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BioC 3.5: CHECK report for goTools on tokay2

This page was generated on 2017-10-18 14:18:53 -0400 (Wed, 18 Oct 2017).

Package 583/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goTools 1.50.0
Agnes Paquet
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/goTools
Branch: RELEASE_3_5
Last Commit: 14b6f54
Last Changed Date: 2017-04-24 15:45:44 -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: goTools
Version: 1.50.0
Command: rm -rf goTools.buildbin-libdir goTools.Rcheck && mkdir goTools.buildbin-libdir goTools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goTools.buildbin-libdir goTools_1.50.0.tar.gz >goTools.Rcheck\00install.out 2>&1 && cp goTools.Rcheck\00install.out goTools-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=goTools.buildbin-libdir --install="check:goTools-install.out" --force-multiarch --no-vignettes --timings goTools_1.50.0.tar.gz
StartedAt: 2017-10-18 00:20:52 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:23:00 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 128.5 seconds
RetCode: 0
Status:  OK  
CheckDir: goTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf goTools.buildbin-libdir goTools.Rcheck && mkdir goTools.buildbin-libdir goTools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goTools.buildbin-libdir goTools_1.50.0.tar.gz >goTools.Rcheck\00install.out 2>&1 && cp goTools.Rcheck\00install.out goTools-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=goTools.buildbin-libdir --install="check:goTools-install.out" --force-multiarch --no-vignettes --timings goTools_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/goTools.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'goTools/DESCRIPTION' ... OK
* this is package 'goTools' version '1.50.0'
* 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 'goTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'GO.db'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
EndNodeList: warning in get("GO:0003674", env = GOMFCHILDREN): partial
  argument match of 'env' to 'envir'
EndNodeList: warning in get("GO:0005575", env = GOCCCHILDREN): partial
  argument match of 'env' to 'envir'
EndNodeList: warning in get("GO:0008150", env = GOBPCHILDREN): partial
  argument match of 'env' to 'envir'
getGOID: warning in mget(x, env = GOenv): partial argument match of
  'env' to 'envir'
goChildren: warning in get(id, env = envi): partial argument match of
  'env' to 'envir'
goParents: warning in get(paste("GO", cat, "PARENTS", sep = ""), env =
  as.environment("package:GO.db")): partial argument match of 'env' to
  'envir'
goParents: warning in get(goid, env = envi): partial argument match of
  'env' to 'envir'
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/goTools.Rcheck/00check.log'
for details.


goTools.Rcheck/00install.out:


install for i386

* installing *source* package 'goTools' ...
** R
** data
** 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 'goTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goTools' as goTools_1.50.0.zip
* DONE (goTools)

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

nameusersystemelapsed
EndNodeList000
ontoCompare000

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

nameusersystemelapsed
EndNodeList000
ontoCompare000