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Package 2/251HostnameOS / ArchBUILDCHECKBUILD BIN
aCGH 1.13.0
Jane Fridlyand
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aCGH
Last Changed Rev: 28557 / Revision: 29143
Last Changed Date: 2007-11-07 23:00:31 -0800 (Wed, 07 Nov 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK [ WARNINGS ]
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  WARNINGS  OK 
Package: aCGH
Version: 1.13.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check aCGH_1.13.0.tar.gz
StartedAt: 2007-12-11 02:40:50 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 02:42:39 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 109.7 seconds
RetCode: 0
Status: WARNINGS
CheckDir: aCGH.Rcheck
Warnings: 1

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/aCGH.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.13.0'
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
floor:
  function(x)
floor.func:
  function(x, floor, x.na)

See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* 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’
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’
plotFreqStatColors: no visible global function definition for
  ‘plotfreq.stat’
plotfreq.stat.final.func: no visible binding for global variable
  ‘.mt.naNUM’
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’
Found possibly global 'T' or 'F' in the following functions:
  combine.func plotfreq.givenstat.final.colors.func
  plotfreq.stat.chrom.final.func plotfreq.stat.final.func
* checking Rd files ... 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
* creating aCGH-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './aCGH.tex' ...
Package natbib Warning: Citation `Snijdersetal01' on page 1 undefined on input 
Package natbib Warning: Citation `Jainetal02' on page 1 undefined on input line
Package natbib Warning: Citation `Nakaoetal04' on page 1 undefined on input lin
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './aCGH.tex' ...
Package natbib Warning: Citation `Snijdersetal01' on page 1 undefined on input 
Package natbib Warning: Citation `Jainetal02' on page 1 undefined on input line
Package natbib Warning: Citation `Nakaoetal04' on page 1 undefined on input lin
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './aCGH.tex' ...
* creating aCGH-manual.tex ... OK
* checking aCGH-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/home/biocbuild/bbs-2.2-bioc/meat/aCGH.Rcheck/00check.log
for details

aCGH.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/aCGH.Rcheck
* Installing *source* package 'aCGH' ...
** libs
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -g3 -I/usr/local/include    -fpic  -g -O2 -Wall -c hmm.cpp -o hmm.o
hmm.cpp: In function ‘double calc_observed_likelihood_iter(std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, double*, bool, double*, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, bool)’:
hmm.cpp:32: warning: deprecated conversion from string constant to ‘char*’
hmm.cpp:42: warning: deprecated conversion from string constant to ‘char*’
hmm.cpp:82: warning: deprecated conversion from string constant to ‘char*’
hmm.cpp:87: warning: deprecated conversion from string constant to ‘char*’
g++ -shared -L/usr/local/lib64 -o aCGH.so hmm.o -lm  -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: multtest
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Loading required package: sma
** help
Note: unmatched right brace in 'aCGH.process' on or after line 28
Note: removing empty section \examples
 >>> Building/Updating help pages for package 'aCGH'
     Formats: text html latex example 
  aCGH                              text    html    latex   example
  aCGH.process                      text    html    latex   example
  aCGH.read.Sprocs                  text    html    latex   example
  aCGH.test                         text    html    latex
  clusterGenome                     text    html    latex   example
  colorectal                        text    html    latex   example
  computeSD.func                    text    html    latex
  fga.func                          text    html    latex   example
  find.genomic.events               text    html    latex
  find.hmm.states                   text    html    latex   example
  findAber.func                     text    html    latex
  findAmplif.func                   text    html    latex
  findOutliers.func                 text    html    latex
  findTrans.func                    text    html    latex
  gainLoss                          text    html    latex   example
  heatmap                           text    html    latex   example
  human.chrom.info.Jul03            text    html    latex
  human.chrom.info.May04            text    html    latex
  impute.HMM                        text    html    latex   example
  impute.lowess                     text    html    latex   example
  mergeFunc                         text    html    latex
  mergeLevels                       text    html    latex   example
  plotFreqStat                      text    html    latex   example
  plotGenome                        text    html    latex   example
  plotHmmStates                     text    html    latex   example
  plotSummaryProfile                text    html    latex   example
  states.hmm.func                   text    html    latex
  summarize.clones                  text    html    latex   example
  threshold.func                    text    html    latex   example
** building package indices ...
* DONE (aCGH)