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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 110/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.56.0  (landing page)
Samuel Zimmerman
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/attract
git_branch: RELEASE_3_19
git_last_commit: bbedc77
git_last_commit_date: 2024-04-30 10:22:07 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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


CHECK results for attract on palomino3

To the developers/maintainers of the attract package:
- 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 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.

raw results


Summary

Package: attract
Version: 1.56.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:attract.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings attract_1.56.0.tar.gz
StartedAt: 2024-06-13 00:24:27 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 00:32:13 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 466.3 seconds
RetCode: 0
Status:   OK  
CheckDir: attract.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:attract.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings attract_1.56.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/attract.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.56.0'
* 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 code 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 ... NOTE
checkRd: (-1) attract-package.Rd:34: Lost braces
    34 | M\"{u}ller F et al. 2008. Regulatory networks define phenotypic classes of human stem cell lines. Nature. 455(7211): 401. 
       |    ^
checkRd: (-1) exprs.dat.Rd:29: Lost braces
    29 | M\"{u}ller F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405.
       |    ^
checkRd: (-1) findOnepwaySynexprs.Rd:15: Lost braces
    15 |                 a single character string denoting the KEGG or reactome ID of the pathway module to be analyzed or a character code{vector} of gene names of a pathway. 
       |                                                                                                                                    ^
checkRd: (-1) findSynexprs.Rd:16: Lost braces
    16 |     It may also be a character code{vector} of gene names of a pathway if defining a custom pathway.
       |                                    ^
checkRd: (-1) loring.eset.Rd:23: Lost braces
    23 | M\"{u}ller, F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405.
       |    ^
checkRd: (-1) samp.info.Rd:28: Lost braces
    28 | M\"{u}ller F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405.
       |    ^
checkRd: (-1) subset.loring.eset.Rd:25: Lost braces
    25 | M\"{u}ller, F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405.
       |    ^
* 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 70.08   5.90   77.86
findAttractors   34.78   5.51   41.73
findCorrPartners  5.49   0.41    6.33
findSynexprs      4.89   0.42    5.75
plotsynexprs      4.52   0.32    5.07
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/attract.Rcheck/00check.log'
for details.


Installation output

attract.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL attract
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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
** 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)

Tests output


Example timings

attract.Rcheck/attract-Ex.timings

nameusersystemelapsed
AttractorModuleSet-class000
SynExpressionSet-class0.010.000.01
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix000
calcFuncSynexprs70.08 5.9077.86
calcInform000
calcModfstat000
calcRss000
exprs.dat0.110.040.14
filterDataSet0.280.060.35
findAttractors34.78 5.5141.73
findCorrPartners5.490.416.33
findOnepwaySynexprs000
findSynexprs4.890.425.75
flagPwayExists000
getCustomGenes000
getPwayGenes000
loring.eset0.090.030.13
plotsynexprs4.520.325.07
removeFlatGenes0.120.030.16
samp.info000
subset.loring.eset0.070.010.08