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BioC 3.4: CHECK report for rGREAT on moscato1

This page was generated on 2016-09-21 03:46:47 -0700 (Wed, 21 Sep 2016).

Package 1014/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rGREAT 1.5.2
Zuguang Gu
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rGREAT
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: rGREAT
Version: 1.5.2
Command: rm -rf rGREAT.buildbin-libdir rGREAT.Rcheck && mkdir rGREAT.buildbin-libdir rGREAT.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rGREAT.buildbin-libdir rGREAT_1.5.2.tar.gz >rGREAT.Rcheck\00install.out 2>&1 && cp rGREAT.Rcheck\00install.out rGREAT-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=rGREAT.buildbin-libdir --install="check:rGREAT-install.out" --force-multiarch --no-vignettes --timings rGREAT_1.5.2.tar.gz
StartedAt: 2016-09-20 15:23:40 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:26:03 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 143.2 seconds
RetCode: 0
Status:  OK  
CheckDir: rGREAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rGREAT.buildbin-libdir rGREAT.Rcheck && mkdir rGREAT.buildbin-libdir rGREAT.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rGREAT.buildbin-libdir rGREAT_1.5.2.tar.gz >rGREAT.Rcheck\00install.out 2>&1 && cp rGREAT.Rcheck\00install.out rGREAT-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=rGREAT.buildbin-libdir --install="check:rGREAT-install.out" --force-multiarch --no-vignettes --timings rGREAT_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/rGREAT.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rGREAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rGREAT' version '1.5.2'
* 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 'rGREAT' 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
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for 'barplot'
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for 'text'
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for 'legend'
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for 'axis'
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for 'par'
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for 'lines'
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for 'arrows'
Undefined global functions or variables:
  arrows axis barplot legend lines par text
Consider adding
  importFrom("graphics", "arrows", "axis", "barplot", "legend", "lines",
             "par", "text")
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
submitGreatJob 0.47   0.08   12.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
submitGreatJob  0.6   0.11   12.99
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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: 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/rGREAT.Rcheck/00check.log'
for details.


rGREAT.Rcheck/00install.out:


install for i386

* installing *source* package 'rGREAT' ...
** 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 'rGREAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rGREAT' as rGREAT_1.5.2.zip
* DONE (rGREAT)

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

nameusersystemelapsed
GreatJob-class000
availableCategories-GreatJob-method0.070.000.06
availableOntologies-GreatJob-method0.040.000.05
getEnrichmentTables-GreatJob-method0.190.020.20
plotRegionGeneAssociationGraphs-GreatJob-method0.220.000.22
submitGreatJob 0.47 0.0812.95

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

nameusersystemelapsed
GreatJob-class000
availableCategories-GreatJob-method0.030.000.03
availableOntologies-GreatJob-method0.050.000.05
getEnrichmentTables-GreatJob-method0.110.000.10
plotRegionGeneAssociationGraphs-GreatJob-method0.480.000.49
submitGreatJob 0.60 0.1112.99