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BioC 3.0: CHECK report for GenomeInfoDb on moscato1

This page was generated on 2015-04-10 09:50:02 -0700 (Fri, 10 Apr 2015).

Package 363/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeInfoDb 1.2.5
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomeInfoDb
Last Changed Rev: 102059 / Revision: 102249
Last Changed Date: 2015-04-07 14:40:44 -0700 (Tue, 07 Apr 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: GenomeInfoDb
Version: 1.2.5
Command: rm -rf GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && mkdir GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.2.5.tar.gz >GenomeInfoDb.Rcheck\00install.out 2>&1 && cp GenomeInfoDb.Rcheck\00install.out GenomeInfoDb-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GenomeInfoDb.buildbin-libdir --install="check:GenomeInfoDb-install.out" --force-multiarch --no-vignettes --timings GenomeInfoDb_1.2.5.tar.gz
StartedAt: 2015-04-10 01:30:40 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:33:41 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 181.0 seconds
RetCode: 0
Status:  OK  
CheckDir: GenomeInfoDb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && mkdir GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.2.5.tar.gz >GenomeInfoDb.Rcheck\00install.out 2>&1 && cp GenomeInfoDb.Rcheck\00install.out GenomeInfoDb-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GenomeInfoDb.buildbin-libdir --install="check:GenomeInfoDb-install.out" --force-multiarch --no-vignettes --timings GenomeInfoDb_1.2.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GenomeInfoDb.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomeInfoDb/DESCRIPTION' ... OK
* this is package 'GenomeInfoDb' version '1.2.5'
* 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 'GenomeInfoDb' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'BiocGenerics' 'S4Vectors'
A package should be listed in only one of these fields.
* 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
Unexported object imported by a ':::' call: 'utils:::.roman2numeric'
  See the note in ?`:::` about the use of this operator.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [22s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
GenomeDescription-class 8.05   0.15     8.2
** running examples for arch 'x64' ... [22s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
GenomeDescription-class 8.22   0.18     8.4
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [8s]
 [8s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [10s]
 [11s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/GenomeInfoDb.Rcheck/00check.log'
for details.

GenomeInfoDb.Rcheck/00install.out:


install for i386

* installing *source* package 'GenomeInfoDb' ...
** 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 'GenomeInfoDb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeInfoDb' as GenomeInfoDb_1.2.5.zip
* DONE (GenomeInfoDb)

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

nameusersystemelapsed
GenomeDescription-class8.050.158.20
Seqinfo-class0.320.020.33
fetchExtendedChromInfoFromUCSC1.230.454.31
rankSeqlevels0.400.030.68
seqinfo2.080.072.14
seqlevels-wrappers2.000.172.17
seqlevelsStyle0.310.060.38

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

nameusersystemelapsed
GenomeDescription-class8.220.188.40
Seqinfo-class0.360.000.36
fetchExtendedChromInfoFromUCSC0.920.332.76
rankSeqlevels0.500.050.55
seqinfo2.330.082.40
seqlevels-wrappers1.580.091.67
seqlevelsStyle0.350.080.42