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BioC experimental data: CHECK report for encoDnaseI on moscato1

This page was generated on 2014-04-04 17:28:59 -0700 (Fri, 04 Apr 2014).

Package 52/181HostnameOS / ArchBUILDCHECKBUILD BIN
encoDnaseI 0.1.18
VJ Carey
Snapshot Date: 2014-04-04 06:15:32 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/encoDnaseI
Last Changed Rev: 2557 / Revision: 2768
Last Changed Date: 2013-11-01 13:36:05 -0700 (Fri, 01 Nov 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: encoDnaseI
Version: 0.1.18
Command: rm -rf encoDnaseI.buildbin-libdir && mkdir encoDnaseI.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=encoDnaseI.buildbin-libdir encoDnaseI_0.1.18.tar.gz >encoDnaseI-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=encoDnaseI.buildbin-libdir --install="check:encoDnaseI-install.out" --force-multiarch --no-vignettes --timings encoDnaseI_0.1.18.tar.gz && mv encoDnaseI.buildbin-libdir/* encoDnaseI.Rcheck/ && rmdir encoDnaseI.buildbin-libdir
StartedAt: 2014-04-04 11:33:11 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 11:40:18 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 427.0 seconds
RetCode: 0
Status:  OK  
CheckDir: encoDnaseI.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-data-experiment/meat/encoDnaseI.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 'encoDnaseI/DESCRIPTION' ... OK
* this is package 'encoDnaseI' version '0.1.18'
* 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 'encoDnaseI' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
* 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
* 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
'library' or 'require' call to 'lattice' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'GGBase' 'GGtools' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... NOTE
WRC: warning in matrix(ans, nr = 2): partial argument match of 'nr' to
  'nrow'
makeHg18track: warning in matrix(dataVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
[,hg18track-ANY-ANY-ANY: warning in matrix(dataVals(x)[kpinds], nc =
  1): partial argument match of 'nc' to 'ncol'
ALICOR: no visible binding for global variable 'rawCD4'
WRC: no visible binding for global variable 'd19'
* 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 ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'snpMatrix'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* 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' ... [24s] OK
** running examples for arch 'x64' ... [26s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
encoDnaseI 3.67   0.08    5.75
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'SNPlocs.Hsapiens.dbSNP.20090506'
* 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

NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-2.13-data-experiment/meat/encoDnaseI.Rcheck/00check.log'
for details.

encoDnaseI.Rcheck/00install.out:


install for i386

* installing *source* package 'encoDnaseI' ...
** 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 'encoDnaseI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'encoDnaseI' as encoDnaseI_0.1.18.zip
* DONE (encoDnaseI)

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

nameusersystemelapsed
encoDnaseI3.840.033.87
hg18track-class4.410.044.46
juxtaPlot0.360.000.36

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

nameusersystemelapsed
encoDnaseI3.670.085.75
hg18track-class4.760.034.79
juxtaPlot0.410.020.42