Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2021-10-15 15:05:52 -0400 (Fri, 15 Oct 2021).

CHECK results for scRepertoire on nebbiolo1

To the developers/maintainers of the scRepertoire package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scRepertoire.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1715/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scRepertoire 1.2.0  (landing page)
Nick Borcherding
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/scRepertoire
git_branch: RELEASE_3_13
git_last_commit: f61c711
git_last_commit_date: 2021-06-16 10:41:12 -0400 (Wed, 16 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: scRepertoire
Version: 1.2.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings scRepertoire_1.2.0.tar.gz
StartedAt: 2021-10-14 11:32:36 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:37:48 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 312.2 seconds
RetCode: 0
Status:   OK  
CheckDir: scRepertoire.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings scRepertoire_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/scRepertoire.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘scRepertoire’ can be installed ... OK
* checking installed package size ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
clonesizeDistribution 14.011  0.060  14.071
alluvialClonotypes    10.802  0.480  11.291
combineTCR             7.911  2.276  10.187
combineExpression      7.772  0.111   7.883
abundanceContig        7.697  0.112   7.811
occupiedscRepertoire   7.725  0.012   7.738
quantContig            7.656  0.012   7.670
compareClonotypes      7.411  0.076   7.488
lengthContig           7.116  0.016   7.131
getCirclize            6.894  0.048   6.942
highlightClonotypes    6.843  0.016   6.858
addVariable            6.469  0.056   6.526
expression2List        6.439  0.028   6.467
clonalDiversity        5.986  0.432   6.422
vizVgenes              6.374  0.000   6.374
clonalHomeostasis      6.064  0.272   6.337
subsetContig           5.661  0.012   5.673
clonalProportion       5.655  0.000   5.657
clonalOverlap          5.399  0.020   5.420
* 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: OK


Installation output

scRepertoire.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL scRepertoire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘scRepertoire’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (scRepertoire)

Tests output


Example timings

scRepertoire.Rcheck/scRepertoire-Ex.timings

nameusersystemelapsed
abundanceContig7.6970.1127.811
addVariable6.4690.0566.526
alluvialClonotypes10.802 0.48011.291
clonalDiversity5.9860.4326.422
clonalHomeostasis6.0640.2726.337
clonalOverlap5.3990.0205.420
clonalProportion5.6550.0005.657
clonesizeDistribution14.011 0.06014.071
combineBCR3.7780.0684.160
combineExpression7.7720.1117.883
combineTCR 7.911 2.27610.187
compareClonotypes7.4110.0767.488
expression2List6.4390.0286.467
getCirclize6.8940.0486.942
highlightClonotypes6.8430.0166.858
lengthContig7.1160.0167.131
occupiedscRepertoire7.7250.0127.738
quantContig7.6560.0127.670
stripBarcode0.8730.7281.600
subsetContig5.6610.0125.673
vizVgenes6.3740.0006.374