Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for PCpheno on merida1

This page was generated on 2021-05-06 12:36:05 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the PCpheno package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1318/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PCpheno 1.52.0  (landing page)
Nolwenn Le Meur
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/PCpheno
Branch: RELEASE_3_12
Last Commit: 3715f48
Last Changed Date: 2020-10-27 10:32:41 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: PCpheno
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PCpheno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PCpheno_1.52.0.tar.gz
StartedAt: 2021-05-06 04:34:57 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:38:06 -0400 (Thu, 06 May 2021)
EllapsedTime: 189.1 seconds
RetCode: 0
Status:   OK  
CheckDir: PCpheno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PCpheno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PCpheno_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/PCpheno.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PCpheno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCpheno’ version ‘1.52.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Category', 'ScISI', 'SLGI', 'ppiStats', 'ppiData', 'annotate'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘PCpheno’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Category’ ‘ScISI’ ‘KEGG.db’ ‘GO.db’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘GO.db’ ‘KEGG.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘SLGI’ ‘annotate’ ‘ppiData’ ‘ppiStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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
graphTheory 5.859  0.132   6.003
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/PCpheno.Rcheck/00check.log’
for details.



Installation output

PCpheno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PCpheno
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘PCpheno’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
** testing if installed package can be loaded from final location
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
** testing if installed package keeps a record of temporary installation path
* DONE (PCpheno)

Tests output


Example timings

PCpheno.Rcheck/PCpheno-Ex.timings

nameusersystemelapsed
CoHyperGResult-class0.5250.0230.549
Dudley0.0060.0040.010
Giaever0.1280.0080.138
HI0.0010.0020.004
KEGG2SCISI0.1070.0130.124
Kastenmayer0.0240.0040.028
Lesage0.0080.0030.011
Osterberg0.0240.0040.029
SGDphenoL0.0270.0020.029
YEASTOHNOLOG0.0100.0030.013
buildFDMat0.1490.0090.158
categoryToEntrezBuilder0.0980.0190.119
complexStatus0.6460.0490.698
deResult-class0.0940.0130.107
densityEstimate0.5040.1160.621
getDescr0.6670.0520.722
getFDgene0.1560.0080.164
graphTheory5.8590.1326.003
gtResult-class4.2640.3104.580
overlap0.0020.0000.003
plot0.6160.0810.699
ppiInteraction3.7620.2113.978
reduceM0.0000.0000.001
truncName0.0000.0000.001