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BioC 3.1: CHECK report for cghMCR on moscato2

This page was generated on 2015-10-09 09:27:40 -0700 (Fri, 09 Oct 2015).

Package 148/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cghMCR 1.26.0
J. Zhang
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cghMCR
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cghMCR
Version: 1.26.0
Command: rm -rf cghMCR.buildbin-libdir cghMCR.Rcheck && mkdir cghMCR.buildbin-libdir cghMCR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cghMCR.buildbin-libdir cghMCR_1.26.0.tar.gz >cghMCR.Rcheck\00install.out 2>&1 && cp cghMCR.Rcheck\00install.out cghMCR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cghMCR.buildbin-libdir --install="check:cghMCR-install.out" --force-multiarch --no-vignettes --timings cghMCR_1.26.0.tar.gz
StartedAt: 2015-10-09 00:08:51 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:12:16 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 205.2 seconds
RetCode: 0
Status:  OK  
CheckDir: cghMCR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cghMCR.buildbin-libdir cghMCR.Rcheck && mkdir cghMCR.buildbin-libdir cghMCR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cghMCR.buildbin-libdir cghMCR_1.26.0.tar.gz >cghMCR.Rcheck\00install.out 2>&1 && cp cghMCR.Rcheck\00install.out cghMCR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cghMCR.buildbin-libdir --install="check:cghMCR-install.out" --force-multiarch --no-vignettes --timings cghMCR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/cghMCR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cghMCR/DESCRIPTION' ... OK
* this is package 'cghMCR' version '1.26.0'
* 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 'cghMCR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 98.1Mb
  sub-directories of 1Mb or more:
    sampleData  97.1Mb
* 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' call to 'DNAcopy' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'CNTools' 'DNAcopy' 'limma' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'adjustSegments' 'alignGenes' 'drawSegs' 'getAdjustments'
  'highlightChrom' 'markChrom'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SGOL: no visible global function definition for 'segBy'
SGOL: no visible global function definition for 'rs'
getSegData: no visible global function definition for 'read.maimages'
getSegData: no visible global function definition for
  'normalizeWithinArrays'
getSegData: no visible global function definition for
  'backgroundCorrect'
getSegData: no visible global function definition for 'CNA'
getSegData: no visible global function definition for 'segment'
getSegData: no visible global function definition for 'smooth.CNA'
* 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' ... [10s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mergeMCRProbes 5.73      0    5.73
** running examples for arch 'x64' ... [9s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mergeMCRProbes 5.18      0    5.17
* 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

Status: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/cghMCR.Rcheck/00check.log'
for details.


cghMCR.Rcheck/00install.out:


install for i386

* installing *source* package 'cghMCR' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'cghMCR' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'cghMCR' as cghMCR_1.26.0.zip
* DONE (cghMCR)

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

nameusersystemelapsed
SGOL-class000
cghMCR-class0.160.000.17
cghMCR0.010.000.02
mergeMCRProbes5.730.005.73
plot.DNAcopy000

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

nameusersystemelapsed
SGOL-class000
cghMCR-class0.130.000.13
cghMCR0.010.000.02
mergeMCRProbes5.180.005.17
plot.DNAcopy000