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This page was generated on 2024-02-22 12:48:17 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 1601/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pwOmics 1.35.0  (landing page)
Torsten Schoeps
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/pwOmics
git_branch: devel
git_last_commit: dfbf89e
git_last_commit_date: 2023-10-24 10:43:28 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for pwOmics on nebbiolo1


To the developers/maintainers of the pwOmics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pwOmics.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: pwOmics
Version: 1.35.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:pwOmics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings pwOmics_1.35.0.tar.gz
StartedAt: 2024-02-22 02:00:05 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 02:04:19 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 254.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pwOmics.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:pwOmics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings pwOmics_1.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/pwOmics.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘pwOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pwOmics’ version ‘1.35.0’
* 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 loading without being on the library search path ... 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 ... NOTE
Invalid package aliases in Rd file 'pwIntOmics-package.Rd':
  ‘pwIntOmics-package’
* 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 Rd file 'plotTimeProfileClusters.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'temp_correlations.Rd':
  ‘...’

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 119.156  1.251  121.29
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/pwOmics.Rcheck/00check.log’
for details.



Installation output

pwOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL pwOmics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 -- Thu Feb 22 02:04:15 2024 
*********************************************** 
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 
  5.728   0.423   6.140 

Example timings

pwOmics.Rcheck/pwOmics-Ex.timings

nameusersystemelapsed
clusterTimeProfiles0.0010.0000.001
consDynamicNet0.0010.0000.000
findSignalingAxes000
generate_DSSignalingBase000
getBiopaxModel0.0000.0010.000
getDS_PWs0.0000.0010.000
getDS_TFs0.0000.0000.001
getDS_TGs0.0000.0000.001
getGenesIntersection0.0010.0000.000
getOmicsDataset000
getOmicsTimepoints0.0000.0000.001
getOmicsallGeneIDs000
getOmicsallProteinIDs000
getProteinIntersection0.0000.0000.001
getTFIntersection0.0010.0000.001
getUS_PWs0.0010.0000.000
getUS_TFs000
getUS_regulators000
get_matching_transcripts000
gettpIntersection0.0000.0010.001
identifyPR0.0000.0010.001
identifyPWTFTGs000
identifyPWs000
identifyRsofTFs000
identifyTFs0.0000.0010.001
infoConsensusGraph0.0000.0010.001
plotConsDynNet000
plotConsensusGraph000
plotConsensusProfiles000
plotTimeProfileClusters0.0000.0010.000
readOmics0.0000.0000.001
readPWdata000
readPhosphodata000
readTFdata0.0000.0010.001
staticConsensusNet0.0010.0000.001
temp_correlations119.156 1.251121.290