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CHECK report for PCpheno on malbec1

This page was generated on 2021-05-05 12:10:29 -0400 (Wed, 05 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: 2021-05-04 14:50:13 -0400 (Tue, 04 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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:PCpheno.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings PCpheno_1.52.0.tar.gz
StartedAt: 2021-05-05 04:25:18 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 04:28:17 -0400 (Wed, 05 May 2021)
EllapsedTime: 178.5 seconds
RetCode: 0
Status:   OK  
CheckDir: PCpheno.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:PCpheno.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings PCpheno_1.52.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/PCpheno.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
graphTheory    6.548  0.112   6.684
gtResult-class 4.808  0.240   5.061
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/PCpheno.Rcheck/00check.log’
for details.



Installation output

PCpheno.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL PCpheno
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-class0.5240.0200.718
Dudley0.0040.0000.006
Giaever0.1240.0000.125
HI0.0040.0000.002
KEGG2SCISI0.0640.0040.153
Kastenmayer0.0160.0000.017
Lesage0.0040.0000.007
Osterberg0.0240.0000.020
SGDphenoL0.0240.0000.023
YEASTOHNOLOG0.0080.0000.009
buildFDMat0.1600.0160.176
categoryToEntrezBuilder0.1160.0080.134
complexStatus0.6960.0320.738
deResult-class0.0880.0120.101
densityEstimate0.5600.1120.676
getDescr0.7000.0200.762
getFDgene0.1920.0080.204
graphTheory6.5480.1126.684
gtResult-class4.8080.2405.061
overlap0.0000.0000.002
plot0.6280.0080.636
ppiInteraction3.5640.0083.629
reduceM0.0000.0000.001
truncName000