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BioC 3.1: CHECK report for HTSanalyzeR on morelia

This page was generated on 2015-10-09 09:39:25 -0700 (Fri, 09 Oct 2015).

Package 471/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSanalyzeR 2.20.0
Xin Wang
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/HTSanalyzeR
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HTSanalyzeR
Version: 2.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.20.0.tar.gz
StartedAt: 2015-10-09 03:01:25 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:04:56 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 210.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: HTSanalyzeR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSanalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSanalyzeR’ version ‘2.20.0’
* 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 ‘HTSanalyzeR’ can be installed ... [16s/17s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
See ‘/Users/biocbuild/bbs-3.1-bioc/meat/HTSanalyzeR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘igraph’
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:
  ‘org.Ce.eg.db’ ‘org.Dm.eg.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’
  ‘org.Rn.eg.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  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 ... NOTE
File ‘HTSanalyzeR/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("/////////////////////////////////////////////////////////////////////////////\n\n//------------------    Thanks for using HTSanalyzeR    -------------------//\n \n//------------please use function changes() to see new changes-------------//\n\n//------------please report any bug to xinwang2hms@gmail.com---------------//\n\n/////////////////////////////////////////////////////////////////////////////\n",     appendLF = FALSE)

See section ‘Good practice’ in '?.onAttach'.

appendGSTerms,GSCA : .local : appendKEGGTerm: warning in mget(gsKEGG,
  env = KEGGPATHID2NAME, ifnotfound = NA): partial argument match of
  'env' to 'envir'
HTSanalyzeR4cellHTS2: no visible global function definition for ‘fData’
KeggGeneSets: no visible binding for global variable ‘KEGGPATHID2EXTID’
cellHTS2OutputStatTests: no visible global function definition for
  ‘fData’
gseaScoresBatchParallel: no visible global function definition for
  ‘parSapply’
appendGSTerms,GSCA : .local : appendKEGGTerm: no visible binding for
  global variable ‘KEGGPATHID2NAME’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/25s] OK
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/HTSanalyzeR.Rcheck/00check.log’
for details.


HTSanalyzeR.Rcheck/00install.out:

* installing *source* package ‘HTSanalyzeR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* DONE (HTSanalyzeR)

HTSanalyzeR.Rcheck/HTSanalyzeR-Ex.timings:

nameusersystemelapsed
FDRcollectionGsea0.7020.0220.725
GOGeneSets1.6990.1401.986
GSCA-class0.0020.0000.003
HTSanalyzeR4cellHTS20.0020.0010.002
KeggGeneSets2.1730.1362.395
NWA-class0.0020.0000.002
aggregatePvals0.0040.0000.005
analyze0.0010.0000.001
analyzeGeneSetCollections0.0020.0000.001
annotationConvertor1.1240.0441.179
appendGSTerms0.0000.0000.001
biogridDataDownload0.0010.0000.000
celAnnotationConvertor1.7140.1782.048
cellHTS2OutputStatTests0.0010.0000.000
changes000
collectionGsea0.2520.0510.303
data-KcViab0.7980.0330.831
drosoAnnotationConvertor1.1760.0251.201
duplicateRemover0.0010.0000.001
getTopGeneSets0.0000.0000.001
gseaPlots0.0010.0000.001
gseaScores0.0140.0010.015
hyperGeoTest2.5100.0452.557
interactome0.0010.0000.001
mammalAnnotationConvertor2.4570.0492.507
multiHyperGeoTest0.0060.0000.006
networkAnalysis0.0010.0000.001
networkPlot0.0000.0000.001
pairwiseGsea0.7770.0510.828
pairwiseGseaPlot0.0000.0000.001
pairwisePhenoMannWhit0.0050.0000.004
permutationPvalueCollectionGsea0.2010.0100.210
plotEnrichMap0.0000.0010.000
plotGSEA0.0010.0000.001
plotSubNet0.0010.0000.001
preprocess0.0000.0000.001
report0.0010.0000.001
reportAll000
summarize0.0010.0000.001
viewEnrichMap0.0010.0000.001
viewGSEA0.0010.0000.001
viewSubNet0.0010.0000.001
writeReportHTSA0.0010.0000.001