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Package 2/233HostnameOS / ArchBUILDCHECKBUILD BIN
aCGH 1.12.0
Jane Fridlyand
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/aCGH
Last Changed Rev: 28558 / Revision: 30966
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 
Package: aCGH
Version: 1.12.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD INSTALL --build --library=aCGH.buildbin-libdir aCGH_1.12.0.tar.gz
StartedAt: 2008-04-09 22:40:54 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 22:42:20 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 86.0 seconds
RetCode: 0
Status: OK
PackageFile: aCGH_1.12.0.zip
PackageFileSize: 6.085 MiB

Command output

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/aCGH.buildbin-libdir

Using auto-selected zip options 'aCGH-ZIPDATA=zip aCGH-HELP=ziponly'

---------- 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
  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
  zipping help files
HHC5012: Error: Cannot create a temporary file in your TEMP path.

HHC4016: Warning: Cannot open "gram Files\Affymetrix\GDAC NetAffx;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\R.INSTALL.4508\aCGH\chm\aCGH.chm



HHC4016: Warning: Cannot open "gram Files\Affymetrix\GDAC NetAffx;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

packaged installation of package 'aCGH' as aCGH_1.12.0.zip
* DONE (aCGH)