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This page was generated on 2021-07-30 15:06:05 -0400 (Fri, 30 Jul 2021).

CHECK results for pwOmics on tokay2

To the developers/maintainers of the pwOmics package:
- Please 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 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 1466/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pwOmics 1.24.0  (landing page)
Maren Sitte
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/pwOmics
Branch: RELEASE_3_13
Last Commit: 9b1e369
Last Changed Date: 2021-05-19 12:13:37 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: pwOmics
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pwOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pwOmics_1.24.0.tar.gz
StartedAt: 2021-07-30 04:14:37 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 04:23:31 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 534.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pwOmics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pwOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pwOmics_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/pwOmics.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pwOmics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pwOmics' version '1.24.0'
* 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
temp_correlations 153.78   1.06  156.82
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
temp_correlations 171.02   0.86  172.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/pwOmics.Rcheck/00check.log'
for details.



Installation output

pwOmics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/pwOmics_1.24.0.tar.gz && rm -rf pwOmics.buildbin-libdir && mkdir pwOmics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pwOmics.buildbin-libdir pwOmics_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pwOmics_1.24.0.zip && rm pwOmics_1.24.0.tar.gz pwOmics_1.24.0.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
 95  893k   95  855k    0     0  2141k      0 --:--:-- --:--:-- --:--:-- 2139k
100  893k  100  893k    0     0  2227k      0 --:--:-- --:--:-- --:--:-- 2228k

install for i386

* installing *source* package 'pwOmics' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pwOmics'
    finding HTML links ... done
    OmicsExampleData                        html  
    PWidentallprots                         html  
    PWidentallprotssub                      html  
    PWidenttps                              html  
    SteinerTree_cons                        html  
    TFidentallgenes                         html  
    TFidenttps                              html  
    addFeedbackLoops                        html  
    clusterTimeProfiles                     html  
    consDynamicNet                          html  
    createBiopaxnew                         html  
    createIntIDs                            html  
    findSignalingAxes                       html  
    findxneighborsoverlap                   html  
    findxnextneighbors                      html  
    genGenelists                            html  
    genGenelistssub                         html  
    genIntIDs                               html  
    generate_DSSignalingBase                html  
    genfullConsensusGraph                   html  
    getAlias_Ensemble                       html  
    getAliasfromSTRINGIDs                   html  
    getBiopaxModel                          html  
    getConsensusSTRINGIDs                   html  
    getDS_PWs                               html  
    getDS_TFs                               html  
    getDS_TGs                               html  
    getFCsplines                            html  
    getGenesIntersection                    html  
    getOmicsDataset                         html  
    getOmicsTimepoints                      html  
    getOmicsallGeneIDs                      html  
    getOmicsallProteinIDs                   html  
    getProteinIntersection                  html  
    getSTRING_graph                         html  
    getTFIntersection                       html  
    getUS_PWs                               html  
    getUS_TFs                               html  
    getUS_regulators                        html  
    get_matching_transcripts                html  
    getbipartitegraphInfo                   html  
    gettpIntersection                       html  
    identPWsofTFs                           html  
    identRegulators                         html  
    identTFTGsinPWs                         html  
    identTFs                                html  
    identifyPR                              html  
    identifyPWTFTGs                         html  
    identifyPWs                             html  
    identifyRsofTFs                         html  
    identifyTFs                             html  
    infoConsensusGraph                      html  
    loadGenelists                           html  
    loadPWs                                 html  
    plotConsDynNet                          html  
    plotConsensusGraph                      html  
    plotConsensusProfiles                   html  
    plotTimeProfileClusters                 html  
    predictFCvals                           html  
    preparePWinfo                           html  
    print.OmicsData                         html  
    pwIntOmics-package                      html  
    readOmics                               html  
    readPWdata                              html  
    readPhosphodata                         html  
    readTFdata                              html  
    readTFtargets                           html  
    selectPWsofTFs                          html  
    staticConsensusNet                      html  
    temp_correlations                       html  
** 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

install for x64

* installing *source* package 'pwOmics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pwOmics' as pwOmics_1.24.0.zip
* DONE (pwOmics)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'pwOmics' successfully unpacked and MD5 sums checked

Tests output

pwOmics.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Fri Jul 30 04:23:14 2021 
*********************************************** 
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 
   6.32    0.56    6.87 

pwOmics.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Fri Jul 30 04:23:21 2021 
*********************************************** 
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 
   6.48    0.42    6.89 

Example timings

pwOmics.Rcheck/examples_i386/pwOmics-Ex.timings

nameusersystemelapsed
clusterTimeProfiles000
consDynamicNet000
findSignalingAxes000
generate_DSSignalingBase000
getBiopaxModel000
getDS_PWs000
getDS_TFs000
getDS_TGs000
getGenesIntersection000
getOmicsDataset000
getOmicsTimepoints000
getOmicsallGeneIDs000
getOmicsallProteinIDs000
getProteinIntersection000
getTFIntersection000
getUS_PWs000
getUS_TFs000
getUS_regulators000
get_matching_transcripts000
gettpIntersection000
identifyPR000
identifyPWTFTGs000
identifyPWs000
identifyRsofTFs000
identifyTFs000
infoConsensusGraph000
plotConsDynNet000
plotConsensusGraph000
plotConsensusProfiles000
plotTimeProfileClusters000
readOmics000
readPWdata000
readPhosphodata000
readTFdata000
staticConsensusNet000
temp_correlations153.78 1.06156.82

pwOmics.Rcheck/examples_x64/pwOmics-Ex.timings

nameusersystemelapsed
clusterTimeProfiles000
consDynamicNet000
findSignalingAxes000
generate_DSSignalingBase000
getBiopaxModel000
getDS_PWs000
getDS_TFs000
getDS_TGs000
getGenesIntersection000
getOmicsDataset000
getOmicsTimepoints000
getOmicsallGeneIDs000
getOmicsallProteinIDs000
getProteinIntersection000
getTFIntersection000
getUS_PWs000
getUS_TFs000
getUS_regulators000
get_matching_transcripts000
gettpIntersection000
identifyPR000
identifyPWTFTGs000
identifyPWs000
identifyRsofTFs000
identifyTFs000
infoConsensusGraph000
plotConsDynNet000
plotConsensusGraph000
plotConsensusProfiles000
plotTimeProfileClusters000
readOmics000
readPWdata000
readPhosphodata000
readTFdata000
staticConsensusNet000
temp_correlations171.02 0.86172.94