Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:23 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 2/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.50.0  (landing page)
Laure Cougnaud
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/a4Base
git_branch: RELEASE_3_18
git_last_commit: 26439bb
git_last_commit_date: 2023-10-24 09:46:28 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for a4Base on kunpeng2


To the developers/maintainers of the a4Base package:
- 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 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: a4Base
Version: 1.50.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings a4Base_1.50.0.tar.gz
StartedAt: 2023-11-02 08:11:24 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 08:16:18 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 294.3 seconds
RetCode: 0
Status:   OK  
CheckDir: a4Base.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings a4Base_1.50.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/a4Base.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.50.0’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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         21.149  2.939  25.686
computeLogRatio      7.125  0.787   8.815
plotLogRatio         6.464  0.295   6.785
boxPlot              2.787  1.159   5.519
plotCombMultSamples  2.488  1.079   5.142
plotComb2Samples     2.472  0.911   5.294
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/a4Base.Rcheck/00check.log’
for details.



Installation output

a4Base.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL a4Base
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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
a4palette0.0360.0000.036
addQuantilesColors1.9100.1682.086
boxPlot2.7871.1595.519
combineTwoExpressionSet0.0000.0000.001
computeLogRatio7.1250.7878.815
createExpressionSet0.0460.0000.046
filterVarInt2.4580.0562.528
heatmap.expressionSet0.0020.0000.002
histPvalue1.8460.0552.071
histpvalueplotter1.8020.0321.836
lassoReg1.7710.0441.825
logReg0.0000.0000.001
nlcvTT000
plot1gene1.6960.0281.726
plotComb2Samples2.4720.9115.294
plotCombMultSamples2.4881.0795.142
plotCombination2genes2.2820.0482.338
plotLogRatio6.4640.2956.785
probabilitiesPlot000
probe2gene1.4020.0511.557
profilesPlot1.6540.0241.767
propdegenescalculation1.8310.0291.863
replicates0.0020.0000.001
spectralMap21.149 2.93925.686
tTest2.5790.0622.815
volcanoPlot2.1200.0402.167