Re: [Bioc-devel] Failing Travis build on 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
mailto:w.l.ne...@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: ... 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
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Re: [Bioc-devel] Failing Travis build on bioc-devel
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
> 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: ... 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]]
>
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[Bioc-devel] Failing Travis build on bioc-devel
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: ... 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]]
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