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BioC 2.14: CHECK report for gage on moscato2

This page was generated on 2014-10-08 08:53:36 -0700 (Wed, 08 Oct 2014).

Package 305/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gage 2.14.4
Weijun Luo
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/gage
Last Changed Rev: 92582 / Revision: 95116
Last Changed Date: 2014-07-16 20:11:46 -0700 (Wed, 16 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: gage
Version: 2.14.4
Command: rm -rf gage.buildbin-libdir && mkdir gage.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gage.buildbin-libdir gage_2.14.4.tar.gz >gage-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=gage.buildbin-libdir --install="check:gage-install.out" --force-multiarch --no-vignettes --timings gage_2.14.4.tar.gz
StartedAt: 2014-10-08 01:14:39 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:17:57 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 197.4 seconds
RetCode: 0
Status:  OK  
CheckDir: gage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gage.buildbin-libdir && mkdir gage.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gage.buildbin-libdir gage_2.14.4.tar.gz >gage-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=gage.buildbin-libdir --install="check:gage-install.out" --force-multiarch --no-vignettes --timings gage_2.14.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/gage.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gage' version '2.14.4'
* 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 'gage' 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
deComp: no visible global function definition for 'annot.db'
eg2sym: no visible binding for global variable 'egSymb'
esset.grp: no visible global function definition for 'make.graph'
go.gsets: no visible global function definition for 'biocLite'
kegg.gsets: no visible binding for global variable 'khier'
kegg.species.code: no visible binding for global variable 'korg'
sym2eg: no visible binding for global variable 'egSymb'
* 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' ... [22s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kegg.gsets 1.26   0.01    5.38
** running examples for arch 'x64' ... [26s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kegg.gsets 1.47   0.02     5.3
* 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/gage.Rcheck/00check.log'
for details.

gage.Rcheck/00install.out:


install for i386

* installing *source* package 'gage' ...
** 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 'gage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gage' as gage_2.14.4.zip
* DONE (gage)

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

nameusersystemelapsed
eg2sym1.300.021.31
egSymb1.070.001.08
essGene0.520.000.53
esset.grp1.740.001.75
gage2.370.032.40
gageComp1.110.001.23
gagePipe1.050.021.06
geneData0.290.000.30
go.gsets0.020.000.02
gs.tTest0.230.000.23
gse168730.320.000.31
heter.gage0.810.000.81
kegg.gs0.980.000.99
kegg.gsets1.260.015.38
readExpData0.020.000.01
readList0.150.000.16
sigGeneSet0.500.020.51

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

nameusersystemelapsed
eg2sym1.640.021.65
egSymb1.320.011.34
essGene0.420.020.58
esset.grp2.310.012.32
gage2.860.002.86
gageComp1.280.001.28
gagePipe1.220.021.24
geneData0.290.030.32
go.gsets000
gs.tTest0.270.000.27
gse168730.340.010.36
heter.gage0.990.000.98
kegg.gs1.180.001.19
kegg.gsets1.470.025.30
readExpData000
readList0.160.000.16
sigGeneSet0.580.000.58