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This page was generated on 2025-03-17 11:40 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1137/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LymphoSeq 1.35.0  (landing page)
David Coffey
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 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 -0400 (Tue, 29 Oct 2024)
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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped


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: 1.35.0
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_1.35.0.tar.gz
StartedAt: 2025-03-16 20:00:20 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 20:01:39 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 79.1 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_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/LymphoSeq.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ... 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    12.881  0.222  13.171
productiveSeq  6.588  0.229   6.946
* 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

##############################################################################
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###
### 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 ‘1.35.0’
** 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
alignSeq0.3800.0100.411
bhattacharyyaCoefficient0.0590.0070.072
bhattacharyyaMatrix0.0670.0030.070
chordDiagramVDJ0.2510.0120.264
clonalRelatedness0.6430.0020.648
clonality0.0210.0030.023
cloneTrack12.881 0.22213.171
commonSeqs0.0610.0040.065
commonSeqsBar0.2960.0260.323
commonSeqsPlot0.1290.0100.141
commonSeqsVenn0.2450.0190.269
differentialAbundance0.8940.0360.930
exportFasta0.0850.0070.093
geneFreq0.3370.0140.355
lorenzCurve0.2800.0090.289
mergeFiles0.0310.0020.033
pairwisePlot0.5910.0100.631
phyloTree0.7700.0110.873
productive0.0250.0020.036
productiveSeq6.5880.2296.946
readImmunoSeq0.0190.0010.023
removeSeq0.0240.0020.027
searchPublished0.0620.0030.067
searchSeq0.1460.0030.150
seqMatrix1.0230.0381.103
similarityMatrix0.0630.0020.070
similarityScore0.0590.0020.063
topFreq0.5200.0350.574
topSeqs0.0600.0020.064
topSeqsPlot0.1290.0040.139
uniqueSeqs0.0750.0030.083