Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:36:08 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 1288/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MMAPPR2 1.16.0 (landing page) Jonathon Hill
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.16.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MMAPPR2 |
StartedAt: 2024-03-27 17:59:07 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 18:00:29 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 82.6 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/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" Smartmatch is experimental at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm line 472. -------------------- 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:177 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:272 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:94 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:200 STACK toplevel /usr/local/ensembl-vep/vep:46 Date (localtime) = Wed Mar 27 18:00:19 2024 Ensembl API version = 110 --------------------------------------------------- Smartmatch is experimental at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm line 472. -------------------- 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:177 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:272 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:94 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:200 STACK toplevel /usr/local/ensembl-vep/vep:46 Date (localtime) = Wed Mar 27 18:00:29 2024 Ensembl API version = 110 --------------------------------------------------- Quitting from lines 128-135 [mmappr-steps] (MMAPPR2.Rmd) Error: processing vignette 'MMAPPR2.Rmd' failed with diagnostics: file(s) do not exist: '/tmp/Rtmph64K3s/filebce966852460b' --- failed re-building ‘MMAPPR2.Rmd’ SUMMARY: processing the following file failed: ‘MMAPPR2.Rmd’ Error: Vignette re-building failed. Execution halted