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BioC 3.5: CHECK report for GGtools on oaxaca

This page was generated on 2016-10-26 16:21:33 -0400 (Wed, 26 Oct 2016).

Package 527/1294HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGtools 5.11.0
VJ Carey
Snapshot Date: 2016-10-25 17:15:05 -0400 (Tue, 25 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools
Last Changed Rev: 122712 / Revision: 123034
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GGtools
Version: 5.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GGtools_5.11.0.tar.gz
StartedAt: 2016-10-26 01:42:02 -0700 (Wed, 26 Oct 2016)
EndedAt: 2016-10-26 01:58:07 -0700 (Wed, 26 Oct 2016)
EllapsedTime: 965.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GGtools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GGtools_5.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GGtools.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGtools/DESCRIPTION’ ... OK
* this is package ‘GGtools’ version ‘5.11.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 72.9Mb
  sub-directories of 1Mb or more:
    data   27.0Mb
    doc     1.6Mb
    parts   2.0Mb
    pup     2.0Mb
    rdas   10.3Mb
    vcf    28.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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' call to 'Homo.sapiens' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Homo.sapiens' 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calfig: no visible global function definition for 'axis'
.calfig: no visible global function definition for 'points'
.calfig: no visible global function definition for 'text'
.calfig: no visible global function definition for 'abline'
.summarize: no visible global function definition for 'ftable'
.summarize: no visible binding for global variable 'npc'
.summarize: no visible binding for global variable 'maf'
.summarize: no visible binding for global variable 'radiusUsed'
.summarize: no visible binding for global variable 'excl'
.transTab: no visible global function definition for 'getSNPlocs'
All.cis.eQTLs: no visible global function definition for 'approx'
SnpMatrixCisToSummex: no visible global function definition for
  'rowRanges'
add878: no visible binding for global variable 'hmm878'
add878: no visible global function definition for 'relevel'
addcadd: no visible binding for global variable 'bindcadd'
addcadd: no visible global function definition for '%dopar%'
addcadd: no visible global function definition for 'foreach'
addcadd: no visible binding for global variable 'x'
addgwhit: no visible binding for global variable 'gwastagger'
addgwhit: no visible global function definition for 'overlapsAny'
appraise : <anonymous>: no visible global function definition for
  'relevel'
appraise : .redu.fdr: no visible global function definition for
  'setkey'
appraise : .redu.fdr: no visible binding for global variable 'snp'
appraise : .redu.fdr: no visible binding for global variable '.N'
appraise : .redu.fdr : <anonymous>: no visible global function
  definition for 'setkeyv'
appraise : .redu.fdr : <anonymous>: no visible binding for global
  variable '.N'
appraise : .discmods: no visible global function definition for
  '%dopar%'
appraise : .discmods: no visible global function definition for
  'foreach'
appraise : .discmods: no visible global function definition for
  'binomial'
appraise : .discmods: no visible global function definition for
  'predict'
appraise : .discmods: no visible global function definition for 'coef'
appraise : .discmods: no visible global function definition for 'vcov'
appraise : .discmods: no visible global function definition for
  'model.matrix'
appraise : .discmods: no visible global function definition for
  'plogis'
binnedQQ: no visible global function definition for 'par'
binnedQQ: no visible global function definition for 'qqplot'
binnedQQ: no visible global function definition for 'mtext'
binqq: no visible global function definition for 'text'
binqq: no visible global function definition for 'segments'
binqq: no visible global function definition for 'abline'
binqq: no visible global function definition for 'axis'
buildConfList : z : <anonymous>: no visible binding for global variable
  'pl'
cgff2dt: no visible global function definition for '%dopar%'
cgff2dt: no visible global function definition for 'foreach'
cgff2dt: no visible global function definition for 'as.data.table'
cgff2dt: no visible binding for global variable 'hmm878'
cgff2dt: no visible global function definition for 'overlapsAny'
cgff2dt: no visible binding for global variable 'gwastagger'
cisAssoc: no visible global function definition for 'rowRanges'
cisAssoc: no visible global function definition for 'assays'
cisAssoc: no visible global function definition for 'as.formula'
cisAssoc: no visible global function definition for 'runif'
cisAssoc: no visible global function definition for 'colData'
cisAssoc: no visible binding for global variable 'chi.squared'
ciseqByCluster : <anonymous>: no visible global function definition for
  'detectCores'
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 : setupSplit : <anonymous>: no visible binding for
  global variable 'mclapply'
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 'ranges<-'
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'
eqBox: no visible global function definition for 'assay'
eqDesc: no visible global function definition for 'assay'
eqsens_dt: no visible global function definition for 'setnames'
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'
eqtlEstimates : <anonymous>: no visible global function definition for
  'formula'
eqtlTests : <anonymous>: no visible global function definition for
  'formula'
eqtlTests.me: no visible binding for global variable 'modelLINEAR'
eqtlTests.me: no visible binding for global variable 'SlicedData'
eqtlTests.me: no visible global function definition for 'model.matrix'
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'
eqtlTests2 : <anonymous>: no visible global function definition for
  'formula'
fplot: no visible global function definition for 'forestplot'
genemodel: no visible global function definition for 'select'
genemodel: no visible binding for global variable 'Homo.sapiens'
get.dffits : maxdf: no visible global function definition for 'dffits'
get.dffits : <anonymous>: no visible global function definition for
  'lm'
getAsSlicedData: no visible binding for global variable 'target'
getCisMap: no visible global function definition for 'snplocs'
get_probechunks: no visible global function definition for 'select'
inflammFilter: no visible binding for global variable 'gwrngs'
inflammFilter: no visible global function definition for 'overlapsAny'
makeSeqinfo: no visible binding for global variable 'hg19.si.df'
meqtlTests : gfun: no visible global function definition for 'formula'
pifdr: no visible global function definition for 'hist'
pifdr.old: no visible global function definition for 'approx'
plotsens: no visible binding for global variable 'mafs'
plotsens: no visible binding for global variable 'value'
plotsens: no visible binding for global variable 'FDR'
pullHits: no visible global function definition for 'ranges<-'
qqhex: no visible global function definition for 'qqplot'
richNull : <anonymous>: no visible global function definition for
  'bindmaf'
simpleTiling: no visible binding for global variable 'Homo.sapiens'
simpleTiling: no visible global function definition for 'tileGenome'
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'
waldtests : <anonymous>: no visible global function definition for
  'wald.test'
plot,gwSnpScreenResult-character: no visible global function definition
  for 'snpcount'
plot,gwSnpScreenResult-character: no visible global function definition
  for 'snplocs'
plot,gwSnpScreenResult-character: no visible binding for global
  variable 'smoothScatter'
plot,gwSnpScreenResult-character: no visible global function definition
  for 'axis'
Undefined global functions or variables:
  %dopar% .N FDR Homo.sapiens Matrix_eQTL_engine SlicedData abline
  approx as.data.table as.formula assay assays axis bindcadd bindmaf
  binomial chi.squared coef colData curp detectCores dffits excl
  export.gff3 firstHalf firstThird foreach forestplot formula ftable
  getSNPlocs gwastagger gwrngs hg19.si.df hist hmm878 i i1 i2 lastThird
  lm maf mafs mclapply midThird model.matrix modelLINEAR mtext npc
  overlapsAny par pl plogis points predict qqplot radiusUsed ranges<-
  relevel rowRanges runOneSplit runif segments select setkey setkeyv
  setnames smoothScatter snp snpcount snplocs target text tileGenome
  value vcov wald.test x
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "mtext", "par",
             "points", "segments", "smoothScatter", "text")
  importFrom("stats", "approx", "as.formula", "binomial", "coef",
             "dffits", "formula", "ftable", "lm", "model.matrix",
             "plogis", "predict", "qqplot", "relevel", "runif", "vcov")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
cisAssoc  43.191  2.528  45.768
eqtlTests  8.330  0.284  18.484
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘cis.R’
  Running ‘eqvgwst.R’
  Running ‘test.meqtlTests.R’
  Running ‘test.meta.trans.R’
  Running ‘testCisMap.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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/GGtools.Rcheck/00check.log’
for details.


GGtools.Rcheck/00install.out:

* installing *source* package ‘GGtools’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
* DONE (GGtools)

GGtools.Rcheck/GGtools-Ex.timings:

nameusersystemelapsed
All.cis0.0020.0000.005
CisConfig-class0.0040.0000.004
EqAppr-class0.0010.0010.001
GGtools-package0.0010.0000.001
TransConfig-class0.0020.0000.002
b10.0510.0030.053
best.cis.eQTLs0.0010.0000.001
best.trans.eQTLs0.0010.0000.000
bindmaf0.0000.0000.001
cgff2dt0.0180.0010.018
cisAssoc43.191 2.52845.768
cisRun-class0.0010.0000.002
ciseqByCluster0.0010.0000.000
collectBest0.0010.0010.001
concatCis0.0000.0000.001
eqBox3.3930.2243.739
eqsens_dt0.0010.0000.001
eqtlTests 8.330 0.28418.484
eqtlTests.me0.0020.0010.001
eqtlTestsManager-class0.0020.0000.002
ex2.2990.0702.370
getCisMap0.0010.0000.001
gwSnpTests3.0670.0803.147
hmm8780.6940.0550.799
pifdr1.3410.0531.548
qqhex0.0940.0070.128
sampsInVCF0.0460.0010.123
sensiCisInput-class0.0010.0000.001
sensiCisOutput-class0.0020.0000.001
simpleTiling0.0020.0010.001
snplocsDefault0.0010.0000.001
strMultPop0.0870.0090.095
transManager-class0.0010.0000.001
transScores0.0010.0000.000
vcf2sm0.0750.0020.076