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BioC 2.14: CHECK report for rols on moscato2

This page was generated on 2014-10-08 08:54:44 -0700 (Wed, 08 Oct 2014).

Package 680/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rols 1.6.1
Laurent Gatto
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/rols
Last Changed Rev: 95096 / Revision: 95116
Last Changed Date: 2014-10-07 14:02:28 -0700 (Tue, 07 Oct 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: rols
Version: 1.6.1
Command: rm -rf rols.buildbin-libdir && mkdir rols.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rols.buildbin-libdir rols_1.6.1.tar.gz >rols-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=rols.buildbin-libdir --install="check:rols-install.out" --force-multiarch --no-vignettes --timings rols_1.6.1.tar.gz
StartedAt: 2014-10-08 04:46:48 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 04:50:13 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 204.5 seconds
RetCode: 0
Status:  OK  
CheckDir: rols.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rols.buildbin-libdir && mkdir rols.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rols.buildbin-libdir rols_1.6.1.tar.gz >rols-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=rols.buildbin-libdir --install="check:rols-install.out" --force-multiarch --no-vignettes --timings rols_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/rols.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 'rols/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rols' version '1.6.1'
* 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 'rols' 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
Found the following possibly unsafe calls:
File 'rols/R/queries.R':
  unlockBinding("ontologies", .rolsEnv)
* 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' ... [74s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
allIds        5.49   0.02   14.80
CVParam-class 1.19   0.07   14.43
isIdObsolete  0.28   0.00   13.62
rootId        0.18   0.00    5.19
term          0.12   0.03   15.16
** running examples for arch 'x64' ... [60s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
allIds        6.13   0.00    9.81
CVParam-class 1.45   0.02   26.87
isIdObsolete  0.24   0.00    8.94
* 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/rols.Rcheck/00check.log'
for details.

rols.Rcheck/00install.out:


install for i386

* installing *source* package 'rols' ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'rols' ...
** testing if installed package can be loaded
Note: the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'rols' as rols_1.6.1.zip
* DONE (rols)

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

nameusersystemelapsed
CVParam-class 1.19 0.0714.43
allIds 5.49 0.0214.80
childrenRelations0.040.000.92
isIdObsolete 0.28 0.0013.62
olsQuery0.350.022.73
olsVersion0.010.000.64
ontologies0.030.000.03
ontologyLoadDate0.080.001.36
ontologyNames0.020.000.01
parents0.080.000.69
rootId0.180.005.19
term 0.12 0.0315.16
termMetadata0.160.002.12

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

nameusersystemelapsed
CVParam-class 1.45 0.0226.87
allIds6.130.009.81
childrenRelations0.080.000.87
isIdObsolete0.240.008.94
olsQuery0.260.002.92
olsVersion0.030.000.62
ontologies0.020.000.02
ontologyLoadDate0.090.001.28
ontologyNames0.030.000.03
parents0.060.000.60
rootId0.200.001.93
term0.110.001.98
termMetadata0.160.001.64