Package: GGtools

Version: 4.0.0

Command: rm -rf GGtools.buildbin-libdir && mkdir GGtools.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGtools.buildbin-libdir GGtools_4.0.0.tar.gz >GGtools-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=GGtools.buildbin-libdir --install="check:GGtools-install.out" --force-multiarch --no-vignettes --timings GGtools_4.0.0.tar.gz && mv GGtools.buildbin-libdir/* GGtools.Rcheck/ && rmdir GGtools.buildbin-libdir

StartedAt: 2012-03-24 01:33:37 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:47:44 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 846.5 seconds

RetCode: 0

Status:  OK

CheckDir: GGtools.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GGtools.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '4.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'GGtools' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 46.8Mb
  sub-directories of 1Mb or more:
    GGEXsite       1.0Mb
    browserTrack   1.8Mb
    data          35.2Mb
    doc            2.4Mb
    parts          2.0Mb
    pup            2.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
.policyFDRtab: no visible binding for global variable 'pm'
eqtlTests : <anonymous> : <anonymous>: possible error in
  snp.rhs.tests(fmla, snp.data = snpdata, data = pData(smlSet), family
  = family, uncertain = uncert, ...): unused argument(s) (uncertain =
  uncert)
getGene2SnpList : setSoloSeq: no visible global function definition for
  'isActiveSeq'
getGene2SnpList : setSoloSeq: no visible global function definition for
  'isActiveSeq<-'
getGene2SnpList: no visible global function definition for
  'transcriptsBy'
getGene2SnpList: no visible global function definition for 'send<-'
ieqtlTests : <anonymous> : <anonymous>: possible error in
  snp.rhs.tests(fmla, snp.data = snpdata, data = pData(smlSet), family
  = family, uncertain = uncert, ...): unused argument(s) (uncertain =
  uncert)
ieqtlTests : <anonymous> : <anonymous>: possible error in
  snp.rhs.tests(fmla, snp.data = snpdata, uncertain = uncert, data =
  pData(smlSet), family = family, rules = rules, ...): unused
  argument(s) (uncertain = uncert, rules = rules)
meqtlTests : <anonymous> : <anonymous>: possible error in
  snp.rhs.tests(fmla, snp.data = snpdata, data = pData(smlSet), family
  = family, uncertain = uncert, ...): unused argument(s) (uncertain =
  uncert)
snp130locs: no visible global function definition for 'GenomicRanges'
topKfeats: no visible binding for global variable 'i1'
topKfeats: no visible binding for global variable 'i2'
* checking Rd files ... NOTE
prepare_Rd: eqtlFDRtab-class.Rd:40-42: Dropping empty section \note
prepare_Rd: eqtlFDRtab-class.Rd:37-39: Dropping empty section \author
prepare_Rd: eqtlFDRtab-class.Rd:34-36: Dropping empty section \references
prepare_Rd: eqtlFDRtab-class.Rd:46-49: Dropping empty section \seealso
prepare_Rd: genewiseFDRtab.Rd:84-86: Dropping empty section \seealso
prepare_Rd: transScores.Rd:86-88: Dropping empty section \details
prepare_Rd: transTab.Rd:23-25: Dropping empty section \details
prepare_Rd: transTab.Rd:40-42: Dropping empty section \note
prepare_Rd: transTab.Rd:37-39: Dropping empty section \author
prepare_Rd: transTab.Rd:34-36: Dropping empty section \references
prepare_Rd: transTab.Rd:46-48: Dropping empty section \seealso
prepare_Rd: transTab.Rd:49-50: 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'eqtest.R'
 OK
** running tests for arch 'x64'
  Running 'eqtest.R'
 OK
* 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

install for i386

* installing *source* package 'GGtools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GGtools_2011.Rnw' 
   'binf09supp.Rnw' 
   'external.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'GGtools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGtools' as GGtools_4.0.0.zip

* DONE (GGtools)