Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-11 11:06:14 -0400 (Thu, 11 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4165
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 attract on palomino4


To the developers/maintainers of the attract package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/attract.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 96/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.49.0  (landing page)
Samuel Zimmerman
Snapshot Date: 2022-08-10 14:00:02 -0400 (Wed, 10 Aug 2022)
git_url: https://git.bioconductor.org/packages/attract
git_branch: master
git_last_commit: 01ae39e
git_last_commit_date: 2022-04-26 11:05:09 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: attract
Version: 1.49.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:attract.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings attract_1.49.0.tar.gz
StartedAt: 2022-08-10 23:22:00 -0400 (Wed, 10 Aug 2022)
EndedAt: 2022-08-10 23:26:52 -0400 (Wed, 10 Aug 2022)
EllapsedTime: 292.2 seconds
RetCode: 0
Status:   OK  
CheckDir: attract.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:attract.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings attract_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/attract.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.49.0'
* 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 whether package 'attract' 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 ... NOTE
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
  partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'adjust' to 'adjust.method'
* 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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
calcFuncSynexprs 65.02   5.80   73.20
findAttractors   39.44   2.62   43.68
findCorrPartners  4.95   0.20    6.32
findSynexprs      4.97   0.15    6.11
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/attract.Rcheck/00check.log'
for details.



Installation output

attract.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/attract_1.49.0.tar.gz && rm -rf attract.buildbin-libdir && mkdir attract.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=attract.buildbin-libdir attract_1.49.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL attract_1.49.0.zip && rm attract_1.49.0.tar.gz attract_1.49.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 58 4204k   58 2467k    0     0  11.5M      0 --:--:-- --:--:-- --:--:-- 11.5M
100 4204k  100 4204k    0     0  14.1M      0 --:--:-- --:--:-- --:--:-- 14.1M
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'attract' ...
** using staged installation
** R
** data
** 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
* MD5 sums
packaged installation of 'attract' as attract_1.49.0.zip
* DONE (attract)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'attract' successfully unpacked and MD5 sums checked

Tests output


Example timings

attract.Rcheck/attract-Ex.timings

nameusersystemelapsed
AttractorModuleSet-class000
SynExpressionSet-class000
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix000
calcFuncSynexprs65.02 5.8073.20
calcInform000
calcModfstat000
calcRss000
exprs.dat0.080.030.11
filterDataSet0.180.020.20
findAttractors39.44 2.6243.68
findCorrPartners4.950.206.32
findOnepwaySynexprs000
findSynexprs4.970.156.11
flagPwayExists000
getCustomGenes000
getPwayGenes000
loring.eset0.160.000.16
plotsynexprs3.860.114.98
removeFlatGenes0.090.020.11
samp.info0.020.000.01
subset.loring.eset0.040.010.07