Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:31 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1276/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Jonathon Hill
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the MMAPPR2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MMAPPR2.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: MMAPPR2 |
Version: 1.17.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MMAPPR2 |
StartedAt: 2024-03-01 20:35:36 -0500 (Fri, 01 Mar 2024) |
EndedAt: 2024-03-01 20:39:49 -0500 (Fri, 01 Mar 2024) |
EllapsedTime: 252.7 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MMAPPR2 ### ############################################################################## ############################################################################## * checking for file ‘MMAPPR2/DESCRIPTION’ ... OK * preparing ‘MMAPPR2’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘MMAPPR2.Rmd’ using rmarkdown running: bash -c "# Cooking show code to account for cases when samtools is not installed echo '#!/bin/bash' > /tmp/samtools chmod 755 /tmp/samtools" -------------------- EXCEPTION -------------------- MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed STACK Bio::EnsEMBL::VEP::AnnotationSource::File::new /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:162 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:228 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:93 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170 STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128 STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199 STACK toplevel /usr/local/ensembl-vep/vep:232 Date (localtime) = Fri Mar 1 20:39:07 2024 Ensembl API version = 109 --------------------------------------------------- -------------------- EXCEPTION -------------------- MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed STACK Bio::EnsEMBL::VEP::AnnotationSource::File::new /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:162 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:228 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:93 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170 STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128 STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199 STACK toplevel /usr/local/ensembl-vep/vep:232 Date (localtime) = Fri Mar 1 20:39:47 2024 Ensembl API version = 109 --------------------------------------------------- Quitting from lines 128-135 [mmappr-steps] (MMAPPR2.Rmd) Error: processing vignette 'MMAPPR2.Rmd' failed with diagnostics: file(s) do not exist: '/tmp/Rtmp1HjxQB/filec7c414209bfb' --- failed re-building ‘MMAPPR2.Rmd’ SUMMARY: processing the following file failed: ‘MMAPPR2.Rmd’ Error: Vignette re-building failed. Execution halted