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BioC 3.2: CHECK report for Ringo on windows1.bioconductor.org

This page was generated on 2015-10-27 17:28:19 -0400 (Tue, 27 Oct 2015).

Package 885/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Ringo 1.34.0
J. Toedling
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Ringo
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: Ringo
Version: 1.34.0
Command: rm -rf Ringo.buildbin-libdir Ringo.Rcheck && mkdir Ringo.buildbin-libdir Ringo.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Ringo.buildbin-libdir Ringo_1.34.0.tar.gz >Ringo.Rcheck\00install.out 2>&1 && cp Ringo.Rcheck\00install.out Ringo-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Ringo.buildbin-libdir --install="check:Ringo-install.out" --force-multiarch --no-vignettes --timings Ringo_1.34.0.tar.gz
StartedAt: 2015-10-27 05:06:15 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:09:08 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 172.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Ringo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Ringo.buildbin-libdir Ringo.Rcheck && mkdir Ringo.buildbin-libdir Ringo.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Ringo.buildbin-libdir Ringo_1.34.0.tar.gz >Ringo.Rcheck\00install.out 2>&1 && cp Ringo.Rcheck\00install.out Ringo-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Ringo.buildbin-libdir --install="check:Ringo-install.out" --force-multiarch --no-vignettes --timings Ringo_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/Ringo.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase' 'RColorBrewer' 'limma' 'Matrix' 'grid' 'lattice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'Ringo' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'limma'
A package should be listed in only one of these fields.
* 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 'grid' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'mclust' 'rtracklayer' 'topGO'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'limma'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Biobase' 'Matrix' 'RColorBrewer' 'grid' 'lattice' 'limma'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'clusters'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for 'addVigs2WinMenu'
asExprSet: no visible global function definition for 'featureNames<-'
asExprSet: no visible global function definition for 'featureData<-'
autocor: no visible global function definition for 'featureNames'
autocor: no visible global function definition for 'exprs'
autocor : <anonymous>: no visible global function definition for
  'matchpt'
chipAlongChrom: no visible global function definition for
  'featureNames'
chipAlongChrom: no visible global function definition for 'exprs'
chipAlongChrom: no visible global function definition for 'brewer.pal'
chipAlongChrom: no visible global function definition for
  'pushViewport'
chipAlongChrom: no visible global function definition for 'viewport'
chipAlongChrom: no visible global function definition for 'grid.layout'
chipAlongChrom: no visible global function definition for
  'dataViewport'
chipAlongChrom: no visible global function definition for 'grid.yaxis'
chipAlongChrom: no visible global function definition for 'gpar'
chipAlongChrom: no visible global function definition for 'grid.text'
chipAlongChrom: no visible global function definition for 'unit'
chipAlongChrom: no visible global function definition for 'draw.key'
chipAlongChrom: no visible global function definition for 'sampleNames'
chipAlongChrom: no visible global function definition for 'popViewport'
chipAlongChrom: no visible global function definition for 'grid.lines'
chipAlongChrom: no visible global function definition for
  'grid.segments'
chipAlongChrom: no visible global function definition for 'arrow'
chipAlongChrom1: no visible global function definition for
  'featureNames'
chipAlongChrom1: no visible global function definition for 'exprs'
chipAlongChrom1: no visible global function definition for 'brewer.pal'
chipAlongChrom1: no visible global function definition for
  'sampleNames'
compute.gc: no visible global function definition for 'listLen'
computeRunningMedians: no visible global function definition for
  'varLabels'
computeRunningMedians: no visible global function definition for
  'pData'
computeRunningMedians: no visible global function definition for
  'sampleNames'
computeRunningMedians: no visible global function definition for
  'exprs'
computeRunningMedians: no visible global function definition for
  'featureNames'
computeRunningMedians: no visible global function definition for
  'phenoData'
computeRunningMedians: no visible global function definition for
  'featureNames<-'
computeRunningMedians: no visible global function definition for
  'featureData<-'
computeRunningMedians: no visible global function definition for
  'featureData'
computeRunningMedians: no visible global function definition for
  'sampleNames<-'
computeSlidingT: no visible global function definition for 'exprs'
computeSlidingT: no visible global function definition for
  'featureNames'
computeSlidingT: no visible global function definition for
  'sampleNames'
computeSlidingT: no visible global function definition for
  'featureNames<-'
computeSlidingT: no visible global function definition for
  'featureData<-'
computeSlidingT: no visible global function definition for
  'featureData'
computeSlidingT: no visible global function definition for
  'sampleNames<-'
corPlot: no visible global function definition for 'exprs'
exportCCData: no visible global function definition for 'exprs'
exportCCData: no visible global function definition for 'exprs<-'
exportCCData: no visible global function definition for
  'package.version'
exportCherList: no visible global function definition for 'IRanges'
exportCherList: no visible global function definition for 'GenomicData'
exportCherList: no visible global function definition for 'export'
findChersOnSmoothed: no visible global function definition for 'pData'
findChersOnSmoothed: no visible global function definition for
  'sampleNames'
findChersOnSmoothed: no visible global function definition for
  'featureNames'
findChersOnSmoothed : <anonymous>: no visible global function
  definition for 'exprs'
image.RGList: no visible global function definition for 'brewer.pal'
merge.RGList: no visible global function definition for 'makeUnique'
newVP: no visible global function definition for 'pushViewport'
newVP: no visible global function definition for 'viewport'
newVP: no visible global function definition for 'grid.layout'
newVP: no visible global function definition for 'grid.text'
newVP: no visible global function definition for 'gpar'
newVP: no visible global function definition for 'popViewport'
normalizeBetweenArraysVSN: no visible global function definition for
  'exprs'
plot.cher: no visible global function definition for 'sampleNames'
plotAlongChromLegend : formatRow: no visible global function definition
  for 'convertWidth'
plotAlongChromLegend : formatRow: no visible global function definition
  for 'stringWidth'
plotAlongChromLegend : formatRow: no visible global function definition
  for 'grid.rect'
plotAlongChromLegend : formatRow: no visible global function definition
  for 'unit'
plotAlongChromLegend : formatRow: no visible binding for global
  variable 'gpar'
plotAlongChromLegend : formatRow: no visible global function definition
  for 'grid.text'
plotAlongChromLegend : formatRow: no visible global function definition
  for 'gpar'
plotAlongChromLegend: no visible global function definition for
  'pushViewport'
plotAlongChromLegend: no visible global function definition for
  'viewport'
plotAlongChromLegend: no visible global function definition for
  'popViewport'
plotFeatures: no visible global function definition for 'pushViewport'
plotFeatures: no visible global function definition for 'dataViewport'
plotFeatures: no visible global function definition for 'grid.segments'
plotFeatures: no visible global function definition for 'gpar'
plotFeatures: no visible global function definition for 'listLen'
plotFeatures: no visible global function definition for 'grid.rect'
plotFeatures: no visible global function definition for 'convertWidth'
plotFeatures: no visible global function definition for 'stringWidth'
plotFeatures: no visible global function definition for 'grid.text'
plotFeatures: no visible global function definition for 'popViewport'
plotOneChIPSample: no visible global function definition for 'unit'
plotOneChIPSample: no visible global function definition for
  'pushViewport'
plotOneChIPSample: no visible global function definition for
  'dataViewport'
plotOneChIPSample: no visible global function definition for
  'grid.yaxis'
plotOneChIPSample: no visible global function definition for 'gpar'
plotOneChIPSample: no visible global function definition for
  'grid.text'
plotOneChIPSample: no visible global function definition for
  'grid.lines'
plotOneChIPSample: no visible global function definition for
  'grid.polyline'
plotOneChIPSample: no visible global function definition for
  'grid.points'
plotOneChIPSample: no visible global function definition for
  'popViewport'
preprocess: no visible global function definition for
  'normalizeWithinArrays'
preprocess: no visible global function definition for
  'normalizeBetweenArrays'
quantilesOverPositions: no visible global function definition for
  'exprs'
quantilesOverPositions: no visible global function definition for
  'sampleNames'
readNgIntensitiesTxt: no visible global function definition for
  'removeExt'
readNimblegen: no visible global function definition for 'readTargets'
readNimblegen: no visible global function definition for
  'readSpotTypes'
readNimblegen: no visible global function definition for
  'controlStatus'
sigGOTable: no visible global function definition for 'mappedkeys'
sigGOTable: no visible binding for global variable 'annFUN.gene2GO'
sigGOTable: no visible binding for global variable 'annFUN.org'
sigGOTable: no visible global function definition for 'runTest'
sigGOTable: no visible global function definition for 'GenTable'
sigGOTable: no visible global function definition for 'usedGO'
sigGOTable: no visible binding for global variable 'p.value'
splitAndSimplify: no visible global function definition for 'listLen'
takeMeanOverGroups: no visible global function definition for 'pData'
takeMeanOverGroups: no visible global function definition for 'exprs'
takeMeanOverGroups: no visible global function definition for
  'featureNames<-'
takeMeanOverGroups: no visible global function definition for
  'featureNames'
twoGaussiansNull: no visible global function definition for 'Mclust'
cbind2,ExpressionSet-ExpressionSet : .local: no visible global function
  definition for 'featureNames'
cbind2,ExpressionSet-ExpressionSet : .local: no visible global function
  definition for 'exprs'
cbind2,ExpressionSet-ExpressionSet : .local: no visible global function
  definition for 'sampleNames'
plot,cher-ExpressionSet : .local: no visible global function definition
  for 'sampleNames'
* checking Rd files ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/biocbld/bbs-3.2-bioc/meat/Ringo.buildbin-libdir/Ringo/libs/i386/Ringo.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/biocbld/bbs-3.2-bioc/meat/Ringo.buildbin-libdir/Ringo/libs/x64/Ringo.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [8s] OK
** running examples for arch 'x64' ... [9s] 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: 5 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/Ringo.Rcheck/00check.log'
for details.


Ringo.Rcheck/00install.out:


install for i386

* installing *source* package 'Ringo' ...
** libs
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp: In function 'SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)':
mmeansd.cpp:27:24: warning: variable 'is' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c mmedian.cpp -o mmedian.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c region_overlap.c -o region_overlap.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ringo_init.c -o ringo_init.o
g++ -m32 -shared -s -static-libgcc -o Ringo.dll tmp.def mmeansd.o mmedian.o region_overlap.o ringo_init.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/Ringo.buildbin-libdir/Ringo/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'ls' from package 'base' in package 'Ringo'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Ringo' ...
** libs
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp: In function 'SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)':
mmeansd.cpp:27:24: warning: variable 'is' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c mmedian.cpp -o mmedian.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c region_overlap.c -o region_overlap.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ringo_init.c -o ringo_init.o
g++ -m64 -shared -s -static-libgcc -o Ringo.dll tmp.def mmeansd.o mmedian.o region_overlap.o ringo_init.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/Ringo.buildbin-libdir/Ringo/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Ringo' as Ringo_1.34.0.zip
* DONE (Ringo)

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

nameusersystemelapsed
arrayImage0.110.000.11
asExprSet0.140.000.14
autocorr0.110.000.11
cherByThreshold0.020.000.01
cherClass0.310.000.31
chipAlongChrom0.100.020.11
chipAlongChromOld0.040.000.05
computeRunningMedians0.270.010.28
compute_gc0.010.000.02
compute_sliding_t0.080.000.07
corrPlot0.020.000.02
exportCherList000
features2Probes1.170.021.19
findChersOnSmoothed0.110.000.11
ftr2xys000
newCER0.010.000.02
nonzero0.020.000.01
plotAutocorr000
plotBM0.020.000.02
posToProbeAnnoEnvironment0.040.000.05
preprocess0.250.000.25
probeAnnoClass0.020.010.03
qopS4000
quantilesOverPositions0.440.030.47
readNimblegen0.060.000.06
regionoverlap0.010.000.01
relateCERs000
sigGOTable000
sliding_meansd000
sliding_quantile0.020.000.02
twoGaussiansNull0.120.000.13
upperBoundNull0.050.000.04
validProbeAnno0.020.000.02

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

nameusersystemelapsed
arrayImage0.130.000.12
asExprSet0.20.00.2
autocorr0.110.000.11
cherByThreshold000
cherClass0.400.000.39
chipAlongChrom0.120.000.13
chipAlongChromOld0.030.000.03
computeRunningMedians0.310.010.32
compute_gc0.020.000.02
compute_sliding_t0.080.000.08
corrPlot0.030.000.03
exportCherList000
features2Probes1.140.001.14
findChersOnSmoothed0.060.000.06
ftr2xys000
newCER0.010.000.01
nonzero000
plotAutocorr000
plotBM0.020.000.02
posToProbeAnnoEnvironment0.030.000.03
preprocess0.170.020.19
probeAnnoClass0.020.000.01
qopS4000
quantilesOverPositions0.510.000.52
readNimblegen0.060.000.06
regionoverlap000
relateCERs000
sigGOTable000
sliding_meansd0.010.000.02
sliding_quantile000
twoGaussiansNull0.120.000.13
upperBoundNull0.050.000.05
validProbeAnno0.020.000.01