# Error: Bioconductor version not changed **URL:** \ **Category:** R\ **Tags:** bug\ **Created:** [May 23, 2019, 6:33pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491 "2019-05-23T18:33:27Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![mjhelf](https://avatars.discourse-cdn.com/v4/letter/m/73ab20/32.png) [@mjhelf](https://travis-ci.community/u/mjhelf)\ **Post date:** [May 23, 2019, 6:33pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/1 "2019-05-23T18:33:27Z")
Hi, I have noticed that bioc-devel builds for a number of packages recently started failing, example: > **[Travis CI - Test and Deploy with Confidence](https://app.travis-ci.com/mjhelf/MassTools/jobs/536419506)** > > Travis CI enables your team to test and ship your apps with confidence. Easily sync your projects with Travis CI and you'll be testing your code in minutes. 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: > [@Bioconductor version error](https://travis-ci.community/t/bioconductor-version-error/3332): > > @jeroen, @jimhester Hi, I am the maintainer of this scMerge package for Bioconductor. The issue that I am having is that Travis seems to be using Bioconductor version 3.8 rather than the newly released 3.9 ([https://travis-ci.org/SydneyBioX/scMerge/jobs/529095216](https://travis-ci.org/SydneyBioX/scMerge/jobs/529095216)). This caused an installation error for a dependent BioC package M3Drop (scMerge requires M3Drop version \>= 1.9.4). I am unsure if this is a bug or not. Thanks 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 ```auto * 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 ``` ---
**Author:** ![xrobin](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/xrobin/32/1843_2.png) [@xrobin](https://travis-ci.community/u/xrobin)\ **Post date:** [May 23, 2019, 8:46pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/2 "2019-05-23T20:46:34Z")
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… ---
**Author:** ![mjhelf](https://avatars.discourse-cdn.com/v4/letter/m/73ab20/32.png) [@mjhelf](https://travis-ci.community/u/mjhelf)\ **Post date:** [May 23, 2019, 9:31pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/3 "2019-05-23T21:31:06Z")
@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… ---
**Author:** ![lgatto](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/lgatto/32/1874_2.png) [@lgatto](https://travis-ci.community/u/lgatto)\ **Post date:** [May 28, 2019, 8:31pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/4 "2019-05-28T20:31:57Z")
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](https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015172.html) ---
**Author:** ![lgatto](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/lgatto/32/1874_2.png) [@lgatto](https://travis-ci.community/u/lgatto)\ **Post date:** [May 29, 2019, 5:01am UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/5 "2019-05-29T05:01:00Z")
Apparently not :-/ ---
**Author:** ![trannhatanh89](https://avatars.discourse-cdn.com/v4/letter/t/958977/32.png) [@trannhatanh89](https://travis-ci.community/u/trannhatanh89)\ **Post date:** [June 1, 2019, 4:43am UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/6 "2019-06-01T04:43:08Z")
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’ ```auto 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’ ```auto > 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 ``` ---
**Author:** ![trannhatanh89](https://avatars.discourse-cdn.com/v4/letter/t/958977/32.png) [@trannhatanh89](https://travis-ci.community/u/trannhatanh89)\ **Post date:** [June 1, 2019, 4:53am UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/7 "2019-06-01T04:53:44Z")
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. ---
**Author:** ![native-api](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/native-api/32/430_2.png) [@native-api](https://travis-ci.community/u/native-api)\ **Post date:** [June 1, 2019, 10:23am UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/8 "2019-06-01T10:23:44Z")
Looking at `R/install.R` from [https://cran.r-project.org/src/contrib/BiocManager\_1.30.4.tar.gz](https://cran.r-project.org/src/contrib/BiocManager_1.30.4.tar.gz) , this should work then: ```auto BiocManager::install(version = "devel", ask = FALSE); ``` ---
**Author:** ![native-api](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/native-api/32/430_2.png) [@native-api](https://travis-ci.community/u/native-api)\ **Post date:** [June 1, 2019, 12:53pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/9 "2019-06-01T12:53:24Z")
> ---
**Author:** ![epurdom](https://avatars.discourse-cdn.com/v4/letter/e/b77776/32.png) [@epurdom](https://travis-ci.community/u/epurdom)\ **Post date:** [June 10, 2019, 7:57pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/10 "2019-06-10T19:57:24Z")
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? ---
**Author:** ![ressy](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/ressy/32/381_2.png) [@ressy](https://travis-ci.community/u/ressy)\ **Post date:** [June 11, 2019, 1:55pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/11 "2019-06-11T13:55:37Z")
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!) ---
**Author:** ![xrobin](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/xrobin/32/1843_2.png) [@xrobin](https://travis-ci.community/u/xrobin)\ **Post date:** [June 14, 2019, 7:36am UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/12 "2019-06-14T07:36:36Z")
It’s been fixed now. I just had to restart the job, but I probably cleaned the cache earlier. ---
**Author:** ![ressy](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/ressy/32/381_2.png) [@ressy](https://travis-ci.community/u/ressy)\ **Post date:** [June 14, 2019, 8:01pm UTC](https://travis-ci.community/t/error-bioconductor-version-not-changed/3491/13 "2019-06-14T20:01:06Z")
Yep, working for me now too after the merge. Thanks @native-api and the devs for getting that going again.