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BioC 3.4: CHECK report for GGtools on moscato1

This page was generated on 2016-09-21 03:41:51 -0700 (Wed, 21 Sep 2016).

Package 514/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGtools 5.9.0
VJ Carey
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: GGtools
Version: 5.9.0
Command: rm -rf GGtools.buildbin-libdir GGtools.Rcheck && mkdir GGtools.buildbin-libdir GGtools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGtools.buildbin-libdir GGtools_5.9.0.tar.gz >GGtools.Rcheck\00install.out 2>&1 && cp GGtools.Rcheck\00install.out GGtools-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GGtools.buildbin-libdir --install="check:GGtools-install.out" --force-multiarch --no-vignettes --timings GGtools_5.9.0.tar.gz
StartedAt: 2016-09-20 09:35:01 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:59:55 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 1494.1 seconds
RetCode: 0
Status:  OK  
CheckDir: GGtools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GGtools.buildbin-libdir GGtools.Rcheck && mkdir GGtools.buildbin-libdir GGtools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGtools.buildbin-libdir GGtools_5.9.0.tar.gz >GGtools.Rcheck\00install.out 2>&1 && cp GGtools.Rcheck\00install.out GGtools-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GGtools.buildbin-libdir --install="check:GGtools-install.out" --force-multiarch --no-vignettes --timings GGtools_5.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/GGtools.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '5.9.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
cisAssoc  48.5    1.0   49.53
eqtlTests  9.0    0.3    9.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
cisAssoc  48.58   1.67   50.27
eqtlTests  8.06   0.39    8.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'cis.R'
  Running 'eqvgwst.R'
  Running 'test.meqtlTests.R'
  Running 'test.meta.trans.R'
  Running 'testCisMap.R'
  Running 'testTrans.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbld/bbs-3.4-bioc/meat/GGtools.Rcheck/00check.log'
for details.


GGtools.Rcheck/00install.out:


install for i386

* 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'

install for x64

* installing *source* package 'GGtools' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::which' by 'Matrix::which' when loading 'GGBase'
* MD5 sums
packaged installation of 'GGtools' as GGtools_5.9.0.zip
* DONE (GGtools)

GGtools.Rcheck/examples_i386/GGtools-Ex.timings:

nameusersystemelapsed
All.cis000
CisConfig-class000
EqAppr-class000
GGtools-package0.010.000.02
TransConfig-class000
b10.060.000.06
best.cis.eQTLs000
best.trans.eQTLs0.020.000.02
bindmaf000
cgff2dt0.020.000.01
cisAssoc48.50 1.0049.53
cisRun-class000
ciseqByCluster000
collectBest0.010.000.02
concatCis000
eqBox3.290.033.32
eqsens_dt000
eqtlTests9.000.309.35
eqtlTests.me000
eqtlTestsManager-class0.020.000.01
ex2.570.052.62
getCisMap000
gwSnpTests3.340.093.43
hmm8780.780.020.79
pifdr1.760.002.11
qqhex0.130.000.12
sampsInVCF0.040.000.05
sensiCisInput-class000
sensiCisOutput-class000
simpleTiling000
snplocsDefault000
strMultPop0.090.000.09
transManager-class000
transScores000
vcf2sm0.090.000.10

GGtools.Rcheck/examples_x64/GGtools-Ex.timings:

nameusersystemelapsed
All.cis000
CisConfig-class000
EqAppr-class000
GGtools-package000
TransConfig-class000
b10.080.000.07
best.cis.eQTLs000
best.trans.eQTLs000
bindmaf0.020.000.02
cgff2dt0.010.000.02
cisAssoc48.58 1.6750.27
cisRun-class000
ciseqByCluster000
collectBest0.020.000.02
concatCis000
eqBox2.620.122.75
eqsens_dt000
eqtlTests8.060.398.72
eqtlTests.me000
eqtlTestsManager-class0.000.020.01
ex2.330.042.37
getCisMap000
gwSnpTests2.900.082.98
hmm8780.620.020.64
pifdr1.830.041.87
qqhex0.110.000.11
sampsInVCF0.040.020.07
sensiCisInput-class000
sensiCisOutput-class000
simpleTiling000
snplocsDefault000
strMultPop0.070.010.07
transManager-class0.010.000.02
transScores000
vcf2sm0.070.000.06