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This page was generated on 2022-04-13 12:05:32 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for LymphoSeq on nebbiolo2


To the developers/maintainers of the LymphoSeq package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1021/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LymphoSeq 1.22.0  (landing page)
David Coffey
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/LymphoSeq
git_branch: RELEASE_3_14
git_last_commit: c0b2fd4
git_last_commit_date: 2021-10-26 12:27:20 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: LymphoSeq
Version: 1.22.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings LymphoSeq_1.22.0.tar.gz
StartedAt: 2022-04-12 08:01:16 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:04:14 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 178.5 seconds
RetCode: 0
Status:   OK  
CheckDir: LymphoSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings LymphoSeq_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/LymphoSeq.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LymphoSeq/DESCRIPTION’ ... OK
* this is package ‘LymphoSeq’ version ‘1.22.0’
* 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 ... NOTE
  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 R 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    24.171  1.644  25.857
productiveSeq 21.198  1.256  22.455
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/LymphoSeq.Rcheck/00check.log’
for details.



Installation output

LymphoSeq.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL LymphoSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘LymphoSeq’ ...
** 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
alignSeq0.6510.0240.685
bhattacharyyaCoefficient0.1620.0160.189
bhattacharyyaMatrix0.1530.0070.161
chordDiagramVDJ0.6950.0360.731
clonalRelatedness1.2570.0440.960
clonality0.0500.0000.051
cloneTrack24.171 1.64425.857
commonSeqs0.1480.0120.159
commonSeqsBar0.6690.1440.813
commonSeqsPlot1.0990.0401.139
commonSeqsVenn0.7250.0240.748
differentialAbundance1.660.041.70
exportFasta0.1930.0200.213
geneFreq1.8780.1001.978
lorenzCurve0.8530.0200.874
mergeFiles0.0670.0040.072
pairwisePlot0.5040.0040.508
phyloTree4.2500.1164.366
productive0.0550.0000.055
productiveSeq21.198 1.25622.455
readImmunoSeq0.0360.0030.040
removeSeq0.050.000.05
searchPublished0.1510.0000.152
searchSeq0.7760.0040.780
seqMatrix1.8390.1321.970
similarityMatrix0.1560.0040.161
similarityScore0.1380.0040.143
topFreq2.1940.1242.318
topSeqs0.1500.0000.149
topSeqsPlot0.2820.0000.281
uniqueSeqs0.1720.0040.175