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Package 89/233HostnameOS / ArchBUILDCHECKBUILD BIN
GLAD 1.12.0
Philippe Hupe
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/GLAD
Last Changed Rev: 27709 / Revision: 30966
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: GLAD
Version: 1.12.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check GLAD_1.12.0.tar.gz
StartedAt: 2008-04-09 19:32:37 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 19:35:28 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 170.9 seconds
RetCode: 0
Status: OK
CheckDir: GLAD.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/GLAD.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '1.12.0'
* 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 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 ... OK
* 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' ... OK
* creating GLAD-manual.tex ... OK
* checking GLAD-manual.tex ... OK

GLAD.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/GLAD.Rcheck


---------- Making package GLAD ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making distance.d from distance.c
making glad-function.d from glad-function.c
making hclust.d from hclust.c
making laws.d from laws.c
making glad.d from glad.cpp
gcc-sjlj  -std=gnu99  -Id:/biocbld/bbs-2.1-bioc/R/include     -O3 -Wall  -c distance.c -o distance.o
gcc-sjlj  -std=gnu99  -Id:/biocbld/bbs-2.1-bioc/R/include     -O3 -Wall  -c glad-function.c -o glad-function.o
gcc-sjlj  -std=gnu99  -Id:/biocbld/bbs-2.1-bioc/R/include     -O3 -Wall  -c hclust.c -o hclust.o
gcc-sjlj  -std=gnu99  -Id:/biocbld/bbs-2.1-bioc/R/include     -O3 -Wall  -c laws.c -o laws.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -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
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include  -i GLAD_res.rc -o GLAD_res.o
g++-sjlj   -shared -s  -o GLAD.dll GLAD.def distance.o glad-function.o hclust.o laws.o glad.o GLAD_res.o  -Ld:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing demos
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'GLAD'
     Formats: text html latex example chm 
  ChrNumeric                        text    html    latex   example chm
  ColorBar                          text    html    latex   example chm
  GLAD-internal                     text    html    latex           chm
  arrayCGH                          text    html    latex   example chm
  arrayPersp                        text    html    latex   example chm
  arrayPlot                         text    html    latex   example chm
  as.data.frame.profileCGH          text    html    latex   example chm
  as.profileCGH                     text    html    latex   example chm
  bladder                           text    html    latex   example chm
  cytoband                          text    html    latex   example chm
  daglad                            text    html    latex   example chm
  glad                              text    html    latex   example chm
  hclust                            text    html    latex   example chm
  kernel                            text    html    latex           chm
  myPalette                         text    html    latex   example chm
  plotProfile                       text    html    latex   example chm
  profileCGH                        text    html    latex   example chm
  snijders                          text    html    latex   example chm
  tkdaglad                          text    html    latex   example chm
  veltman                           text    html    latex   example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "x;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\GLAD.Rcheck\00_pkg_src\GLAD\chm\GLAD.chm

HHC4016: Warning: Cannot open "x;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:
  preparing package GLAD for lazy loading
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
  adding MD5 sums

* DONE (GLAD)