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This page was generated on 2022-06-27 11:10:08 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 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? 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 1790/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scRepertoire 1.6.0  (landing page)
Nick Borcherding
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/scRepertoire
git_branch: RELEASE_3_15
git_last_commit: 7ba1676
git_last_commit_date: 2022-04-26 12:10:40 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: scRepertoire
Version: 1.6.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings scRepertoire_1.6.0.tar.gz
StartedAt: 2022-06-26 21:50:47 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 21:57:05 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 378.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scRepertoire.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings scRepertoire_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/scRepertoire.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.6.0’
* 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
combineBCR            52.827  1.132  40.251
clusterTCR            16.477  0.060  16.299
clonesizeDistribution 13.852  0.084  13.937
clonalDiversity       11.576  0.200  11.776
alluvialClonotypes     9.228  0.183   9.413
combineTCR             7.023  2.168   9.192
abundanceContig        8.086  0.143   8.231
combineExpression      7.551  0.280   7.831
addVariable            6.442  0.137   6.578
compareClonotypes      6.418  0.128   6.547
occupiedscRepertoire   6.334  0.140   6.474
clonalOverlay          6.325  0.036   6.361
clonalHomeostasis      6.192  0.012   6.206
quantContig            5.996  0.100   6.096
clonalOverlap          5.975  0.080   6.056
expression2List        5.912  0.052   5.963
clonalProportion       5.757  0.052   5.810
lengthContig           5.565  0.060   5.625
getCirclize            5.299  0.080   5.379
highlightClonotypes    5.309  0.008   5.317
subsetContig           5.226  0.035   5.263
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL scRepertoire
###
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* installing to library ‘/home/biocbuild/bbs-3.15-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
StartracDiversity0.0000.0000.001
abundanceContig8.0860.1438.231
addVariable6.4420.1376.578
alluvialClonotypes9.2280.1839.413
clonalDiversity11.576 0.20011.776
clonalHomeostasis6.1920.0126.206
clonalOverlap5.9750.0806.056
clonalOverlay6.3250.0366.361
clonalProportion5.7570.0525.810
clonesizeDistribution13.852 0.08413.937
clusterTCR16.477 0.06016.299
combineBCR52.827 1.13240.251
combineExpression7.5510.2807.831
combineTCR7.0232.1689.192
compareClonotypes6.4180.1286.547
expression2List5.9120.0525.963
getCirclize5.2990.0805.379
highlightClonotypes5.3090.0085.317
lengthContig5.5650.0605.625
occupiedscRepertoire6.3340.1406.474
quantContig5.9960.1006.096
stripBarcode0.8710.7321.603
subsetContig5.2260.0355.263