curatedBreastData 1.5.0
Katie Planey
| Snapshot Date: 2016-05-28 09:20:19 -0700 (Sat, 28 May 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/curatedBreastData | | Last Changed Rev: 3763 / Revision: 3781 | | Last Changed Date: 2016-05-03 14:48:02 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf curatedBreastData.buildbin-libdir curatedBreastData.Rcheck && mkdir curatedBreastData.buildbin-libdir curatedBreastData.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=curatedBreastData.buildbin-libdir curatedBreastData_1.5.0.tar.gz >curatedBreastData.Rcheck\00install.out 2>&1 && cp curatedBreastData.Rcheck\00install.out curatedBreastData-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=curatedBreastData.buildbin-libdir --install="check:curatedBreastData-install.out" --force-multiarch --no-vignettes --timings curatedBreastData_1.5.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-data-experiment/meat/curatedBreastData.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'curatedBreastData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'curatedBreastData' version '1.5.0'
* 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 'curatedBreastData' can be installed ... OK
* checking installed package size ... NOTE
installed size is 283.0Mb
sub-directories of 1Mb or more:
data 282.6Mb
* 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
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
collapseDupProbes: no visible global function definition for 'cov'
filterAndImputeSamples: no visible global function definition for
'na.omit'
filterGenesByVariance : <anonymous>: no visible global function
definition for 'var'
filterGenesByVariance: no visible global function definition for
'median'
filterGenesByVariance: no visible global function definition for
'quantile'
processExpressionSet: no visible global function definition for
'validObject'
processExpressionSet: no visible global function definition for
'na.omit'
removeDuplicatedPatients : <anonymous>: no visible global function
definition for 'var'
Undefined global functions or variables:
cov median na.omit quantile validObject var
Consider adding
importFrom("methods", "validObject")
importFrom("stats", "cov", "median", "na.omit", "quantile", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
collapseDupProbes 81.23 0.59 83.21
processExpressionSet 44.77 0.65 45.96
filterAndImputeSamples 42.10 1.18 44.37
removeDuplicatedPatients 37.61 0.38 37.98
filterGenesByVariance 37.15 0.44 37.59
curatedBreastDataExprSetList 36.29 0.55 36.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
collapseDupProbes 93.37 0.68 94.05
processExpressionSet 42.16 0.64 42.93
filterAndImputeSamples 39.96 1.14 41.12
curatedBreastDataExprSetList 34.51 0.58 35.09
filterGenesByVariance 34.57 0.44 35.46
removeDuplicatedPatients 33.96 0.54 34.51
* checking for unstated dependencies in vignettes ... OK
* 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: 2 NOTEs
See
'D:/biocbld/bbs-3.4-data-experiment/meat/curatedBreastData.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'curatedBreastData' ...
** 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 'curatedBreastData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'curatedBreastData' as curatedBreastData_1.5.0.zip
* DONE (curatedBreastData)