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Package 217/514HostnameOS / ArchBUILDCHECKBUILD BIN
GGtools 4.0.0
Vince Carey
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GGtools
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GGtools
Version: 4.0.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGtools_4.0.0.tar.gz
StartedAt: 2012-03-24 01:29:06 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:43:20 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 853.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GGtools.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/GGtools.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 ... OK
* 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 46.5Mb
  sub-directories of 1Mb or more:
    GGEXsite       1.0Mb
    browserTrack   1.8Mb
    data          35.2Mb
    doc            2.1Mb
    parts          2.0Mb
    pup            2.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'lab2010.pdf' from 1426Kb to 812Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  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

GGtools.Rcheck/00install.out:

* 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

* DONE (GGtools)

GGtools.Rcheck/GGtools-Ex.timings:

nameusersystemelapsed
X2chunk0.0010.0010.001
cisProxScores-class0.0020.0010.003
cisProxScores0.0010.0000.001
clipPCs77.550 3.88082.757
degnerASE010.0190.0080.027
dropMonomorphies6.7890.4857.357
eqtlEstimatesManager-class25.787 3.14523.807
eqtlFDRtab-class0.0010.0000.001
eqtlTests110.671 2.081114.260
eqtlTestsManager-class0.0010.0010.018
ex60.3330.0120.370