Dear fellow developers,
I have a package which has been failing on Travis CI's bioc-devel build since the release of R 4.0.0 and Bioconductor 3.11. The bioc-release build is still working fine.
The error happens when installing the SummarizedExperiment dependency (or, apparently, when installing its dependency, GenomicRanges). Here is the relevant part of the log:
* installing *source* package ?SummarizedExperiment? ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ?GenomicRanges?:
.onLoad failed in loadNamespace() for 'XVector', details:
call: NULL
error: (converted from warning) undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL")
Error: package ?GenomicRanges? could not be loaded
Execution halted
ERROR: lazy loading failed for package ?SummarizedExperiment?
* removing ?/home/travis/R/Library/SummarizedExperiment?
* restoring previous ?/home/travis/R/Library/SummarizedExperiment?
Error in i.p(...) :
(converted from warning) installation of package ?SummarizedExperiment? had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
travis_time:end:0be4d543:start=1588839621760310466,finish=1588839851948469642,duration=230188159176,event=
[0K[31;1mThe command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::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 was wondering if anyone else went through this or can offer a solution.
Best regards,
Waldir
[Bioc-devel] Failing Travis build on bioc-devel
3 messages · Waldir Leoncio Netto, Charlotte Soneson
Hi Waldir, try to delete the travis cache (under More Options - Caches) and restart the build. That helped for me. Best, Charlotte
On 7 May 2020, at 11:33, Waldir Leoncio Netto <w.l.netto at medisin.uio.no> wrote:
Dear fellow developers,
I have a package which has been failing on Travis CI's bioc-devel build since the release of R 4.0.0 and Bioconductor 3.11. The bioc-release build is still working fine.
The error happens when installing the SummarizedExperiment dependency (or, apparently, when installing its dependency, GenomicRanges). Here is the relevant part of the log:
* installing *source* package ?SummarizedExperiment? ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ?GenomicRanges?:
.onLoad failed in loadNamespace() for 'XVector', details:
call: NULL
error: (converted from warning) undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL")
Error: package ?GenomicRanges? could not be loaded
Execution halted
ERROR: lazy loading failed for package ?SummarizedExperiment?
* removing ?/home/travis/R/Library/SummarizedExperiment?
* restoring previous ?/home/travis/R/Library/SummarizedExperiment?
Error in i.p(...) :
(converted from warning) installation of package ?SummarizedExperiment? had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
travis_time:end:0be4d543:start=1588839621760310466,finish=1588839851948469642,duration=230188159176,event=
[0K[31;1mThe command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::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 was wondering if anyone else went through this or can offer a solution.
Best regards,
Waldir
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Thank you Charlotte, that was it!
On Thu, 2020-05-07 at 11:39 +0200, Charlotte Soneson wrote:
Hi Waldir, try to delete the travis cache (under More Options - Caches) and restart the build. That helped for me. Best, Charlotte
On 7 May 2020, at 11:33, Waldir Leoncio Netto <w.l.netto at medisin.uio.no<mailto:w.l.netto at medisin.uio.no>> wrote:
Dear fellow developers,
I have a package which has been failing on Travis CI's bioc-devel build since the release of R 4.0.0 and Bioconductor 3.11. The bioc-release build is still working fine.
The error happens when installing the SummarizedExperiment dependency (or, apparently, when installing its dependency, GenomicRanges). Here is the relevant part of the log:
* installing *source* package ?SummarizedExperiment? ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ?GenomicRanges?:
.onLoad failed in loadNamespace() for 'XVector', details:
call: NULL
error: (converted from warning) undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL")
Error: package ?GenomicRanges? could not be loaded
Execution halted
ERROR: lazy loading failed for package ?SummarizedExperiment?
* removing ?/home/travis/R/Library/SummarizedExperiment?
* restoring previous ?/home/travis/R/Library/SummarizedExperiment?
Error in i.p(...) :
(converted from warning) installation of package ?SummarizedExperiment? had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
travis_time:end:0be4d543:start=1588839621760310466,finish=1588839851948469642,duration=230188159176,event=
[0K[31;1mThe command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::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 was wondering if anyone else went through this or can offer a solution.
Best regards,
Waldir
_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel