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 |
* 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
/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)