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This page was generated on 2025-08-15 12:08 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1142/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LymphoSeq 1.37.0  (landing page)
David Coffey
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025)
git_url: https://git.bioconductor.org/packages/LymphoSeq
git_branch: devel
git_last_commit: 61ac6ca
git_last_commit_date: 2025-04-15 11:01:17 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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 13.7.7 Ventura / arm64  ERROR    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for LymphoSeq on lconway

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: 1.37.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LymphoSeq_1.37.0.tar.gz
StartedAt: 2025-08-14 21:37:57 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 21:41:34 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 216.5 seconds
RetCode: 0
Status:   OK  
CheckDir: LymphoSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LymphoSeq_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/LymphoSeq.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LymphoSeq/DESCRIPTION’ ... OK
* this is package ‘LymphoSeq’ version ‘1.37.0’
* 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 ... INFO
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
* 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 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    26.60  1.108  27.889
productiveSeq 22.17  0.757  23.071
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

LymphoSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LymphoSeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘LymphoSeq’ ...
** this is package ‘LymphoSeq’ version ‘1.37.0’
** 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
alignSeq1.2550.0261.304
bhattacharyyaCoefficient0.1810.0160.215
bhattacharyyaMatrix0.1970.0110.208
chordDiagramVDJ0.9470.0360.988
clonalRelatedness0.6770.0080.690
clonality0.0600.0050.066
cloneTrack26.600 1.10827.889
commonSeqs0.1720.0180.193
commonSeqsBar1.0030.1191.127
commonSeqsPlot0.4220.0460.472
commonSeqsVenn0.6820.0780.769
differentialAbundance3.1890.0663.273
exportFasta0.2470.0210.270
geneFreq1.1260.0411.171
lorenzCurve2.0800.0422.135
mergeFiles0.0770.0040.081
pairwisePlot0.7280.0110.748
phyloTree2.6880.0292.736
productive0.0580.0040.063
productiveSeq22.170 0.75723.071
readImmunoSeq0.0440.0050.050
removeSeq0.0570.0050.062
searchPublished0.1850.0120.199
searchSeq0.4510.0130.467
seqMatrix4.7710.1014.904
similarityMatrix0.1760.0070.183
similarityScore0.1690.0060.177
topFreq1.5150.0131.536
topSeqs0.1790.0080.188
topSeqsPlot0.4680.0180.489
uniqueSeqs0.2410.0090.249