GLAD 1.13.0
Philippe Hupe
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GLAD | | Last Changed Rev: 29013 / Revision: 29143 | | Last Changed Date: 2007-12-04 06:21:00 -0800 (Tue, 04 Dec 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/GLAD.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '1.13.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GLAD' 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotProfile.profileCGH: no visible binding for global variable
‘cytoband’
* checking Rd files ... WARNING
Rd files without 'description':
GLAD-internal.Rd
These entries are required in an Rd file.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'arrayPersp':
arrayPersp.default arrayPersp.arrayCGH
S3 methods shown with full name in documentation object 'arrayPlot':
arrayPlot.default arrayPlot.arrayCGH
S3 methods shown with full name in documentation object 'as.data.frame.profileCGH':
as.data.frame.profileCGH
S3 methods shown with full name in documentation object 'as.profileCGH':
as.profileCGH.data.frame
S3 methods shown with full name in documentation object 'daglad':
daglad.profileCGH
S3 methods shown with full name in documentation object 'glad':
glad.profileCGH
S3 methods shown with full name in documentation object 'plotProfile':
plotProfile.profileCGH
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 use of $BLAS_LIBS ... OK
* creating GLAD-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' './GLAD.tex' ...
Package natbib Warning: Citation `pinkel98' on page 1 undefined on input line 4
Package natbib Warning: Citation `snijders01' on page 1 undefined on input line
Package natbib Warning: Citation `solinas97' on page 1 undefined on input line
Package natbib Warning: Citation `ishkanian04' on page 1 undefined on input lin
Package natbib Warning: Citation `hupe04' on page 1 undefined on input line 40.
Package natbib Warning: Citation `snijders01' on page 1 undefined on input line
Package natbib Warning: Citation `veltman03' on page 1 undefined on input line
Package natbib Warning: Citation `billerey01' on page 1 undefined on input line
Package natbib Warning: Citation `snijders01' on page 3 undefined on input line
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './GLAD.tex' ...
Package natbib Warning: Citation `pinkel98' on page 1 undefined on input line 4
Package natbib Warning: Citation `snijders01' on page 1 undefined on input line
Package natbib Warning: Citation `solinas97' on page 1 undefined on input line
Package natbib Warning: Citation `ishkanian04' on page 1 undefined on input lin
Package natbib Warning: Citation `hupe04' on page 1 undefined on input line 40.
Package natbib Warning: Citation `snijders01' on page 1 undefined on input line
Package natbib Warning: Citation `veltman03' on page 1 undefined on input line
Package natbib Warning: Citation `billerey01' on page 2 undefined on input line
Package natbib Warning: Citation `snijders01' on page 3 undefined on input line
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './GLAD.tex' ...
* creating GLAD-manual.tex ... OK
* checking GLAD-manual.tex ... OK
WARNING: There was 1 warning, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/GLAD.Rcheck/00check.log
for details
/loc/home/biocbuild/bbs-2.2-bioc/meat/GLAD.Rcheck
* Installing *source* package 'GLAD' ...
Configuring variable environment
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c distance.c -o distance.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c glad.cpp -o glad.o
glad.cpp: In function ‘void detectOutliers(double*, int*, int*, int*, int*, int*, double*, int*)’:
glad.cpp:112: warning: comparison between signed and unsigned integer expressions
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c glad-function.c -o glad-function.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c hclust.c -o hclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c laws.c -o laws.o
g++ -shared -L/usr/local/lib64 -o GLAD.so distance.o glad.o glad-function.o hclust.o laws.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
** help
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \usage
Note: removing empty section \value
Note: removing empty section \description
Note: removing empty section \seealso
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
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Note: removing empty section \value
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \details
Note: removing empty section \seealso
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
>>> Building/Updating help pages for package 'GLAD'
Formats: text html latex example
ChrNumeric text html latex example
ColorBar text html latex example
GLAD-internal text html latex
arrayCGH text html latex example
arrayPersp text html latex example
arrayPlot text html latex example
as.data.frame.profileCGH text html latex example
as.profileCGH text html latex example
bladder text html latex example
cytoband text html latex example
daglad text html latex example
glad text html latex example
hclust text html latex example
kernel text html latex
myPalette text html latex example
plotProfile text html latex example
profileCGH text html latex example
snijders text html latex example
tkdaglad text html latex example
veltman text html latex example
** building package indices ...
* DONE (GLAD)