BioC 2.12: CHECK report for gwascat on moscato2

Package: gwascat

Version: 1.4.0

Command: rm -rf gwascat.buildbin-libdir && mkdir gwascat.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_1.4.0.tar.gz >gwascat-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_1.4.0.tar.gz && mv gwascat.buildbin-libdir/* gwascat.Rcheck/ && rmdir gwascat.buildbin-libdir

StartedAt: 2013-10-02 02:32:16 -0700 (Wed, 02 Oct 2013)

EndedAt: 2013-10-02 02:43:14 -0700 (Wed, 02 Oct 2013)

EllapsedTime: 657.7 seconds

RetCode: 0

Status: OK

CheckDir: gwascat.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/gwascat.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'SNPlocs.Hsapiens.dbSNP.20111119'
* 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 'gwascat' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.7Mb
  sub-directories of 1Mb or more:
    data  20.4Mb
    obo    1.3Mb
    tab    1.1Mb
* 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 for unstated 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
chklocs: no visible global function definition for 'getSNPlocs'
snpGenos: no visible global function definition for 'getSNPlocs'
traitsManh: no visible binding for global variable 'Pvalue_mlog'
traitsManh: no visible binding for global variable 'Trait'
* 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 examples ...
** running examples for arch 'i386' ... [64s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
riskyAlleleCount 21.80   0.13   21.92
gwcex2gviz       11.00   0.30   11.42
traitsManh        5.18   0.12    5.30
** running examples for arch 'x64' ... [65s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
riskyAlleleCount 18.56   0.14   18.71
gwcex2gviz       13.40   0.42   13.84
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/gwascat.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'gwascat' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
NOTE: input data had non-ASCII characters replaced by '*'.

install for x64

* installing *source* package 'gwascat' ...
** testing if installed package can be loaded
NOTE: input data had non-ASCII characters replaced by '*'.
* MD5 sums
packaged installation of 'gwascat' as gwascat_1.4.0.zip
* DONE (gwascat)

BioC 2.12: CHECK report for gwascat on moscato2

Summary

Command output