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BioC 3.4: CHECK report for Risa on tokay1

This page was generated on 2017-04-15 16:17:26 -0400 (Sat, 15 Apr 2017).

Package 1054/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.16.0
Alejandra Gonzalez-Beltran
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Risa
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Risa
Version: 1.16.0
Command: rm -rf Risa.buildbin-libdir Risa.Rcheck && mkdir Risa.buildbin-libdir Risa.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Risa.buildbin-libdir Risa_1.16.0.tar.gz >Risa.Rcheck\00install.out 2>&1 && cp Risa.Rcheck\00install.out Risa-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Risa.buildbin-libdir --install="check:Risa-install.out" --force-multiarch --no-vignettes --timings Risa_1.16.0.tar.gz
StartedAt: 2017-04-15 00:32:10 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:36:20 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 250.6 seconds
RetCode: 0
Status:  OK  
CheckDir: Risa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Risa.buildbin-libdir Risa.Rcheck && mkdir Risa.buildbin-libdir Risa.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Risa.buildbin-libdir Risa_1.16.0.tar.gz >Risa.Rcheck\00install.out 2>&1 && cp Risa.Rcheck\00install.out Risa-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Risa.buildbin-libdir --install="check:Risa-install.out" --force-multiarch --no-vignettes --timings Risa_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/Risa.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Risa/DESCRIPTION' ... OK
* this is package 'Risa' version '1.16.0'
* 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 'Risa' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
getPackagesInBiocView: no visible global function definition for 'data'
readISAtabZip: no visible global function definition for 'unzip'
suggestBiocPackage: no visible global function definition for
  'read.csv'
write.assay.file: no visible global function definition for
  'write.table'
write.investigation.file: no visible global function definition for
  'write.table'
write.study.file: no visible global function definition for
  'write.table'
initialize,ISATab: no visible global function definition for
  'count.fields'
initialize,ISATab: no visible global function definition for
  'read.table'
initialize,ISATab : <anonymous>: no visible global function definition
  for 'read.table'
initialize,ISATab : <anonymous> : <anonymous>: no visible global
  function definition for 'read.table'
initialize,ISATab: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  count.fields data na.omit read.csv read.table unzip write.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "count.fields", "data", "read.csv", "read.table",
             "unzip", "write.table")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
Risa-package                0.16   0.08   10.03
processAssayXcmsSet.1factor 0.06   0.02   15.69
processAssayXcmsSet         0.07   0.00   16.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
processAssayXcmsSet.1factor 0.11   0.00   20.97
processAssayXcmsSet         0.08   0.02   22.14
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/Risa.Rcheck/00check.log'
for details.


Risa.Rcheck/00install.out:


install for i386

* installing *source* package 'Risa' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Risa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Risa' as Risa_1.16.0.zip
* DONE (Risa)

Risa.Rcheck/examples_i386/Risa-Ex.timings:

nameusersystemelapsed
AssayTab-class000
ISAtab-class000
Risa-package 0.16 0.0810.03
getAnnotatedDataFrameAssay0.150.000.16
getExpressionSet0.070.010.17
getMIAMEMetadata0.090.020.11
getMSAssayFilenames0.010.000.01
getMicroarrayAssayFilenames0.070.010.08
getStudyFilename0.030.000.03
isMSAssay0.010.000.02
isMicroarrayAssay0.080.000.08
processAssayXcmsSet.1factor 0.06 0.0215.69
processAssayXcmsSet 0.07 0.0016.95
readISAtab0.080.110.19
updateAssayMetadata0.090.000.09
write.assay.file0.010.000.02
write.investigation.file0.040.000.03
write.isatab0.030.000.03
write.study.file0.030.000.03

Risa.Rcheck/examples_x64/Risa-Ex.timings:

nameusersystemelapsed
AssayTab-class000
ISAtab-class000
Risa-package0.090.110.21
getAnnotatedDataFrameAssay0.110.030.14
getExpressionSet0.050.030.08
getMIAMEMetadata0.090.000.09
getMSAssayFilenames0.020.000.02
getMicroarrayAssayFilenames0.030.030.06
getStudyFilename0.030.000.04
isMSAssay0.040.000.03
isMicroarrayAssay0.060.020.07
processAssayXcmsSet.1factor 0.11 0.0020.97
processAssayXcmsSet 0.08 0.0222.14
readISAtab0.120.150.29
updateAssayMetadata0.130.030.15
write.assay.file0.040.000.05
write.investigation.file0.070.000.06
write.isatab0.040.000.05
write.study.file0.030.000.03