BioC 2.14: CHECK report for GGtools on petty

Package: GGtools

Version: 5.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGtools_5.0.0.tar.gz

StartedAt: 2014-10-07 22:14:34 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:37:14 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 1360.1 seconds

RetCode: 0

Status:  OK

CheckDir: GGtools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGtools_5.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GGtools.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘5.0.0’
* 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 ... [73s/75s] OK
* checking installed package size ... NOTE
  installed size is 44.6Mb
  sub-directories of 1Mb or more:
    data   26.8Mb
    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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
appraise : .discmods: warning in bigglm(discfmlas[[i]], data = train,
  fam = binomial(), chunksize = 50000, maxit = inmaxit): partial
  argument match of 'fam' to 'family'
add878: no visible binding for global variable ‘hmm878’
addgwhit: no visible binding for global variable ‘gwastagger’
appraise : .redu.fdr: no visible binding for global variable ‘snp’
appraise : .discmods: no visible global function definition for
  ‘%dopar%’
appraise : .discmods: no visible global function definition for
  ‘foreach’
bindmaf.simple: no visible binding for global variable ‘smchr.init’
buildConfList : z : <anonymous>: no visible binding for global variable
  ‘pl’
calfig.old: no visible binding for global variable ‘MOREAPPR_coeflist’
calfig.old: no visible binding for global variable ‘MOREAPPR_tabs’
cgff2dt: no visible global function definition for ‘%dopar%’
cgff2dt: no visible global function definition for ‘foreach’
cgff2dt: no visible binding for global variable ‘hmm878’
cgff2dt: no visible binding for global variable ‘gwastagger’
cisAssoc: no visible global function definition for ‘ScanVcfParam’
cisAssoc: no visible global function definition for ‘readVcf’
cisAssoc: no visible global function definition for
  ‘genotypeToSnpMatrix’
ciseqByCluster: no visible binding for '<<-' assignment to ‘firstHalf’
ciseqByCluster: no visible binding for '<<-' assignment to ‘secondHalf’
ciseqByCluster: no visible binding for '<<-' assignment to ‘firstThird’
ciseqByCluster: no visible binding for '<<-' assignment to ‘lastThird’
ciseqByCluster: no visible binding for '<<-' assignment to ‘midThird’
ciseqByCluster: no visible binding for '<<-' assignment to
  ‘runOneSplit’
ciseqByCluster : <anonymous>: no visible binding for global variable
  ‘firstHalf’
ciseqByCluster : <anonymous> : cr2gff: no visible global function
  definition for ‘export.gff3’
ciseqByCluster: no visible binding for global variable ‘firstThird’
ciseqByCluster: no visible binding for global variable ‘midThird’
ciseqByCluster: no visible binding for global variable ‘lastThird’
ciseqByCluster : <anonymous>: no visible global function definition for
  ‘runOneSplit’
eqsens_dt: no visible global function definition for ‘%dopar%’
eqsens_dt: no visible global function definition for ‘foreach’
eqsens_dt: no visible binding for global variable ‘curp’
eqtlscan: no visible binding for global variable ‘ex’
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’
genemodel: no visible binding for global variable ‘Homo.sapiens’
getAsSlicedData: no visible binding for global variable ‘target’
inflammFilter: no visible binding for global variable ‘gwrngs’
makeSeqinfo: no visible binding for global variable ‘hg19.si.df’
plotsens: no visible global function definition for ‘melt’
plotsens: no visible global function definition for ‘ggplot’
plotsens: no visible global function definition for ‘geom_point’
plotsens: no visible global function definition for ‘aes’
plotsens: no visible binding for global variable ‘mafs’
plotsens: no visible binding for global variable ‘value’
plotsens: no visible binding for global variable ‘FDR’
plotsens: no visible global function definition for ‘facet_grid’
plotsens: no visible global function definition for ‘theme’
plotsens: no visible global function definition for ‘element_text’
plotsens: no visible global function definition for ‘labs’
richNull : <anonymous>: no visible global function definition for
  ‘bindmaf’
simpleTiling: no visible binding for global variable ‘Homo.sapiens’
snvsOnly: no visible global function definition for ‘ref’
snvsOnly: no visible global function definition for ‘alt’
topKfeats: no visible binding for global variable ‘i1’
topKfeats: no visible binding for global variable ‘i2’
tscan2df: no visible global function definition for ‘%dopar%’
tscan2df: no visible global function definition for ‘foreach’
tscan2df: no visible binding for global variable ‘i’
tscan2gr: no visible global function definition for ‘%dopar%’
tscan2gr: no visible global function definition for ‘foreach’
tscan2gr: no visible binding for global variable ‘i’
* checking Rd files ... NOTE
prepare_Rd: appraise.Rd:97-98: Dropping empty section \examples
prepare_Rd: calfig.Rd:70-71: Dropping empty section \examples
prepare_Rd: transeqByCluster.Rd:82-83: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘MatrixEQTL’
* 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 ... [74s/75s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
eqtlTests  21.15  0.591  21.968
gwSnpTests  5.59  0.182   5.857
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘cis.R’ [208s/182s]
  Running ‘eqvgwst.R’ [50s/51s]
  Running ‘test.meqtlTests.R’ [55s/56s]
  Running ‘test.meta.trans.R’ [1s/1s]
  Running ‘testCisMap.R’ [93s/95s]
  Running ‘testTrans.R’ [138s/140s]
 [547s/525s] 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-2.14-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	0.003	0.001	0.004
CisConfig-class	0.007	0.001	0.007
GGtools-package	0.002	0.000	0.002
TransConfig-class	0.003	0.000	0.004
b1	0.254	0.003	0.266
best.cis.eQTLs	0.003	0.001	0.003
best.trans.eQTLs	0.002	0.001	0.002
bindmaf	0.001	0.000	0.001
cgff2dt	0.057	0.001	0.125
cisRun-class	0.003	0.000	0.003
ciseqByCluster	0.001	0.000	0.001
collectBest	0.003	0.000	0.004
concatCis	0.001	0.001	0.001
eqsens_dt	0.001	0.000	0.001
eqtlTests	21.150	0.591	21.968
eqtlTests.me	0.005	0.001	0.006
eqtlTestsManager-class	0.002	0.000	0.003
ex	4.255	0.142	4.412
getCisMap	0.002	0.001	0.001
gwSnpTests	5.590	0.182	5.857
hmm878	2.210	0.085	2.300
pifdr	4.065	0.168	4.251
qqhex	0.190	0.018	0.232
sampsInVCF	0.215	0.004	0.223
sensiCisInput-class	0.002	0.000	0.002
sensiCisOutput-class	0.002	0.000	0.003
simpleTiling	0.002	0.000	0.003
snplocsDefault	0.001	0.000	0.001
strMultPop	0.134	0.017	0.152
transManager-class	0.001	0.001	0.002
transScores	0.001	0.000	0.002
vcf2sm	0.208	0.004	0.213