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Package 2/353HostnameOS / ArchBUILDCHECKBUILD BIN
aCGH 1.22.0
Peter Dimitrov
Snapshot Date: 2010-04-02 23:28:25 -0700 (Fri, 02 Apr 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/aCGH
Last Changed Rev: 42684 / Revision: 45705
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: aCGH
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/2.10/Resources/bin/R CMD check --no-vignettes aCGH_1.22.0.tar.gz
StartedAt: 2010-04-03 04:17:55 -0700 (Sat, 03 Apr 2010)
EndedAt: 2010-04-03 04:19:47 -0700 (Sat, 03 Apr 2010)
EllapsedTime: 111.5 seconds
RetCode: 0
Status: OK
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.5-bioc/meat/aCGH.Rcheck'
* using R version 2.10.1 Patched (2009-12-14 r50738)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.22.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aCGH' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[.aCGH: no visible binding for global variable ‘joan’
changeProp.func: no visible binding for global variable
  ‘data.screen.norm.thres’
computeSD.func: no visible binding for global variable ‘states.bic’
findAber.func: no visible binding for global variable ‘states.bic’
findAmplif.func: no visible binding for global variable ‘res3’
findAmplif.func: no visible binding for global variable ‘res2’
findAmplif.func: no visible binding for global variable ‘res1’
findAmplif.func: no visible binding for global variable ‘states.bic’
findOutliers.func: no visible binding for global variable ‘madGenome’
findOutliers.func: no visible binding for global variable ‘states.bic’
findTrans.func: no visible binding for global variable ‘res1’
findTrans.func: no visible binding for global variable ‘res2’
findTrans.func: no visible binding for global variable ‘states.bic’
mergeFunc: no visible binding for global variable ‘states.bic’
plotCGH.func: no visible binding for global variable ‘data.cgh’
plotCGH.func: no visible binding for global variable ‘map.cgh’
plotCGH.hmm.func: no visible binding for global variable ‘dat’
plotCGH.hmm.func: no visible binding for global variable ‘states.bic’
plotCGH.hmm.func: no visible binding for global variable ‘res4’
plotCGH.hmm.func: no visible binding for global variable ‘res2’
plotCGH.hmm.func: no visible binding for global variable ‘res1’
plotCGH.hmm.func: no visible binding for global variable ‘res3’
plotChrom.grey.samples.func: no visible binding for global variable
  ‘states.bic’
plotChrom.grey.samples.func: no visible binding for global variable
  ‘res4’
plotChrom.grey.samples.func: no visible binding for global variable
  ‘res2’
plotChrom.grey.samples.func: no visible binding for global variable
  ‘res1’
plotChrom.grey.samples.func: no visible binding for global variable
  ‘res3’
plotChrom.hmm.func: no visible binding for global variable ‘states.bic’
plotChrom.hmm.func: no visible binding for global variable ‘res4’
plotChrom.hmm.func: no visible binding for global variable ‘res2’
plotChrom.hmm.func: no visible binding for global variable ‘res1’
plotChrom.hmm.func: no visible binding for global variable ‘res3’
plotChrom.samples.func: no visible binding for global variable
  ‘states.bic’
plotChrom.samples.func: no visible binding for global variable ‘res4’
plotChrom.samples.func: no visible binding for global variable ‘res2’
plotChrom.samples.func: no visible binding for global variable ‘res1’
plotChrom.samples.func: no visible binding for global variable ‘res3’
plotFreqStatColors: no visible global function definition for
  ‘plotfreq.stat’
plotFreqStatGrey: no visible global function definition for
  ‘plotfreq.stat’
plotGeneSign: no visible binding for global variable ‘.mt.naNUM’
plotSummaryProfile: no visible binding for global variable
  ‘numchromgain’
plotSummaryProfile: no visible binding for global variable
  ‘numchromloss’
plotSummaryProfile: no visible binding for global variable ‘numtrans’
plotSummaryProfile: no visible binding for global variable
  ‘numtrans.binary’
plotSummaryProfile: no visible binding for global variable ‘numaber’
plotSummaryProfile: no visible binding for global variable ‘numamplif’
plotSummaryProfile: no visible binding for global variable
  ‘numamplif.binary’
plotSummaryProfile: no visible binding for global variable
  ‘numamplicon’
plotSummaryProfile: no visible binding for global variable
  ‘sizeamplicon’
plotfreq.givenstat.final.colors.func: no visible binding for global
  variable ‘stats’
plotfreq.givenstat.final.colors.func: no visible binding for global
  variable ‘statsPerm’
plotfreq.givenstat.final.colors.func: possible error in gainLoss(dat =
  data, cols = cols, thres = thres, quant = quant.col): unused
  argument(s) (quant = quant.col)
plotfreq.stat.chrom.final.func: no visible binding for global variable
  ‘.mt.naNUM’
plotfreq.stat.chrom.final.func: no visible global function definition
  for ‘exit’
plotfreq.stat.final.func: no visible binding for global variable
  ‘.mt.naNUM’
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

aCGH.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package ‘aCGH’ ...
** libs
** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -g3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c hmm.cpp -o hmm.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -g3 -I/usr/local/include    -fPIC  -g -O2 -c hmm.cpp -o hmm.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: splines
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
* DONE (aCGH)