R-travis: error when installing dependencies: "ERROR: no packages specified"

[drisso]

Dear @craigcitro and @jimhester.

I'm seeing the following error when installing and checking the clusterExperiment package (cc @epurdom).

trying URL 'https://cloud.r-project.org/src/contrib/abind_1.4-5.tar.gz'
Content type 'application/x-gzip' length 21810 bytes (21 KB)
==================================================
downloaded 21 KB

Installing abind
Running command /home/travis/R-bin/lib/R/bin/R 
Arguments:
CMD
INSTALL
'/tmp/Rtmp28daE3/devtools3edc4dd74d7d/abind'

Warning: invalid package ‘'/tmp/Rtmp28daE3/devtools3edc4dd74d7d/abind'’
Error: ERROR: no packages specified
Installation failed: NULL : Command failed:
  
 Warning: invalid package ‘'/tmp/Rtmp28daE3/devtools3edc4dd74d7d/abind'’
Error: ERROR: no packages specified

This error is repeated many times for all the dependencies that it tries to install, I presume. The full log is here: https://s3.amazonaws.com/archive.travis-ci.org/jobs/218910640/log.txt

It ends with the following error:

missing: abind, ade4, ape, bold, colorspace, crul, data.table, DBI, dendextend, DEoptimR, dichromat, diptest, doParallel, dplyr, flexmix, foreach, fpc, GenomeInfoDb, GenomicRanges, ggplot2, gridBase, gridExtra, gtable, howmany, httpcode, IRanges, iterators, kernlab, labeling, limma, locfdr, MAST, matrixStats, mclust, modeltools, munsell, mvtnorm, natserv, NMF, phylobase, pkgmaker, plyr, prabclus, prettyunits, progress, RColorBrewer, registry, rentrez, reshape, reshape2, ritis, rncl, RNeXML, rngtools, robustbase, rotl, rredlist, S4Vectors, scales, solrium, SummarizedExperiment, taxize, tibble, tidyr, triebeard, trimcluster, urltools, uuid, viridis, viridisLite, worrms, xtable, XVector, zlibbioc

travis_time:end:15835d73:start=1491404781230721022,finish=1491405880231069963,duration=1099000348941
�[0K
�[31;1mThe command "Rscript -e 'deps <- devtools::dev_package_deps(dependencies = NA);devtools::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .�[0m

Your build has been stopped.

I've tried to remove the cached packages, in case that was a problem, but it didn't solve it.

The .travis.yml file is the same that we have been using for some time and never resulted in these errors.

Any idea of what's going on? Any help will be much appreciated!

[jimhester]

It looks like a change in devel devtools has broke something. I would use CRAN devtools in the meantime, i.e. take out https://github.com/epurdom/clusterExperiment/blob/10cb9ba33198172979044fbd0e26e04da06a0e1f/.travis.yml#L32-L34

[drisso]

Thank you for the quick reply. I also suspected that it was an issue with the devel devtools package, but unfortunately, the CRAN version of devtools give us a different error:

Installing diagram
Error in FUN(X[[i]], ...) : 
  Invalid comparison operator in dependency: >= 

which I believe is a known issue addressed in the devel version.

[jimhester]

Ah yes, if you go back a few commits in the devtools version you install it should work then.

## Use patched devtools
r_github_packages:
  - hadley/devtools@efa894ffa

[drisso]

Thank you, @jimhester ! Going back to that commit, everything works!

[BanzaiMan]

Looks like we can close this.

[f0nzie]

still getting these issues with Travis and devtools. Should I use the same commit efa894ffa?

[f0nzie]

Not good (getting this from Travis) in two packages:

missing: rhdf5, S4Vectors
The command "Rscript -e 'deps <- devtools::dev_package_deps(dependencies = NA);devtools::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .
missing: rhdf5, S4VectorsThe command "Rscript -e 'deps <- devtools::dev_package_deps(dependencies = NA);devtools::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { 
```message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .

[f0nzie]

Has devtools changed something the past week?

Now, I am getting these new errors in Travis:

nstalling *source* package ‘devtools’ ...
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (devtools)
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
$ Rscript -e 'deps <- devtools::dev_package_deps(dependencies = NA);devtools::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'
trying URL 'http://cloud.r-project.org/src/contrib/acepack_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34848 bytes (34 KB)
==================================================
downloaded 34 KB
Installing acepack
Installation failed: NULL : 'rcmd_safe_env' is not an exported object from 'namespace:callr'