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BioC 3.0: CHECK report for COPDSexualDimorphism on moscato1

This page was generated on 2015-04-10 09:50:12 -0700 (Fri, 10 Apr 2015).

Package 196/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COPDSexualDimorphism 1.2.0
J Fah Sathirapongsasuti
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/COPDSexualDimorphism
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: COPDSexualDimorphism
Version: 1.2.0
Command: rm -rf COPDSexualDimorphism.buildbin-libdir COPDSexualDimorphism.Rcheck && mkdir COPDSexualDimorphism.buildbin-libdir COPDSexualDimorphism.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COPDSexualDimorphism.buildbin-libdir COPDSexualDimorphism_1.2.0.tar.gz >COPDSexualDimorphism.Rcheck\00install.out 2>&1 && cp COPDSexualDimorphism.Rcheck\00install.out COPDSexualDimorphism-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=COPDSexualDimorphism.buildbin-libdir --install="check:COPDSexualDimorphism-install.out" --force-multiarch --no-vignettes --timings COPDSexualDimorphism_1.2.0.tar.gz
StartedAt: 2015-04-10 00:05:30 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:08:50 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 200.1 seconds
RetCode: 0
Status:  OK  
CheckDir: COPDSexualDimorphism.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf COPDSexualDimorphism.buildbin-libdir COPDSexualDimorphism.Rcheck && mkdir COPDSexualDimorphism.buildbin-libdir COPDSexualDimorphism.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COPDSexualDimorphism.buildbin-libdir COPDSexualDimorphism_1.2.0.tar.gz >COPDSexualDimorphism.Rcheck\00install.out 2>&1 && cp COPDSexualDimorphism.Rcheck\00install.out COPDSexualDimorphism-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=COPDSexualDimorphism.buildbin-libdir --install="check:COPDSexualDimorphism-install.out" --force-multiarch --no-vignettes --timings COPDSexualDimorphism_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/COPDSexualDimorphism.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 'COPDSexualDimorphism/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COPDSexualDimorphism' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'COPDSexualDimorphism.data' 'NCBI2R' 'RColorBrewer' 'beeswarm'
  'limma' 'GenomicRanges' 'gplots' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'COPDSexualDimorphism' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'GenomicRanges' 'NCBI2R' 'RColorBrewer' 'beeswarm'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'COPDSexualDimorphism.data' 'NCBI2R' 'RColorBrewer' 'gplots' 'limma'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getNeighbors: no visible global function definition for 'Rle'
getNeighbors: no visible global function definition for 'IRanges'
my.smart.plot: no visible global function definition for 'brewer.pal'
sdcd: no visible binding for global variable 'chromosome_name'
sdcd.vmr: no visible global function definition for 'GetNeighGenes'
sdcd.vmr: no visible binding for global variable 'vmr'
* 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' ... [20s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
COPDSexualDimorphism-package 4.46   0.18    6.59
** running examples for arch 'x64' ... [14s] 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 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/COPDSexualDimorphism.Rcheck/00check.log'
for details.

COPDSexualDimorphism.Rcheck/00install.out:


install for i386

* installing *source* package 'COPDSexualDimorphism' ...
** 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 'COPDSexualDimorphism' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COPDSexualDimorphism' as COPDSexualDimorphism_1.2.0.zip
* DONE (COPDSexualDimorphism)

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

nameusersystemelapsed
COPDSexualDimorphism-package4.460.186.59
do.sdcd.boxplot0.450.030.48
lgrc.sdcd.genes0.020.000.01
sdcd4.100.174.29

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

nameusersystemelapsed
COPDSexualDimorphism-package4.190.134.32
do.sdcd.boxplot0.520.000.52
lgrc.sdcd.genes0.030.000.03
sdcd3.460.173.65