BioC 2.12: CHECK report for GGtools on petty

Package: GGtools

Version: 4.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGtools_4.8.0.tar.gz

StartedAt: 2013-10-08 22:34:46 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:49:07 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 860.7 seconds

RetCode: 0

Status:  OK

CheckDir: GGtools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GGtools.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '4.8.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GGtools' can be installed ... [55s/56s] 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 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
unified.col.summary: warning in matrix(NA, nr = length(oksn), nc =
  npacks): partial argument match of 'nr' to 'nrow'
unified.col.summary: warning in matrix(NA, nr = length(oksn), nc =
  npacks): partial argument match of 'nc' to 'ncol'
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 ... NOTE
prepare_Rd: richNull.Rd:75-77: Dropping empty section \note
prepare_Rd: richNull.Rd:81-83: Dropping empty section \seealso
prepare_Rd: richNull.Rd:84-85: Dropping empty section \examples
prepare_Rd: sensanal.Rd:56-57: Dropping empty section \examples
prepare_Rd: sensiCisOutput-class.Rd:56-59: Dropping empty section \seealso
* 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 ... [63s/63s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
eqtlTests  22.382  0.824  23.401
gwSnpTests  6.344  0.331   6.730
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'eqvgwst.R' [41s/45s]
  Running 'test.meqtlTests.R' [47s/47s]
  Running 'test.meta.trans.R' [1s/1s]
  Running 'testCisMap.R' [86s/89s]
  Running 'testTrans.R' [94s/96s]
 [269s/278s] 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 4 notes.
See
  '/Users/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (GGtools)

name	user	system	elapsed
All.cis	0.008	0.004	0.012
GGtools-package	0.628	0.007	0.637
best.cis.eQTLs	0.010	0.006	0.016
best.trans.eQTLs	0.008	0.008	0.015
bindmaf	0.008	0.004	0.011
eqtlTests	22.382	0.824	23.401
eqtlTestsManager-class	0.004	0.005	0.009
ex	3.646	0.199	3.873
getCisMap	0.003	0.006	0.009
gwSnpTests	6.344	0.331	6.730
sensiCisInput-class	0.041	0.008	0.048
sensiCisOutput-class	0.003	0.005	0.008
snplocsDefault	0.002	0.003	0.006
strMultPop	0.169	0.027	0.197
transManager-class	0.040	0.007	0.048
transScores	0.003	0.004	0.007
vcf2sm	0.248	0.008	0.257