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 |
* 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
* 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)