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This page was generated on 2022-01-24 11:06:48 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 riesling1


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? 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 94/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.47.0  (landing page)
Samuel Zimmerman
Snapshot Date: 2022-01-23 13:55:15 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/attract
git_branch: master
git_last_commit: b7601f8
git_last_commit_date: 2021-10-26 11:56:18 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: attract
Version: 1.47.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:attract.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings attract_1.47.0.tar.gz
StartedAt: 2022-01-23 18:17:38 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 18:21:52 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 253.9 seconds
RetCode: 0
Status:   OK  
CheckDir: attract.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:attract.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings attract_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/attract.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.47.0'
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
calcFuncSynexprs 57.27   7.47   65.97
findAttractors   38.16   2.57   41.89
findCorrPartners  3.95   0.52    5.44
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/attract.Rcheck/00check.log'
for details.



Installation output

attract.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL attract
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'attract' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'attract'
    finding HTML links ... done
    AttractorModuleSet-class                html  
    SynExpressionSet-class                  html  
    attract-package                         html  
    buildCorMatrix                          html  
    buildCustomIncidenceMatrix              html  
    buildKeggIncidenceMatrix                html  
    calcFuncSynexprs                        html  
    calcInform                              html  
    calcModfstat                            html  
    calcRss                                 html  
    exprs.dat                               html  
    filterDataSet                           html  
    findAttractors                          html  
    findCorrPartners                        html  
    findOnepwaySynexprs                     html  
    findSynexprs                            html  
    flagPwayExists                          html  
    getCustomGenes                          html  
    getPwayGenes                            html  
    loring.eset                             html  
    plotsynexprs                            html  
    removeFlatGenes                         html  
    samp.info                               html  
    subset.loring.eset                      html  
** 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 (attract)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MetID' is missing or broken
 done

Tests output


Example timings

attract.Rcheck/attract-Ex.timings

nameusersystemelapsed
AttractorModuleSet-class000
SynExpressionSet-class000
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix000
calcFuncSynexprs57.27 7.4765.97
calcInform000
calcModfstat000
calcRss000
exprs.dat0.120.030.16
filterDataSet0.200.070.26
findAttractors38.16 2.5741.89
findCorrPartners3.950.525.44
findOnepwaySynexprs000
findSynexprs3.740.084.78
flagPwayExists000
getCustomGenes000
getPwayGenes000
loring.eset0.10.00.1
plotsynexprs3.180.074.20
removeFlatGenes0.100.030.13
samp.info000
subset.loring.eset0.060.000.06