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This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 1303/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMAPPR2 1.18.0  (landing page)
Jonathon Hill
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/MMAPPR2
git_branch: RELEASE_3_19
git_last_commit: c652044
git_last_commit_date: 2024-04-30 11:15:31 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for MMAPPR2 on nebbiolo1

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.

raw results


Summary

Package: MMAPPR2
Version: 1.18.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MMAPPR2
StartedAt: 2024-10-16 19:33:12 -0400 (Wed, 16 Oct 2024)
EndedAt: 2024-10-16 19:34:38 -0400 (Wed, 16 Oct 2024)
EllapsedTime: 86.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-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 Oct 16 19:34:25 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 Oct 16 19:34:37 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/RtmpJs9RMJ/file3fe25d64738de'
--- failed re-building ‘MMAPPR2.Rmd’

SUMMARY: processing the following file failed:
  ‘MMAPPR2.Rmd’

Error: Vignette re-building failed.
Execution halted