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BioC 3.1: CHECK report for GGtools on moscato2

This page was generated on 2015-10-09 09:27:45 -0700 (Fri, 09 Oct 2015).

Package 412/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGtools 5.4.0
VJ Carey
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GGtools
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GGtools
Version: 5.4.0
Command: rm -rf GGtools.buildbin-libdir GGtools.Rcheck && mkdir GGtools.buildbin-libdir GGtools.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGtools.buildbin-libdir GGtools_5.4.0.tar.gz >GGtools.Rcheck\00install.out 2>&1 && cp GGtools.Rcheck\00install.out GGtools-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GGtools.buildbin-libdir --install="check:GGtools-install.out" --force-multiarch --no-vignettes --timings GGtools_5.4.0.tar.gz
StartedAt: 2015-10-09 02:17:22 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:36:59 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 1176.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GGtools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GGtools.buildbin-libdir GGtools.Rcheck && mkdir GGtools.buildbin-libdir GGtools.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGtools.buildbin-libdir GGtools_5.4.0.tar.gz >GGtools.Rcheck\00install.out 2>&1 && cp GGtools.Rcheck\00install.out GGtools-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GGtools.buildbin-libdir --install="check:GGtools-install.out" --force-multiarch --no-vignettes --timings GGtools_5.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/GGtools.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '5.4.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by 'reshape2::melt' when loading 'GGtools'
See 'E:/biocbld/bbs-3.1-bioc/meat/GGtools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 73.0Mb
  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 'parallel' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Homo.sapiens' 'MatrixEQTL' 'aod' 'foreach' 'gwascat'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: '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
plot,gwSnpScreenResult-character : .local: warning in axis(3, at =
  genePosition(x@gene, annlib = x@annotation), col = "red", lwd = 2,
  label = " "): partial argument match of 'label' to 'labels'
.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'
SnpMatrixCisToSummex: no visible global function definition for
  'rowRanges'
add878: no visible binding for global variable 'hmm878'
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 : .redu.fdr: no visible binding for global variable 'snp'
appraise : .redu.fdr: no visible binding for global variable 'score'
appraise : .discmods: no visible global function definition for
  '%dopar%'
appraise : .discmods: no visible global function definition for
  'foreach'
bindmaf.legacy: no visible global function definition for 'strand<-'
bindmaf.simple: no visible global function definition for 'strand<-'
bindprops: no visible global function definition for 'strand<-'
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 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 'colData'
cisAssoc: no visible binding for global variable 'chi.squared'
ciseqByCluster: no visible global function definition for
  'clusterApply'
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: no visible global function definition for
  'clusterApply'
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 global function definition for
  'clusterExport'
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: no visible global function definition for
  'clusterApplyLB'
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 '%dopar%'
eqsens_dt: no visible global function definition for 'foreach'
eqsens_dt: no visible binding for global variable 'curp'
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'
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'
getAsSlicedData: no visible binding for global variable 'target'
getCisMap: no visible global function definition for 'getSNPlocs'
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'
meta.bindmaf: no visible global function definition for 'strand<-'
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<-'
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'
snpsCisToGenes: no visible global function definition for 'start<-'
topKfeats: no visible binding for global variable 'i1'
topKfeats: no visible binding for global variable 'i2'
transeqByCluster: no visible global function definition for
  'clusterExport'
transeqByCluster: no visible global function definition for
  'clusterApplyLB'
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'
update_fdr_filt: no visible binding for global variable 'score'
waldtests : <anonymous>: no visible global function definition for
  'wald.test'
plot,gwSnpScreenResult-character : .local: no visible global function
  definition for 'getSNPcount'
plot,gwSnpScreenResult-character : .local: no visible global function
  definition for 'getSNPlocs'
* 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' ... [70s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
cisAssoc  29.59   0.63   30.34
eqtlTests  9.64   0.23   11.02
** running examples for arch 'x64' ... [67s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
cisAssoc  28.36   0.75   29.22
eqtlTests  9.38   0.21    9.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'cis.R' [113s]
  Running 'eqvgwst.R' [20s]
  Running 'test.meqtlTests.R' [24s]
  Running 'test.meta.trans.R' [0s]
  Running 'testCisMap.R' [41s]
  Running 'testTrans.R' [69s]
 [267s] OK
** running tests for arch 'x64' ...
  Running 'cis.R' [96s]
  Running 'eqvgwst.R' [24s]
  Running 'test.meqtlTests.R' [23s]
  Running 'test.meta.trans.R' [0s]
  Running 'testCisMap.R' [41s]
  Running 'testTrans.R' [81s]
 [266s] 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: 1 WARNING, 6 NOTEs
See
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'reshape2::melt' when loading 'GGtools'
No methods found in "IRanges" for requests: aggregate
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'reshape2::melt' when loading 'GGtools'
No methods found in "IRanges" for requests: aggregate

install for x64

* installing *source* package 'GGtools' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'reshape2::melt' when loading 'GGtools'
No methods found in "IRanges" for requests: aggregate
* MD5 sums
packaged installation of 'GGtools' as GGtools_5.4.0.zip
* DONE (GGtools)

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

nameusersystemelapsed
All.cis000
CisConfig-class000
EqAppr-class000
GGtools-package000
TransConfig-class000
b10.110.000.11
best.cis.eQTLs000
best.trans.eQTLs0.010.000.01
bindmaf000
cgff2dt0.020.000.02
cisAssoc29.59 0.6330.34
cisRun-class0.020.000.01
ciseqByCluster000
collectBest000
concatCis000
eqBox2.980.093.08
eqsens_dt000
eqtlTests 9.64 0.2311.02
eqtlTests.me000
eqtlTestsManager-class000
ex2.560.112.67
getCisMap000
gwSnpTests3.710.133.84
hmm8781.120.031.15
pifdr2.940.053.18
qqhex0.170.000.18
sampsInVCF0.080.000.07
sensiCisInput-class000
sensiCisOutput-class000
simpleTiling000
snplocsDefault000
strMultPop0.130.000.12
transManager-class000
transScores000
vcf2sm0.070.000.06

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

nameusersystemelapsed
All.cis000
CisConfig-class0.010.000.02
EqAppr-class000
GGtools-package000
TransConfig-class000
b10.090.000.09
best.cis.eQTLs0.020.000.02
best.trans.eQTLs000
bindmaf000
cgff2dt0.020.000.01
cisAssoc28.36 0.7529.22
cisRun-class000
ciseqByCluster000
collectBest0.010.000.02
concatCis000
eqBox3.570.113.94
eqsens_dt000
eqtlTests9.380.219.75
eqtlTests.me000
eqtlTestsManager-class000
ex2.340.072.40
getCisMap000
gwSnpTests3.360.073.43
hmm8780.650.020.67
pifdr1.970.021.98
qqhex0.110.010.13
sampsInVCF0.040.000.04
sensiCisInput-class000
sensiCisOutput-class0.020.000.02
simpleTiling000
snplocsDefault000
strMultPop0.120.000.12
transManager-class000
transScores000
vcf2sm0.080.000.08