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BioC 3.5: CHECK report for PCpheno on malbec2

This page was generated on 2017-08-16 13:13:02 -0400 (Wed, 16 Aug 2017).

Package 964/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PCpheno 1.38.0
Nolwenn Le Meur
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/PCpheno
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PCpheno
Version: 1.38.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PCpheno_1.38.0.tar.gz
StartedAt: 2017-08-16 01:13:19 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:15:43 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 144.2 seconds
RetCode: 0
Status:  OK 
CheckDir: PCpheno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PCpheno_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/PCpheno.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.38.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
graphTheory 5.084  0.032   5.119
* 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-3.5-bioc/meat/PCpheno.Rcheck/00check.log’
for details.


PCpheno.Rcheck/00install.out:

* installing *source* package ‘PCpheno’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
* DONE (PCpheno)

PCpheno.Rcheck/PCpheno-Ex.timings:

nameusersystemelapsed
CoHyperGResult-class0.4000.0040.451
Dudley0.0040.0040.007
Giaever0.1080.0040.112
HI0.0000.0000.001
KEGG2SCISI0.3560.0040.379
Kastenmayer0.0160.0000.017
Lesage0.0080.0000.006
Osterberg0.0200.0000.018
SGDphenoL0.0240.0000.025
YEASTOHNOLOG0.0080.0000.008
buildFDMat0.1360.0080.145
categoryToEntrezBuilder0.3600.0080.380
complexStatus0.5240.0040.533
deResult-class0.0680.0040.070
densityEstimate1.0600.0001.062
getDescr0.7840.0080.843
getFDgene0.1440.0000.142
graphTheory5.0840.0325.119
gtResult-class3.1200.0883.210
overlap0.0000.0000.001
plot0.8840.0120.895
ppiInteraction2.8480.0202.919
reduceM0.0000.0000.001
truncName0.0000.0000.001