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This page was generated on 2025-10-20 12:04 -0400 (Mon, 20 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1159/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LymphoSeq 1.37.0  (landing page)
David Coffey
Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 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 12.7.6 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LymphoSeq_1.37.0.tar.gz
StartedAt: 2025-10-20 01:25:49 -0400 (Mon, 20 Oct 2025)
EndedAt: 2025-10-20 01:29:38 -0400 (Mon, 20 Oct 2025)
EllapsedTime: 229.4 seconds
RetCode: 0
Status:   OK  
CheckDir: LymphoSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LymphoSeq_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/LymphoSeq.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* 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 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    23.540  1.742  25.325
productiveSeq 14.102  1.259  15.362
phyloTree      7.153  0.124   7.279
* 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-3.22-bioc/R/bin/R CMD INSTALL LymphoSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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
alignSeq0.6980.0070.714
bhattacharyyaCoefficient0.2670.0260.303
bhattacharyyaMatrix0.5440.0240.569
chordDiagramVDJ0.7270.0920.817
clonalRelatedness0.7110.0080.382
clonality0.0500.0050.056
cloneTrack23.540 1.74225.325
commonSeqs0.1380.0290.167
commonSeqsBar1.0600.2001.261
commonSeqsPlot1.1570.0921.249
commonSeqsVenn0.6920.0370.724
differentialAbundance1.7280.0341.762
exportFasta0.2030.0160.219
geneFreq1.6810.1181.799
lorenzCurve1.1470.0061.153
mergeFiles0.0710.0010.072
pairwisePlot0.9530.0020.956
phyloTree7.1530.1247.279
productive0.0570.0020.060
productiveSeq14.102 1.25915.362
readImmunoSeq0.0450.0070.052
removeSeq0.0540.0070.061
searchPublished0.1550.0110.167
searchSeq0.7450.0010.747
seqMatrix2.4650.3012.766
similarityMatrix0.1460.0030.148
similarityScore0.1370.0010.137
topFreq1.2120.1021.313
topSeqs0.1430.0030.146
topSeqsPlot0.5980.0060.605
uniqueSeqs0.1730.0030.177