Package: GGtools

Version: 4.6.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGtools_4.6.2.tar.gz

StartedAt: 2013-03-24 23:45:47 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-25 00:00:03 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 855.9 seconds

RetCode: 0

Status:  OK

CheckDir: GGtools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GGtools.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '4.6.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'MatrixEQTL'
* 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 45.4Mb
  sub-directories of 1Mb or more:
    data     21.5Mb
    doc       1.6Mb
    olddata  13.7Mb
    olddoc    2.7Mb
    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 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
* 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
vcf2sm,TabixFile-GRanges-integer: warning in matrix(as.raw(0), nr =
  length(sampids), ncol = nsnp): partial argument match of 'nr' to
  'nrow'
eqtlTests.me: no visible binding for global variable 'modelLINEAR'
eqtlTests.me: no visible binding for global variable 'SlicedData'
eqtlTests.me: no visible binding for global variable
  'Matrix_eQTL_engine'
eqtlTests.meText: no visible binding for global variable 'modelLINEAR'
eqtlTests.meText: no visible binding for global variable 'SlicedData'
eqtlTests.meText: no visible binding for global variable
  'Matrix_eQTL_engine'
getAsSlicedData: no visible binding for global variable 'target'
topKfeats: no visible binding for global variable 'i1'
topKfeats: no visible binding for global variable 'i2'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
best.trans.eQTLs 300.075 21.214 327.952
eqtlTests         10.754  0.624  11.534
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'eqvgwst.R'
  Running 'test.meqtlTests.R'
  Running 'test.meta.trans.R'
  Running 'testTrans.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

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/GGtools.Rcheck/00check.log'
for details.

* installing *source* package 'GGtools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GGtools_2012.Rnw' 
** testing if installed package can be loaded

* DONE (GGtools)

name	user	system	elapsed
GGtools-package	0.000	0.000	0.001
best.cis.eQTLs	0.001	0.001	0.001
best.trans.eQTLs	300.075	21.214	327.952
eqtlTests	10.754	0.624	11.534
eqtlTestsManager-class	0.001	0.001	0.001
ex	2.990	0.228	3.503
getCisMap	0	0	0
gwSnpTests	4.215	0.348	4.813
strMultPop	0.099	0.011	0.136
transManager-class	0.001	0.001	0.000
transScores	0	0	0
vcf2sm	0.131	0.009	0.142