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This page was generated on 2025-08-30 12:07 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1144/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LymphoSeq 1.37.0  (landing page)
David Coffey
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for LymphoSeq on kjohnson3

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: 2025-08-29 20:06:51 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 20:08:09 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 78.0 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 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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    11.716  0.215  12.414
productiveSeq  7.912  0.277   8.253
* 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-arm64/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
alignSeq0.3760.0070.389
bhattacharyyaCoefficient0.0650.0060.076
bhattacharyyaMatrix0.1020.0030.105
chordDiagramVDJ0.2460.0100.257
clonalRelatedness0.6460.0020.649
clonality0.0210.0020.022
cloneTrack11.716 0.21512.414
commonSeqs0.0600.0050.072
commonSeqsBar0.3030.0270.354
commonSeqsPlot0.1330.0130.192
commonSeqsVenn0.2560.0280.349
differentialAbundance0.9450.0190.991
exportFasta0.0880.0140.121
geneFreq0.3470.0200.423
lorenzCurve0.7180.0200.820
mergeFiles0.0310.0020.035
pairwisePlot0.2240.0060.275
phyloTree0.7810.0120.918
productive0.0240.0020.037
productiveSeq7.9120.2778.253
readImmunoSeq0.0170.0010.019
removeSeq0.0210.0010.022
searchPublished0.0610.0030.065
searchSeq0.1470.0030.150
seqMatrix0.6690.0270.696
similarityMatrix0.0650.0050.071
similarityScore0.0620.0060.068
topFreq0.9120.0450.961
topSeqs0.0580.0020.061
topSeqsPlot0.1300.0030.135
uniqueSeqs0.0810.0020.089