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BioC 2.13: CHECK report for GGtools on perceval

This page was generated on 2014-04-05 09:51:52 -0700 (Sat, 05 Apr 2014).

Package 309/750HostnameOS / ArchBUILDCHECKBUILD BIN
GGtools 4.10.0
VJ Carey
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GGtools
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

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

Command output

* 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.

GGtools.Rcheck/00install.out:

* 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)

GGtools.Rcheck/GGtools-Ex.timings:

nameusersystemelapsed
All.cis0.0090.0070.016
CisConfig-class0.0180.0100.030
GGtools-package0.0100.0050.014
b10.1570.0060.165
best.cis.eQTLs0.0150.0050.021
best.trans.eQTLs0.0160.0060.023
bindmaf0.0020.0030.005
cisRun-class0.0090.0040.013
collectBest0.0260.0140.041
eqtlTests19.476 0.84020.741
eqtlTestsManager-class0.0710.0190.091
ex2.5110.1962.733
getCisMap0.0030.0060.008
gwSnpTests6.5190.3396.947
pifdr0.0090.0070.017
sensiCisInput-class0.0030.0050.008
sensiCisOutput-class0.0440.0060.051
snplocsDefault0.0020.0040.007
strMultPop0.0880.0250.113
transManager-class0.0020.0030.005
transScores0.0030.0060.009
vcf2sm0.1620.0100.173