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BioC experimental data: CHECK report for davidTiling on moscato1

This page was generated on 2016-04-20 20:26:19 -0700 (Wed, 20 Apr 2016).

Package 59/257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
davidTiling 1.10.0
Wolfgang Huber
Snapshot Date: 2016-04-20 09:20:20 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_2/experiment/pkgs/davidTiling
Last Changed Rev: 3460 / Revision: 3730
Last Changed Date: 2015-10-13 13:14:23 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK 

Summary

Package: davidTiling
Version: 1.10.0
Command: rm -rf davidTiling.buildbin-libdir davidTiling.Rcheck && mkdir davidTiling.buildbin-libdir davidTiling.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=davidTiling.buildbin-libdir davidTiling_1.10.0.tar.gz >davidTiling.Rcheck\00install.out 2>&1 && cp davidTiling.Rcheck\00install.out davidTiling-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=davidTiling.buildbin-libdir --install="check:davidTiling-install.out" --force-multiarch --no-vignettes --timings davidTiling_1.10.0.tar.gz
StartedAt: 2016-04-20 13:07:14 -0700 (Wed, 20 Apr 2016)
EndedAt: 2016-04-20 13:25:28 -0700 (Wed, 20 Apr 2016)
EllapsedTime: 1093.6 seconds
RetCode: 0
Status:  OK  
CheckDir: davidTiling.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf davidTiling.buildbin-libdir davidTiling.Rcheck && mkdir davidTiling.buildbin-libdir davidTiling.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=davidTiling.buildbin-libdir davidTiling_1.10.0.tar.gz >davidTiling.Rcheck\00install.out 2>&1 && cp davidTiling.Rcheck\00install.out davidTiling-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=davidTiling.buildbin-libdir --install="check:davidTiling-install.out" --force-multiarch --no-vignettes --timings davidTiling_1.10.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-data-experiment/meat/davidTiling.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 'davidTiling/DESCRIPTION' ... OK
* this is package 'davidTiling' version '1.10.0'
* 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 'davidTiling' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 538.0Mb
  sub-directories of 1Mb or more:
    celfiles  305.9Mb
    data      229.5Mb
    website     2.3Mb
* 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
** 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
Packages in Depends field not imported from:
  'Biobase' 'GO.db' 'tilingArray'
  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
GOHyperG: no visible binding for global variable 'GOTERM'
GOHyperG: no visible global function definition for
  'replaceSystematicByCommonName'
GOHyperG: no visible global function definition for 'Term'
getAllGO: no visible binding for global variable 'GOMFANCESTOR'
getAllGO: no visible binding for global variable 'GOBPANCESTOR'
getAllGO: no visible binding for global variable 'GOCCANCESTOR'
scoreSegments: no visible binding for global variable 'yeastFeatures'
scoreSegments: no visible binding for global variable 'chrs'
scoreSegments: no visible global function definition for 'otherStrand'
scoreSegments: no visible global function definition for 'posMin'
* checking Rd files ... NOTE
prepare_Rd: GOHyperG.Rd:34-35: Dropping empty section \examples
prepare_Rd: getGO.Rd:32-33: Dropping empty section \examples
prepare_Rd: scatterWithHist.Rd:19-20: Dropping empty section \details
prepare_Rd: scoreSegments.Rd:103-104: Dropping empty section \examples
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [49s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
davidTiling 34.43   0.53   34.98
probeAnno    6.41   0.29    7.50
** running examples for arch 'x64' ... [64s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
davidTiling     32.60   0.36   32.96
probeAnno        5.65   0.28    5.92
scatterWithHist  0.03   0.01   17.96
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'D:/biocbld/bbs-3.2-data-experiment/meat/davidTiling.Rcheck/00check.log'
for details.


davidTiling.Rcheck/00install.out:


install for i386

* installing *source* package 'davidTiling' ...
** 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 'davidTiling' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'davidTiling' as davidTiling_1.10.0.zip
* DONE (davidTiling)

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

nameusersystemelapsed
davidTiling34.43 0.5334.98
getAttributeField000
gff0.540.000.55
probeAnno6.410.297.50
scatterWithHist0.020.000.03
showDens0.000.000.03
yeastFeatures0.000.020.02

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

nameusersystemelapsed
davidTiling32.60 0.3632.96
getAttributeField0.020.000.02
gff0.480.020.50
probeAnno5.650.285.92
scatterWithHist 0.03 0.0117.96
showDens000
yeastFeatures000