Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O [P] Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for paxtoolsr on tokay2

This page was generated on 2017-08-16 13:23:50 -0400 (Wed, 16 Aug 2017).

Package 956/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.10.0
Augustin Luna
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/paxtoolsr
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  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: paxtoolsr
Version: 1.10.0
Command: rm -rf paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && mkdir paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=paxtoolsr.buildbin-libdir paxtoolsr_1.10.0.tar.gz >paxtoolsr.Rcheck\00install.out 2>&1 && cp paxtoolsr.Rcheck\00install.out paxtoolsr-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=paxtoolsr.buildbin-libdir --install="check:paxtoolsr-install.out" --force-multiarch --no-vignettes --timings paxtoolsr_1.10.0.tar.gz
StartedAt: 2017-08-16 01:49:24 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:52:00 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 156.0 seconds
RetCode: 0
Status:  OK  
CheckDir: paxtoolsr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && mkdir paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=paxtoolsr.buildbin-libdir paxtoolsr_1.10.0.tar.gz >paxtoolsr.Rcheck\00install.out 2>&1 && cp paxtoolsr.Rcheck\00install.out paxtoolsr-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=paxtoolsr.buildbin-libdir --install="check:paxtoolsr-install.out" --force-multiarch --no-vignettes --timings paxtoolsr_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/paxtoolsr.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'paxtoolsr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'paxtoolsr' version '1.10.0'
* 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 'paxtoolsr' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 30.7Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    java     24.5Mb
* 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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'jsonlite'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onLoad: no visible global function definition for 'write.table'
downloadFile: no visible global function definition for 'URLencode'
downloadFile: no visible global function definition for 'read.table'
downloadFile: no visible global function definition for 'write.table'
downloadPc2: no visible global function definition for 'select.list'
downloadSignedPC: no visible global function definition for
  'read.table'
getPcRequest: no visible global function definition for 'URLencode'
readSifnx: no visible global function definition for 'read.table'
splitSifnxByPathway: no visible global function definition for
  'txtProgressBar'
splitSifnxByPathway: no visible global function definition for
  '%dopar%'
splitSifnxByPathway: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  %dopar% URLencode read.table select.list setTxtProgressBar
  txtProgressBar write.table
Consider adding
  importFrom("utils", "URLencode", "read.table", "select.list",
             "setTxtProgressBar", "txtProgressBar", "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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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/paxtoolsr.Rcheck/00check.log'
for details.


paxtoolsr.Rcheck/00install.out:


install for i386

* installing *source* package 'paxtoolsr' ...
** 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 'paxtoolsr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'paxtoolsr' as paxtoolsr_1.10.0.zip
* DONE (paxtoolsr)

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

nameusersystemelapsed
downloadFile0.200.030.56
downloadPc2000
downloadSignedPC000
extractIds0.020.000.02
fetch1.140.131.54
filterSif0.230.000.24
getCacheFiles000
getErrorMessage000
getNeighbors0.250.000.25
getPc000
getPcUrl000
getSifInteractionCategories000
graphPc000
integrateBiopax1.230.031.27
loadSifInIgraph0.080.000.08
mapValues000
mergeBiopax1.080.011.03
pcDirections000
pcFormats000
pcGraphQueries000
processPcRequest0.000.020.08
readBiopax000
readGmt0.010.000.01
readSbgn0.000.020.02
readSif000
readSifnx0.020.000.01
searchListOfVectors0.010.000.02
searchPc000
summarize0.110.000.15
summarizeSif000
toGSEA0.070.000.49
toLevel30.090.000.14
toSBGN0.830.093.92
toSif0.790.000.92
toSifnx0.460.000.58
topPathways000
traverse000
validate0.330.164.72

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

nameusersystemelapsed
downloadFile0.260.010.54
downloadPc2000
downloadSignedPC000
extractIds0.030.000.03
fetch4.440.271.28
filterSif0.620.000.30
getCacheFiles000
getErrorMessage000
getNeighbors1.000.030.25
getPc000
getPcUrl000
getSifInteractionCategories000
graphPc000
integrateBiopax3.130.120.80
loadSifInIgraph0.120.000.06
mapValues000
mergeBiopax1.210.030.42
pcDirections000
pcFormats000
pcGraphQueries000
processPcRequest0.090.000.08
readBiopax000
readGmt0.030.000.02
readSbgn000
readSif0.020.000.01
readSifnx0.010.000.02
searchListOfVectors000
searchPc000
summarize0.210.000.09
summarizeSif000
toGSEA0.180.040.19
toLevel30.490.010.13
toSBGN1.780.101.96
toSif3.090.091.43
toSifnx1.630.030.78
topPathways000
traverse000
validate1.220.203.08