Error when travis install BiocManager for Linux / R - release

r

#1

Details: https://github.com/travis-ci/travis-ci/issues/10321.
Another example: https://travis-ci.org/ropensci/drake/jobs/451189229#L904
I believe the double quotes around BiocManager should not be escaped.


#2

Hi,

We’re also getting this error recently:

https://api.travis-ci.org/v3/job/451770581/log.txt

Thanks,

Victoria


#3

+1 I’m seeing this for all of my R packages:

e[0Ke[33;1mInstalling Bioconductore[0m
travis_time:start:090cf15f
e[0K$ Rscript -e 'if (!requireNamespace(\"BiocManager\", quietly=TRUE))  install.packages("BiocManager");if (FALSE) BiocManager::install(version = "devel");cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocManager::repositories());")'
Error: unexpected input in "if (!requireNamespace(\"
Execution halted

#4

Experiencing the same issue. CC @jeroen @jimhester


#5

I’m seeing a different failed command but the same result. In version “oldrel” my jobs succeed, running this:

Rscript -e 'source("https://bioconductor.org/biocLite.R");tryCatch( useDevel(FALSE), error=function(e) {if (!grepl("already in use", e$message)) {e}} );cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocInstaller::biocinstallRepos());")'

In the release/devel/bioc-devel versions it fails with the error:

Error in contrib.url(repos, type) :
trying to use CRAN without setting a mirror
Calls: install.packages -> startsWith -> contrib.url
Execution halted

The command in this case is:

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

(The if (FALSE) above is if (TRUE) for the “bioc-devel” version, but the failure is still the same.)

Example: https://travis-ci.org/ShawHahnLab/chiimp/builds/452066703


#6

I’m experiencing the same issue: https://travis-ci.org/ropensci/smapr/jobs/452219892


#7

I restarted my jobs today and all (oldrel/release/devel/bioc-devel) ran to completion with no changes to those Rscript commands. So maybe that wasn’t the issue in the first place. (But maybe it’s working again, at least for me?)