Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 94/251HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: GLAD
Version: 1.13.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check GLAD_1.13.0.tar.gz
StartedAt: 2007-12-11 03:42:21 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:43:01 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 40.2 seconds
RetCode: 0
Status: WARNINGS
CheckDir: GLAD.Rcheck
Warnings: 1

Command output

* 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

GLAD.Rcheck/00install.out:

/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
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
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)