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BioC 2.13: CHECK report for gage on moscato1

This page was generated on 2014-04-05 09:50:11 -0700 (Sat, 05 Apr 2014).

Package 272/750HostnameOS / ArchBUILDCHECKBUILD BIN
gage 2.12.3
Weijun Luo
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/gage
Last Changed Rev: 87473 / Revision: 88450
Last Changed Date: 2014-03-14 15:52:36 -0700 (Fri, 14 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: gage
Version: 2.12.3
Command: rm -rf gage.buildbin-libdir && mkdir gage.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gage.buildbin-libdir gage_2.12.3.tar.gz >gage-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=gage.buildbin-libdir --install="check:gage-install.out" --force-multiarch --no-vignettes --timings gage_2.12.3.tar.gz && mv gage.buildbin-libdir/* gage.Rcheck/ && rmdir gage.buildbin-libdir
StartedAt: 2014-04-05 03:58:46 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:02:33 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 226.6 seconds
RetCode: 0
Status:  OK  
CheckDir: gage.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/gage.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '2.12.3'
* 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'
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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'RNA-seqWorkflow.Rnw', 'dataPrep.Rnw', 'gage.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kegg.gsets 1.13   0.05     5.4
** running examples for arch 'x64' ... [28s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.13-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_2.12.3.zip
* DONE (gage)

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

nameusersystemelapsed
eg2sym1.440.001.44
egSymb1.100.001.11
essGene0.510.020.59
esset.grp1.810.001.81
gage2.590.002.59
gageComp1.080.022.46
gagePipe0.940.030.97
geneData0.400.000.41
gs.tTest0.200.020.22
gse168730.310.010.33
heter.gage0.810.000.82
kegg.gs0.940.000.93
kegg.gsets1.130.055.40
readExpData0.020.000.02
readList0.210.000.22
sigGeneSet0.470.000.47

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

nameusersystemelapsed
eg2sym1.460.061.52
egSymb1.270.011.28
essGene0.600.031.08
esset.grp2.350.023.06
gage2.920.012.93
gageComp1.610.002.17
gagePipe1.060.051.10
geneData0.450.010.47
gs.tTest0.250.020.26
gse168730.350.010.36
heter.gage0.840.020.86
kegg.gs1.330.001.33
kegg.gsets1.150.054.97
readExpData0.030.000.03
readList0.190.000.19
sigGeneSet0.820.001.82