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This page was generated on 2025-02-04 11:40 -0500 (Tue, 04 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4716
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4478
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4489
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4442
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 1128/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LymphoSeq 1.35.0  (landing page)
David Coffey
Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025)
git_url: https://git.bioconductor.org/packages/LymphoSeq
git_branch: devel
git_last_commit: 1b80972
git_last_commit_date: 2024-10-29 10:10:14 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for LymphoSeq on nebbiolo1

To the developers/maintainers of the LymphoSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LymphoSeq.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: LymphoSeq
Version: 1.35.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings LymphoSeq_1.35.0.tar.gz
StartedAt: 2025-02-03 23:49:05 -0500 (Mon, 03 Feb 2025)
EndedAt: 2025-02-03 23:52:56 -0500 (Mon, 03 Feb 2025)
EllapsedTime: 231.4 seconds
RetCode: 0
Status:   OK  
CheckDir: LymphoSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings LymphoSeq_1.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/LymphoSeq.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘LymphoSeq/DESCRIPTION’ ... OK
* this is package ‘LymphoSeq’ version ‘1.35.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘LymphoSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
cloneTrack    26.131  1.714  27.852
productiveSeq 14.634  1.406  16.046
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

LymphoSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL LymphoSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘LymphoSeq’ ...
** this is package ‘LymphoSeq’ version ‘1.35.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LymphoSeq)

Tests output


Example timings

LymphoSeq.Rcheck/LymphoSeq-Ex.timings

nameusersystemelapsed
alignSeq0.6740.0470.728
bhattacharyyaCoefficient0.1470.0060.167
bhattacharyyaMatrix0.1700.0050.174
chordDiagramVDJ0.7650.0270.792
clonalRelatedness0.7150.0060.383
clonality0.0510.0070.058
cloneTrack26.131 1.71427.852
commonSeqs0.1580.0260.184
commonSeqsBar0.8170.1630.981
commonSeqsPlot0.3640.0560.420
commonSeqsVenn0.7230.1060.822
differentialAbundance2.5170.1722.689
exportFasta0.2150.0050.221
geneFreq0.9420.0180.960
lorenzCurve0.8890.0060.896
mergeFiles0.0720.0050.078
pairwisePlot1.4150.0021.417
phyloTree3.2380.0373.276
productive0.0540.0030.057
productiveSeq14.634 1.40616.046
readImmunoSeq0.0470.0020.049
removeSeq0.0540.0020.055
searchPublished0.1530.0080.161
searchSeq0.8840.0060.889
seqMatrix2.4930.1712.664
similarityMatrix0.1590.0030.162
similarityScore0.1510.0020.153
topFreq1.1880.1161.303
topSeqs0.7490.0330.782
topSeqsPlot0.3850.0030.387
uniqueSeqs0.1830.0030.185