In R version 4.0.0 library path not writable

c-mertes · August 27, 2020, 6:25pm

Hey all,

I noticed today that my builds failed for only R >= 4.0.0 versions on travis. As we did not changed anything in the travis.yml and it still works for 3.6.3 I assume it might be the setup script.

you can see the failing jobs here:

https://travis-ci.com/github/c-mertes/FRASER/builds/181678791

The error we face is:

Installing Bioconductor
$ Rscript -e 'if (!requireNamespace("BiocManager", quietly=TRUE))  
install.packages("BiocManager");if (TRUE) BiocManager::install(version = "devel", ask = FALSE);cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocManager::repositories());")'
Warning in install.packages("BiocManager") :
  'lib = "/opt/R/4.0.0/lib/R/library"' is not writable
Error in install.packages("BiocManager") : unable to install packages
Execution halted
The command "eval Rscript -e 'if (!requireNamespace("BiocManager", quietly=TRUE))  
install.packages("BiocManager");if (TRUE) BiocManager::install(version = "devel", ask = FALSE);cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocManager::repositories());")' " failed. Retrying, 2 of 3.

Any idea @jeroen and @jimhester what could be the cause and how to fix it?

jeroen · August 27, 2020, 6:47pm

Did you try to wipe the cache?

c-mertes · August 27, 2020, 7:16pm

yes I did this already. Under the cache option I clicked Delete all repository caches.

bbimber · August 27, 2020, 8:32pm

We just starting to hit this with R 3.6.3 as well:

https://travis-ci.com/github/bimberlabinternal/OOSAP/jobs/378528732

The command "eval Rscript -e 'if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager");if (FALSE) BiocManager::install(version = "devel", ask = FALSE);cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocManager::repositories());")' " failed. Retrying, 3 of 3.

Warning in install.packages("BiocManager") :
 'lib = "/opt/R/3.6.3/lib/R/library"' is not writable
Error in install.packages("BiocManager") : unable to install packages
Execution halted

adigherman · August 27, 2020, 8:37pm

I am also seeing this on all my new unix builds from R 3.4 to R 4.0. My guess is that since you guys are now using a Debian package to install R it’s probably installing it in a different path than it used to when you were unzipping it directly.

muschellij2 · August 27, 2020, 8:44pm

I’m not sure that export is being invoked from https://github.com/travis-ci/travis-build/blob/master/lib/travis/build/script/r.rb#L47 or if the gdebi installation is overwriting these?

harpomaxx · August 28, 2020, 9:57pm

Same problem here. The build fails because it can’t write the library path for R >=4.0.

https://travis-ci.org/github/harpomaxx/GSgalgoR/builds/722161711

Any idea for bypassing the problem, at least for now?

mdozmorov · August 29, 2020, 7:51pm

Same error. It started to appear around August 27, 2020. Google currently points only to this thread. Looking for advice what to do.
https://travis-ci.com/github/dozmorovlab/preciseTAD/jobs/379115179#L758

Installing Bioconductor
$ Rscript -e 'if (!requireNamespace("BiocManager", quietly=TRUE))  install.packages("BiocManager");if (TRUE) BiocManager::install(version = "devel", ask = FALSE);cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocManager::repositories());")'
Warning in install.packages("BiocManager") :
  'lib = "/opt/R/4.0.0/lib/R/library"' is not writable
Error in install.packages("BiocManager") : unable to install packages
Execution halted

c-mertes · August 31, 2020, 7:34am

I think @muschellij2 is right that somehow the export is not invoked.
Based on my little test it seems like its only coming up with bioc versions.

https://travis-ci.com/github/c-mertes/test-ci/builds/182026369

So I guess a workaround is to use base R versions and install the bioconductor packages yourself.

LiNk-NY · August 31, 2020, 2:32pm

It seems that the PATH variable was changed in a recent commit.
I’ve asked Jim @jimhester for more info here https://github.com/travis-ci/travis-build/commit/51f5f85ad56a6cfea94a3ce71d8ced29c26d4e45

AnneSoBen · September 1, 2020, 2:37pm

We have the same error here:
https://travis-ci.org/github/metabaRfactory/metabaR/builds/723096728

Has anyone found a solution to bypass the problem?

bbimber · September 1, 2020, 4:00pm

@c-mertes had a good point above - we just switched our config to use base R (require_bioc=False), and installed bioconductor ourselves.

adigherman · September 1, 2020, 5:26pm

I traced this to the R package installer config options options, specifically the libR.pc file.

pkg-config retrieves information about packages from special metadata files. These files are named after the package, and have a .pc extension.

The previous R install had
rhome=/home/travis/R-bin/lib/R rlibdir=${rhome}/lib rincludedir=/home/travis/R-bin/lib/R/include

the new installer (using gdebi) has
rhome=/opt/R/4.0.0/lib/R rlibdir=${rhome}/lib rincludedir=/opt/R/4.0.0/lib/R/include

AnneSoBen · September 2, 2020, 8:34am

Thanks! I tried this solution but, as a beginner, I think I didn’t do it right… At which step should we install BiocManager? Could you give a config example?

bbimber · September 2, 2020, 1:36pm

This is possibly not the most elegant way, and it includes more code than you need, but I think if you add a before_install that runs a script like this (ignore the rest of what’s in this):

github.com

bimberlabinternal/OOSAP/blob/Dev/.travis.yml

# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
# and: https://github.com/travis-ci/travis-build/blob/master/lib/travis/build/script/r.rb

dist: bionic
language: r
r: 3.6.3

# See: https://travis-ci.community/t/in-r-version-4-0-0-library-path-not-writable/9744/9
bioc_required: false

cache:
  - packages
  - pip
  - ccache

python:
  - "3.6"

os:
  - linux

This file has been truncated. show original

and in your script you install the right Bioconductor version, and then update Rprofile (lines 67-77):

github.com

bimberlabinternal/OOSAP/blob/Dev/travis-config.sh

#!/bin/bash

# See:
# http://dirk.eddelbuettel.com/blog/2017/11/27/
# https://www.jumpingrivers.com/blog/speeding-up-package-installation/
# https://github.com/travis-ci/travis-build/blob/master/lib/travis/build/script/r.rb
echo 'Running travis setup'

mkdir $HOME/.R

export R_BIOC_VERSION='3.10'

# Force python3:
python3 -m pip install --upgrade pip

python3 --version
python --version
pip3 --version
pip --version

This file has been truncated. show original

That will probably do it.

native-api · September 6, 2020, 9:51am

@jeroen @jimhester this PR should resolve the issue by installing packages into per-user location (option 2 below)

A workaround is to install packages manually in the install: phase, passing lib = Sys.getenv("R_LIBS_USER") to install functions everywhere.

https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages:

lib <…> If missing, defaults to the first element of .libPaths().

https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/libPaths:

The library search path is initialized at startup from the environment variable R_LIBS <…> followed by those in environment variable R_LIBS_USER .

R_LIBS is never set, so the above-mentioned default that the package is configured with must be being used instead.

So we have a few options:

install packages system-wide with sudo
install packages per-user
set R_LIBS (probably not a good idea as there might be something on the default paths already)

jeroen · September 6, 2020, 12:37pm

I hope this will fix it: https://github.com/travis-ci/travis-build/pull/1957

native-api · September 14, 2020, 5:04pm

12 posts were split to a new topic: BiocCheck installation cannot install scripts; thus “R CMD BiocCheck” fails

richelbilderbeek · September 9, 2020, 8:50am

Issue appears solved to me: my Bioconductor builds pass . Thanks @jeroen and @native-api!

jeroen · September 9, 2020, 9:38am

OK, thank you for letting us know!

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In R version 4.0.0 library path not writable

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