BioC 2.13: CHECK report for GGtools on perceval

Package: GGtools

Version: 4.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGtools_4.10.0.tar.gz

StartedAt: 2014-04-05 01:38:42 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:52:19 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 817.1 seconds

RetCode: 0

Status:  OK

CheckDir: GGtools.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GGtools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGtools/DESCRIPTION’ ... OK
* this is package ‘GGtools’ version ‘4.10.0’
* 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 ... [50s/52s] OK
* checking installed package size ... NOTE
  installed size is 39.1Mb
  sub-directories of 1Mb or more:
    data   21.5Mb
    doc     1.6Mb
    parts   2.0Mb
    pup     2.0Mb
    rdas   10.3Mb
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘GenomicRanges’ ‘IRanges’
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘methods’ ‘utils’
  All declared Imports should be used.
Package in Depends field not imported from: ‘GGBase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
‘:::’ calls which should be ‘::’:
  ‘IRanges:::as.data.frame’ ‘IRanges:::end’ ‘IRanges:::start’
  ‘Rsamtools:::close.TabixFile’ ‘Rsamtools:::isOpen’
  ‘Rsamtools:::open.TabixFile’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘namelist’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getFDR: warning in dir(patt = "^pop.*rda$"): partial argument match of
  'patt' to 'pattern'
hns : <anonymous>: warning in dir(patt = chrtag, system.file("rdas",
  package = x), full = TRUE): partial argument match of 'patt' to
  'pattern'
hns : <anonymous>: warning in dir(patt = chrtag, system.file("rdas",
  package = x), full = TRUE): partial argument match of 'full' to
  'full.names'
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’
hns : <anonymous>: possible error in convertCis(x, MAFlb = MAFlb,
  radius = inradius): unused argument (MAFlb = MAFlb)
topKfeats: no visible binding for global variable ‘i1’
topKfeats: no visible binding for global variable ‘i2’
* checking Rd files ... NOTE
prepare_Rd: cisRun-class.Rd:36-38: Dropping empty section \references
prepare_Rd: cisRun-class.Rd:49-52: Dropping empty section \seealso
prepare_Rd: collectBest.Rd:69-71: Dropping empty section \seealso
prepare_Rd: pifdr.Rd:64-66: Dropping empty section \seealso
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 files in ‘vignettes’ ... OK
* checking examples ... [58s/59s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
eqtlTests  19.476  0.840  20.741
gwSnpTests  6.519  0.339   6.947
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘eqvgwst.R’ [41s/42s]
  Running ‘test.meqtlTests.R’ [44s/45s]
  Running ‘test.meta.trans.R’ [0s/0s]
  Running ‘testCisMap.R’ [87s/88s]
  Running ‘testTrans.R’ [79s/80s]
 [252s/256s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.009	0.007	0.016
CisConfig-class	0.018	0.010	0.030
GGtools-package	0.010	0.005	0.014
b1	0.157	0.006	0.165
best.cis.eQTLs	0.015	0.005	0.021
best.trans.eQTLs	0.016	0.006	0.023
bindmaf	0.002	0.003	0.005
cisRun-class	0.009	0.004	0.013
collectBest	0.026	0.014	0.041
eqtlTests	19.476	0.840	20.741
eqtlTestsManager-class	0.071	0.019	0.091
ex	2.511	0.196	2.733
getCisMap	0.003	0.006	0.008
gwSnpTests	6.519	0.339	6.947
pifdr	0.009	0.007	0.017
sensiCisInput-class	0.003	0.005	0.008
sensiCisOutput-class	0.044	0.006	0.051
snplocsDefault	0.002	0.004	0.007
strMultPop	0.088	0.025	0.113
transManager-class	0.002	0.003	0.005
transScores	0.003	0.006	0.009
vcf2sm	0.162	0.010	0.173