      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-as
CC                      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-cc
CFLAGS                  -march=nocona -mtune=haswell -ftree-vectorize
                        -fPIC -fstack-protector-strong -fno-plt -O2
                        -pipe
COLUMNS                 198
CONDA_BACKUP_HOST       x86_64-conda_cos6-linux-gnu
CONDA_DEFAULT_ENV       base
CONDA_EXE               /home/lab/conda/bin/conda
CONDA_PREFIX            /home/lab/conda
CONDA_PROMPT_MODIFIER   (base)
CONDA_PYTHON_EXE        /home/lab/conda/bin/python
CONDA_SHLVL             1
CPP                     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-cpp
CPPFLAGS                -DNDEBUG -D_FORTIFY_SOURCE=2 -O2
CXX                     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-c++
CXXFILT                 /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-c++filt
CXXFLAGS                -fvisibility-inlines-hidden -std=c++17
                        -fmessage-length=0 -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
DEBUG_CFLAGS            -march=nocona -mtune=haswell -ftree-vectorize
                        -fPIC -fstack-protector-all -fno-plt -Og -g
                        -Wall -Wextra -fvar-tracking-assignments -pipe
DEBUG_CPPFLAGS          -D_DEBUG -D_FORTIFY_SOURCE=2 -Og
DEBUG_CXXFLAGS          -fvisibility-inlines-hidden -std=c++17
                        -fmessage-length=0 -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-all
                        -fno-plt -Og -g -Wall -Wextra
                        -fvar-tracking-assignments -pipe
DEBUG_FFLAGS            -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe -fopenmp -march=nocona
                        -mtune=haswell -ftree-vectorize -fPIC
                        -fstack-protector-all -fno-plt -Og -g -Wall
                        -Wextra -fcheck=all -fbacktrace -fimplicit-none
                        -fvar-tracking-assignments -pipe
DEBUG_FORTRANFLAGS      -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe -fopenmp -march=nocona
                        -mtune=haswell -ftree-vectorize -fPIC
                        -fstack-protector-all -fno-plt -Og -g -Wall
                        -Wextra -fcheck=all -fbacktrace -fimplicit-none
                        -fvar-tracking-assignments -pipe
EDITOR                  vi
ELFEDIT                 /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-elfedit
F77                     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gfortran
F95                     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-f95
FC                      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gfortran
FFLAGS                  -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
FORTRANFLAGS            -fopenmp -march=nocona -mtune=haswell
                        -ftree-vectorize -fPIC -fstack-protector-strong
                        -fno-plt -O2 -pipe
GCC                     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gcc
GCC_AR                  /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
GCC_NM                  /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
GCC_RANLIB              /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
GFORTRAN                /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gfortran
GPROF                   /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-gprof
GXX                     /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-g++
HOME                    /home/balter
HOST                    x86_64-conda_cos6-linux-gnu
LANG                    C.UTF-8
LD                      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-ld
LD_GOLD                 /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-ld.gold
LDFLAGS                 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed
                        -Wl,-z,relro -Wl,-z,now
LESSCLOSE               /usr/bin/lesspipe %s %s
LESSOPEN                | /usr/bin/lesspipe %s
LINES                   57
LN_S                    ln -s
LOGNAME                 balter
LS_COLORS               rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*
.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:
*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01
;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35
:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.m
pg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=0
1;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.m
id=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
MAIL                    /var/mail/balter
MAKE                    make
NM                      /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-nm
OBJCOPY                 /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-objcopy
OBJDUMP                 /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-objdump
OLDPWD                  /home/balter
PAGER                   /usr/bin/less
PATH                    /home/lab/conda/envs/r35/bin:/home/lab/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PWD                     /home/balter/rsenvtest
R_ARCH
R_BROWSER               /usr/bin/open
R_BZIPCMD               /home/lab/conda/bin/bzip2
R_DOC_DIR               /home/lab/conda/lib/R/doc
R_GZIPCMD               /usr/bin/gzip
R_HOME                  /home/lab/conda/envs/r35/lib/R
R_INCLUDE_DIR           /home/lab/conda/envs/r35/lib/R/include/
R_LIBS_SITE             /home/lab/conda/envs/r35/lib/R/library/
R_LIBS_USER             /home/balter/R/
R_PAPERSIZE             a4
R_PDFVIEWER             /usr/bin/open
R_PLATFORM              x86_64-conda_cos6-linux-gnu
R_PRINTCMD
R_RD4PDF                times,hyper
R_SESSION_TMPDIR        /tmp/Rtmp9I3Q44
R_SHARE_DIR             /home/lab/conda/envs/r35/lib/R/share
R_SYSTEM_ABI            linux,gcc,gxx,gfortran,?
R_TEXI2DVICMD           texi2dvi
R_UNZIPCMD              /usr/bin/unzip
R_ZIPCMD
RANLIB                  /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-ranlib
READELF                 /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-readelf
SED                     /bin/sed
SHELL                   /bin/bash
SHLVL                   1
SIZE                    /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-size
SSH_CLIENT              73.11.33.164 50893 22
SSH_CONNECTION          73.11.33.164 50893 178.128.190.17 22
SSH_TTY                 /dev/pts/1
STRINGS                 /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-strings
STRIP                   /home/lab/conda/bin/x86_64-conda_cos6-linux-gnu-strip
TAR                     /bin/gtar
TERM                    xterm-256color
USER                    balter
XDG_DATA_DIRS           /usr/local/share:/usr/share:/var/lib/snapd/desktop
XDG_RUNTIME_DIR         /run/user/1000
XDG_SESSION_ID          491
> source("https://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
  internet routines cannot be loaded

The environment variables are very different.


RStudio Server open source not running .Renviron
#2

2 posts were merged into an existing topic: RStudio Server open source not running .Renviron


#3