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BioC 2.13: CHECK report for GSEABase on moscato1

This page was generated on 2014-04-05 09:49:32 -0700 (Sat, 05 Apr 2014).

Package 330/750HostnameOS / ArchBUILDCHECKBUILD BIN
GSEABase 1.24.0
Bioconductor Package Maintainer
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/GSEABase
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
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: GSEABase
Version: 1.24.0
Command: rm -rf GSEABase.buildbin-libdir && mkdir GSEABase.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSEABase.buildbin-libdir GSEABase_1.24.0.tar.gz >GSEABase-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=GSEABase.buildbin-libdir --install="check:GSEABase-install.out" --force-multiarch --no-vignettes --timings GSEABase_1.24.0.tar.gz && mv GSEABase.buildbin-libdir/* GSEABase.Rcheck/ && rmdir GSEABase.buildbin-libdir
StartedAt: 2014-04-05 04:27:21 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:32:51 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 330.1 seconds
RetCode: 0
Status:  OK  
CheckDir: GSEABase.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GSEABase.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 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '1.24.0'
* 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 'GSEABase' 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.checkRequired' '.constructors_Simple'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'GSEABase.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [22s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
GeneSetCollection-methods 10.7   0.25      11
** running examples for arch 'x64' ... [27s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GeneSetCollection-methods 13.71   0.26   14.02
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'unitTests.R' [51s]
 [52s] OK
** running tests for arch 'x64'
  Running 'unitTests.R' [50s]
 [50s] 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/GSEABase.Rcheck/00check.log'
for details.

GSEABase.Rcheck/00install.out:


install for i386

* installing *source* package 'GSEABase' ...
** 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 'GSEABase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSEABase' as GSEABase_1.24.0.zip
* DONE (GSEABase)

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

nameusersystemelapsed
CollectionType-class0.920.040.98
CollectionType-constructors0.360.000.35
GSEABase-package0.270.030.30
GeneColorSet-class0.350.040.38
GeneIdentifierType-class0.20.00.2
GeneIdentifierType-constructors0.500.040.55
GeneSet-class0.730.030.77
GeneSet-methods0.470.000.47
GeneSetCollection-class0.080.000.07
GeneSetCollection-methods10.70 0.2511.00
OBOCollection-class0.170.000.17
getOBOCollection0.140.000.14
getObjects0.130.000.12
goSlim-methods1.200.031.23
incidence-methods0.060.000.07

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

nameusersystemelapsed
CollectionType-class1.360.081.44
CollectionType-constructors0.260.030.29
GSEABase-package0.260.000.26
GeneColorSet-class0.300.010.31
GeneIdentifierType-class0.360.000.36
GeneIdentifierType-constructors0.610.000.61
GeneSet-class0.870.050.92
GeneSet-methods0.310.020.33
GeneSetCollection-class0.110.000.11
GeneSetCollection-methods13.71 0.2614.02
OBOCollection-class0.220.000.22
getOBOCollection0.160.000.16
getObjects0.120.000.12
goSlim-methods0.900.020.92
incidence-methods0.030.010.05