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BioC 3.2: CHECK report for tilingArray on zin1

This page was generated on 2016-04-23 10:10:18 -0700 (Sat, 23 Apr 2016).

Package 1052/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tilingArray 1.48.0
Zhenyu Xu
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/tilingArray
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 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
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tilingArray
Version: 1.48.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings tilingArray_1.48.0.tar.gz
StartedAt: 2016-04-23 06:08:41 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:10:29 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 108.6 seconds
RetCode: 0
Status:  OK 
CheckDir: tilingArray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings tilingArray_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/tilingArray.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tilingArray/DESCRIPTION’ ... OK
* this is package ‘tilingArray’ version ‘1.48.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘tilingArray’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘pixmap’
  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
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
myPixmap: no visible global function definition for ‘pixmapGrey’
myWrite: no visible global function definition for ‘write.pnm’
normalizeByReference: no visible global function definition for ‘exprs’
normalizeByReference: no visible global function definition for
  ‘exprs<-’
plotFeatures: no visible global function definition for ‘listLen’
qcPlots: no visible global function definition for ‘pData’
qcPlots: no visible global function definition for ‘exprs’
readCel2eSet: no visible global function definition for ‘varLabels’
segChrom: no visible global function definition for ‘exprs’
plot,segmentation-ANY : .local: no visible global function definition
  for ‘note’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/tilingArray.Rcheck/00check.log’
for details.


tilingArray.Rcheck/00install.out:

* installing *source* package ‘tilingArray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c findsegments.c -o findsegments.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sampleStep.c -o sampleStep.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o tilingArray.so findsegments.o sampleStep.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/tilingArray.Rcheck/tilingArray/libs
** 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 (tilingArray)

tilingArray.Rcheck/tilingArray-Ex.timings:

nameusersystemelapsed
PMindex000
class-segmentation0.0470.0000.047
comparisonPlot000
costMatrix0.0530.0040.060
findsegments0.0010.0000.001
gffSub0.0940.0120.106
normalizeByReference0.0010.0000.001
otherStrand000
plotAlongChrom0.1720.0000.172
plotAlongChromLegend0.0010.0000.000
plotSegmentationHeatmap0.0740.0000.074
plotpenLL0.0230.0040.028
posMin0.0000.0040.000
qcPlots0.0000.0000.001
readCel2eSet0.0000.0000.001
sampleStep0.0000.0000.001
segChrom0.0000.0000.001
segment0.0000.0040.001
segnf0.2840.0000.286