Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4358
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 247/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.74.0  (landing page)
Hervé Pagès
Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025)
git_url: https://git.bioconductor.org/packages/BSgenome
git_branch: RELEASE_3_20
git_last_commit: 7ab2eb4
git_last_commit_date: 2024-10-29 09:26:26 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for BSgenome on taishan

To the developers/maintainers of the BSgenome package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BSgenome.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: BSgenome
Version: 1.74.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BSgenome_1.74.0.tar.gz
StartedAt: 2025-01-08 23:40:10 -0000 (Wed, 08 Jan 2025)
EndedAt: 2025-01-08 23:40:20 -0000 (Wed, 08 Jan 2025)
EllapsedTime: 10.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BSgenome.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BSgenome_1.74.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BSgenome.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.74.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Packages suggested but not available:
  'BSgenome.Rnorvegicus.UCSC.rn5',
  'XtraSNPlocs.Hsapiens.dbSNP144.GRCh38'

Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'Biostrings', 'BiocIO', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BSgenome.Rcheck/00check.log’
for details.


Installation output


Tests output


Example timings