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BioC 3.2: CHECK report for CGHbase on moscato1

This page was generated on 2016-04-23 10:16:38 -0700 (Sat, 23 Apr 2016).

Package 153/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHbase 1.30.0
Mark van de Wiel
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CGHbase
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CGHbase
Version: 1.30.0
Command: rm -rf CGHbase.buildbin-libdir CGHbase.Rcheck && mkdir CGHbase.buildbin-libdir CGHbase.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHbase.buildbin-libdir CGHbase_1.30.0.tar.gz >CGHbase.Rcheck\00install.out 2>&1 && cp CGHbase.Rcheck\00install.out CGHbase-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CGHbase.buildbin-libdir --install="check:CGHbase-install.out" --force-multiarch --no-vignettes --timings CGHbase_1.30.0.tar.gz
StartedAt: 2016-04-23 00:27:34 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:29:12 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 97.9 seconds
RetCode: 0
Status:  OK  
CheckDir: CGHbase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CGHbase.buildbin-libdir CGHbase.Rcheck && mkdir CGHbase.buildbin-libdir CGHbase.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHbase.buildbin-libdir CGHbase_1.30.0.tar.gz >CGHbase.Rcheck\00install.out 2>&1 && cp CGHbase.Rcheck\00install.out CGHbase-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CGHbase.buildbin-libdir --install="check:CGHbase-install.out" --force-multiarch --no-vignettes --timings CGHbase_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CGHbase.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGHbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHbase' version '1.30.0'
* 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 'CGHbase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'Biobase:::assayDataElement'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'Biobase:::assayDataDims'
  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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [3s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/CGHbase.Rcheck/00check.log'
for details.


CGHbase.Rcheck/00install.out:


install for i386

* installing *source* package 'CGHbase' ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'CGHbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHbase' as CGHbase_1.30.0.zip
* DONE (CGHbase)

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

nameusersystemelapsed
class.cghCall0.10.00.1
class.cghRaw0.250.030.28
class.cghRegions0.390.000.39
class.cghSeg0.040.000.04
copynumber0.070.000.06
frequencyPlot000
frequencyPlotCalls000
make_cghRaw0.140.020.16
summaryPlot000

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

nameusersystemelapsed
class.cghCall0.070.000.08
class.cghRaw0.270.010.28
class.cghRegions0.310.001.10
class.cghSeg0.040.000.04
copynumber0.050.000.05
frequencyPlot000
frequencyPlotCalls000
make_cghRaw0.130.000.12
summaryPlot000