aCGH 1.12.0
Jane Fridlyand
| Snapshot Date: 2008-04-02 12:12:36 -0700 (Wed, 02 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/aCGH | | Last Changed Rev: 28558 / Revision: 30807 | | Last Changed Date: 2007-11-07 23:08:50 -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 |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/aCGH.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.12.0'
* 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 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'
plotfreq.stat.final.func: no visible binding for global variable
'.mt.naNUM'
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'
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' ... OK
* creating aCGH-manual.tex ... OK
* checking aCGH-manual.tex ... OK
WARNING: There was 1 warning, see
D:/biocbld/bbs-2.1-bioc/meat/aCGH.Rcheck/00check.log
for details
installing R.css in D:/biocbld/bbs-2.1-bioc/meat/aCGH.Rcheck
---------- Making package aCGH ------------
adding build stamp to DESCRIPTION
making DLL ...
making hmm.d from hmm.cpp
g++-sjlj -g3 -Id:/biocbld/bbs-2.1-bioc/R/include -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*'
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include -i aCGH_res.rc -o aCGH_res.o
g++-sjlj -shared -s -o aCGH.dll aCGH.def hmm.o aCGH_res.o -Ld:/biocbld/bbs-2.1-bioc/R/bin -lm -lR
... DLL made
installing DLL
installing R files
installing demos
installing inst files
installing data files
preparing package aCGH 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
installing man source files
installing indices
not zipping data
installing help
Note: unmatched right brace in 'aCGH.process' on or after line 28
Note: unmatched right brace in 'aCGH.process.Rd' on or after line 28
>>> Building/Updating help pages for package 'aCGH'
Formats: text html latex example chm
aCGH text html latex example chm
aCGH.process text html latex example chm
aCGH.read.Sprocs text html latex example chm
aCGH.test text html latex example chm
clusterGenome text html latex example chm
colorectal text html latex example chm
computeSD.func text html latex chm
fga.func text html latex example chm
find.genomic.events text html latex chm
find.hmm.states text html latex example chm
findAber.func text html latex chm
findAmplif.func text html latex chm
findOutliers.func text html latex chm
findTrans.func text html latex chm
gainLoss text html latex example chm
heatmap text html latex example chm
human.chrom.info.Jul03 text html latex chm
human.chrom.info.May04 text html latex chm
impute.HMM text html latex example chm
impute.lowess text html latex example chm
mergeFunc text html latex chm
mergeLevels text html latex example chm
plotFreqStat text html latex example chm
plotGenome text html latex example chm
plotHmmStates text html latex example chm
plotSummaryProfile text html latex example chm
states.hmm.func text html latex chm
summarize.clones text html latex example chm
threshold.func text html latex example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open ";c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\aCGH.Rcheck\00_pkg_src\aCGH\chm\aCGH.chm
HHC4016: Warning: Cannot open ";c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
The following files were not compiled:
adding MD5 sums
* DONE (aCGH)