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BioC 2.13: CHECK report for CGHbase on moscato1

This page was generated on 2014-04-05 09:49:42 -0700 (Sat, 05 Apr 2014).

Package 120/750HostnameOS / ArchBUILDCHECKBUILD BIN
CGHbase 1.22.0
Mark van de Wiel
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CGHbase
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: CGHbase
Version: 1.22.0
Command: rm -rf CGHbase.buildbin-libdir && mkdir CGHbase.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHbase.buildbin-libdir CGHbase_1.22.0.tar.gz >CGHbase-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=CGHbase.buildbin-libdir --install="check:CGHbase-install.out" --force-multiarch --no-vignettes --timings CGHbase_1.22.0.tar.gz && mv CGHbase.buildbin-libdir/* CGHbase.Rcheck/ && rmdir CGHbase.buildbin-libdir
StartedAt: 2014-04-05 02:51:51 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:53:10 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 78.9 seconds
RetCode: 0
Status:  OK  
CheckDir: CGHbase.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/CGHbase.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '1.22.0'
* 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 ... 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 ... 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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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' ... [3s] OK
** running examples for arch 'x64' ... [4s] OK
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-2.13-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_1.22.0.zip
* DONE (CGHbase)

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

nameusersystemelapsed
class.cghCall0.10.00.1
class.cghRaw0.390.010.41
class.cghRegions0.330.000.32
class.cghSeg0.060.000.07
copynumber0.050.000.05
frequencyPlot0.010.000.01
frequencyPlotCalls000
make_cghRaw0.250.000.25
summaryPlot0.010.000.02

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

nameusersystemelapsed
class.cghCall0.110.000.11
class.cghRaw0.460.000.45
class.cghRegions0.360.000.36
class.cghSeg0.070.000.08
copynumber0.050.000.04
frequencyPlot0.020.000.02
frequencyPlotCalls000
make_cghRaw0.140.000.14
summaryPlot0.010.000.01