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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1591/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pwOmics 1.32.0  (landing page)
Maren Sitte
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/pwOmics
git_branch: RELEASE_3_17
git_last_commit: b7a7328
git_last_commit_date: 2023-04-25 10:39:39 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for pwOmics on kjohnson2


To the developers/maintainers of the pwOmics package:
- 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: pwOmics
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pwOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pwOmics_1.32.0.tar.gz
StartedAt: 2023-10-18 16:33:55 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 16:42:13 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 497.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pwOmics.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pwOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pwOmics_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pwOmics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pwOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pwOmics’ version ‘1.32.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pwOmics’ 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 ... NOTE
identifyPWTFTGs: no visible binding for global variable ‘upreg’
identifyPWTFTGs: no visible binding for global variable ‘phosphoeffect’
infoConsensusGraph: no visible global function definition for ‘from’
Undefined global functions or variables:
  from phosphoeffect upreg
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotTimeProfileClusters':
  ‘...’

Documented arguments not in \usage in documentation object 'temp_correlations':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
temp_correlations 152.454  1.962 239.987
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pwOmics.Rcheck/00check.log’
for details.



Installation output

pwOmics.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pwOmics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘pwOmics’ ...
** 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 (pwOmics)

Tests output

pwOmics.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("pwOmics")


RUNIT TEST PROTOCOL -- Wed Oct 18 16:41:55 2023 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
pwOmics RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  7.060   0.403  11.467 

Example timings

pwOmics.Rcheck/pwOmics-Ex.timings

nameusersystemelapsed
clusterTimeProfiles0.0000.0000.001
consDynamicNet0.0000.0010.001
findSignalingAxes0.0010.0000.001
generate_DSSignalingBase0.0000.0010.001
getBiopaxModel0.0000.0000.002
getDS_PWs0.0000.0000.001
getDS_TFs0.0000.0010.000
getDS_TGs0.0010.0000.001
getGenesIntersection0.0000.0000.001
getOmicsDataset0.0000.0000.001
getOmicsTimepoints000
getOmicsallGeneIDs000
getOmicsallProteinIDs0.0000.0010.003
getProteinIntersection0.0000.0010.001
getTFIntersection000
getUS_PWs0.0010.0000.000
getUS_TFs0.0000.0000.001
getUS_regulators0.0000.0010.001
get_matching_transcripts000
gettpIntersection0.0000.0000.002
identifyPR000
identifyPWTFTGs0.0000.0010.001
identifyPWs0.0000.0000.001
identifyRsofTFs000
identifyTFs0.0010.0000.000
infoConsensusGraph000
plotConsDynNet0.0000.0010.000
plotConsensusGraph0.0000.0000.001
plotConsensusProfiles0.0000.0000.001
plotTimeProfileClusters000
readOmics000
readPWdata0.0000.0000.001
readPhosphodata000
readTFdata000
staticConsensusNet0.0000.0000.003
temp_correlations152.454 1.962239.987