Error: Bioconductor version not changed

Hi,
I have noticed that bioc-devel builds for a number of packages recently started failing, example:

https://travis-ci.org/mjhelf/MassTools/jobs/536419506

This seems to happen to packages from other people too, and has only been going on for about 2 days. I can’t tell if this is a problem with Bioconductor or Travis, and I couldn’t find anything on this on the support forums (Bioconductor or Travis) so far…

Edit:

Actually, @xrobin posted a build with the same error in this thread:

The thread was originally about a different error though, and the (short-term) fix posted there by @kevinwang09 does not seem to work for this new error

* DONE (BiocManager)
The downloaded source packages are in
	‘/tmp/Rtmp7dKqN4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Error: Bioconductor version not changed
Execution halted
The command "eval Rscript -e 'if (!requireNamespace("BiocManager", quietly=TRUE))  install.packages("BiocManager");if (TRUE) BiocManager::install(version = "devel");cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocManager::repositories());")' " failed. Retrying, 2 of 3.
Error: Bioconductor version not changed
Execution halted
1 Like

Indeed this is fairly new. I had a successful build 10 days ago… apparently the R version was changed from R-devel to R-3.6.0 in between, I guess it might be related…

@jeroen, @jimhester
My last successful build with bioc-devel finished on May 21 around 4 am EST. The R version in the successful build was R under development r76551, which is post R-3.6.0.
Bioconductor devel changed from 3.9 to 3.10 on May 3, so the BiocManager::install(version = "devel") part should have started behaving differently at that time…

I am experiencing the same problems. The issue might be on Bioconductor’s side, which I reported on the Bioc-devel mailing list (see [1]). If the issue on travis is related to the missing index of Bioc packages, it should be sorted out very soon.

[1] https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015172.html

Apparently not :-/

So I tried running the code with error in my R terminal, and I found that if I answered “n” to upgrading packages to version 3.10, I would get that Error: Bioconductor version not changed error. If i said “y”, everything seemed alright. I don’t know what exactly happens behind the scene for Travis-CI, but I guess that’s where the error comes from.

‘n’

if (!requireNamespace("BiocManager", quietly=TRUE))  install.packages("BiocManager");if (TRUE) BiocManager::install(version = "devel");cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocManager::repositories());
Installing package into ‘C:/Users/Anh/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/BiocManager_1.30.4.zip'
Content type 'application/zip' length 292998 bytes (286 KB)
downloaded 286 KB

package ‘BiocManager’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Anh\AppData\Local\Temp\RtmpyoHsBB\downloaded_packages
Upgrade 17 packages to Bioconductor version '3.10'? [y/n]: 
n
Error: Bioconductor version not changed

‘y’

> if (!requireNamespace("BiocManager", quietly=TRUE))  install.packages("BiocManager");if (TRUE) BiocManager::install(version = "devel");cat(append = TRUE, file = "~/.Rprofile.site", "options(repos = BiocManager::repositories());
Upgrade 17 packages to Bioconductor version '3.10'? [y/n]: 
y
Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'BiocVersion'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/BiocVersion_3.10.0.zip'
Content type 'application/zip' length 8941 bytes
downloaded 8941 bytes

package ‘BiocVersion’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Anh\AppData\Local\Temp\RtmpyoHsBB\downloaded_packages
1 Like

Right now I test my package against bioc-release to make sure my incremental additions to the package do not introduce fatal errors, which seems to work for now. I hope the issue will be resolved soon.

Looking at R/install.R from https://cran.r-project.org/src/contrib/BiocManager_1.30.4.tar.gz , this should work then:

BiocManager::install(version = "devel", ask = FALSE);

It’s unclear to me whether this has been fixed, but I am still experiencing this error. I am wondering if I need to clear a cache or something to get this fix to appear on my travisCI?

No, it hasn’t been fixed yet; @native-api’s pull request (adding ask = FALSE as mentioned above) still needs to be merged. I’m still seeing this error too. (And no, clearing the cache doesn’t help either, from my experience a minute ago before bothering to look here!)

It’s been fixed now. I just had to restart the job, but I probably cleaned the cache earlier.

Yep, working for me now too after the merge. Thanks @native-api and the devs for getting that going again.