Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-06 11:04:58 -0500 (Mon, 06 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 a4Base on nebbiolo1


To the developers/maintainers of the a4Base package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/a4Base.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 2/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.47.0  (landing page)
Laure Cougnaud
Snapshot Date: 2023-02-05 14:00:11 -0500 (Sun, 05 Feb 2023)
git_url: https://git.bioconductor.org/packages/a4Base
git_branch: master
git_last_commit: 06934f7
git_last_commit_date: 2022-11-01 11:05:49 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: a4Base
Version: 1.47.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings a4Base_1.47.0.tar.gz
StartedAt: 2023-02-05 18:51:59 -0500 (Sun, 05 Feb 2023)
EndedAt: 2023-02-05 18:55:01 -0500 (Sun, 05 Feb 2023)
EllapsedTime: 182.1 seconds
RetCode: 0
Status:   OK  
CheckDir: a4Base.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings a4Base_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/a4Base.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.47.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘JavaGD’
* 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 ‘a4Base’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
checkRd: (-1) filterVarInt.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) histPvalue.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) lassoReg.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) spectralMap.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) volcanoPlot.Rd:45: Escaped LaTeX specials: \&
* 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 data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
spectralMap 10.932   0.28  11.212
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/a4Base.Rcheck/00check.log’
for details.



Installation output

a4Base.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL a4Base
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘a4Base’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (a4Base)

Tests output


Example timings

a4Base.Rcheck/a4Base-Ex.timings

nameusersystemelapsed
a4palette0.0280.0000.028
addQuantilesColors1.9170.2042.120
boxPlot2.5380.1192.658
combineTwoExpressionSet0.0010.0000.000
computeLogRatio4.670.264.93
createExpressionSet0.0340.0000.034
filterVarInt1.6980.0561.754
heatmap.expressionSet0.0000.0020.002
histPvalue2.3050.1552.461
histpvalueplotter1.6630.0441.707
lassoReg1.8140.0641.878
logReg000
nlcvTT000
plot1gene1.7160.0631.780
plotComb2Samples1.9560.0442.000
plotCombMultSamples3.4050.1113.517
plotCombination2genes2.5600.0992.660
plotLogRatio4.1060.0804.185
probabilitiesPlot000
probe2gene1.4960.0481.545
profilesPlot1.6110.0561.667
propdegenescalculation1.7250.0291.755
replicates0.0010.0000.001
spectralMap10.932 0.28011.212
tTest2.8180.1032.922
volcanoPlot2.1420.0272.170