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BioC experimental data: CHECK report for encoDnaseI on moscato2

This page was generated on 2015-10-07 16:21:10 -0700 (Wed, 07 Oct 2015).

Package 73/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
encoDnaseI 0.6.0
VJ Carey
Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/encoDnaseI
Last Changed Rev: 3279 / Revision: 3442
Last Changed Date: 2015-04-16 13:16:53 -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 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: encoDnaseI
Version: 0.6.0
Command: rm -rf encoDnaseI.buildbin-libdir encoDnaseI.Rcheck && mkdir encoDnaseI.buildbin-libdir encoDnaseI.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=encoDnaseI.buildbin-libdir encoDnaseI_0.6.0.tar.gz >encoDnaseI.Rcheck\00install.out 2>&1 && cp encoDnaseI.Rcheck\00install.out encoDnaseI-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=encoDnaseI.buildbin-libdir --install="check:encoDnaseI-install.out" --force-multiarch --no-vignettes --timings encoDnaseI_0.6.0.tar.gz
StartedAt: 2015-10-07 10:24:49 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 10:36:11 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 682.1 seconds
RetCode: 0
Status:  OK  
CheckDir: encoDnaseI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf encoDnaseI.buildbin-libdir encoDnaseI.Rcheck && mkdir encoDnaseI.buildbin-libdir encoDnaseI.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=encoDnaseI.buildbin-libdir encoDnaseI_0.6.0.tar.gz >encoDnaseI.Rcheck\00install.out 2>&1 && cp encoDnaseI.Rcheck\00install.out encoDnaseI-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=encoDnaseI.buildbin-libdir --install="check:encoDnaseI-install.out" --force-multiarch --no-vignettes --timings encoDnaseI_0.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-data-experiment/meat/encoDnaseI.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 'encoDnaseI/DESCRIPTION' ... OK
* this is package 'encoDnaseI' version '0.6.0'
* 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 '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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 '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.
* 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'
ALICOR: no visible global function definition for 'p.value'
WRC: no visible binding for global variable 'd19'
juxtaPlot: no visible global function definition for 'p.value'
juxtaPlot: no visible global function definition for 'xyplot'
* 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' ... [35s] OK
** running examples for arch 'x64' ... [20s] OK
* 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
* DONE

Status: 6 NOTEs
See
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'reshape2::melt' when loading 'GGtools'
No methods found in "IRanges" for requests: aggregate
** 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'
Warning: replacing previous import by 'reshape2::melt' when loading 'GGtools'
No methods found in "IRanges" for requests: aggregate

install for x64

* installing *source* package 'encoDnaseI' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'reshape2::melt' when loading 'GGtools'
No methods found in "IRanges" for requests: aggregate
* MD5 sums
packaged installation of 'encoDnaseI' as encoDnaseI_0.6.0.zip
* DONE (encoDnaseI)

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

nameusersystemelapsed
encoDnaseI2.140.002.14
hg18track-class3.010.003.16
juxtaPlot000

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

nameusersystemelapsed
encoDnaseI2.580.012.59
hg18track-class2.590.052.64
juxtaPlot000