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Package 90/251HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.1.0
Gregor Gorjanc
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsPed
Last Changed Rev: 28616 / Revision: 29143
Last Changed Date: 2007-11-09 11:11:24 -0800 (Fri, 09 Nov 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  ERROR 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  ERROR 
wellington Linux (openSUSE 10.3) / i686  OK  ERROR 
liverpool Windows Server 2003 R2 (32-bit) / x64 [ OK ] ERROR  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  ERROR  OK 
Package: GeneticsPed
Version: 1.1.0
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD build GeneticsPed
StartedAt: 2007-12-11 03:46:52 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:47:39 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 47.7 seconds
RetCode: 0
Status: OK
PackageFile: GeneticsPed_1.1.0.tar.gz
PackageFileSize: 286 KiB

Command output

* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* preparing 'GeneticsPed':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.2-bioc/tmpdir/Rinst535691763


---------- Making package GeneticsPed ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making sargolzaei.d from sargolzaei.c
making ainverse.d from ainverse.cc
making eibd.d from eibd.cc
making inbreed.d from inbreed.cc
making inverseAdditive.d from inverseAdditive.cc
making meuwissen.d from meuwissen.cc
making pedSort.d from pedSort.cc
making pedtemplate.d from pedtemplate.cc
making register.d from register.cc
making sortped.d from sortped.cc
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function 'sargolzaei':
sargolzaei.c:96: warning: comparison between pointer and integer
sargolzaei.c:19: warning: 'S' may be used uninitialized in this function
sargolzaei.c:19: warning: 'MIP' may be used uninitialized in this function
gfortran-sjlj   -O3  -c ggmatmult.f -o ggmatmult.o
gfortran-sjlj   -O3  -c gpi.f -o gpi.o
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c ainverse.cc -o ainverse.o
In file included from ../include/inbreed.h:21,
                 from ../include/ainverse.h:23,
                 from ainverse.cc:9:
../include/math_utilities.h: In function 'double dabs(double)':
../include/math_utilities.h:86: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double erfinv(double)':
../include/math_utilities.h:104: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double incomplete_beta(double, double, double)':
../include/math_utilities.h:170: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double betacf(double, double, double)':
../include/math_utilities.h:243: warning: deprecated conversion from string constant to 'char*'
ainverse.cc: In function 'void AddCoeff(EIBDMat&, Pedigree&, VecMap&)':
ainverse.cc:59: warning: deprecated conversion from string constant to 'char*'
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c eibd.cc -o eibd.o
eibd.cc: In member function 'void EIBDMember::Show()':
eibd.cc:90: warning: deprecated conversion from string constant to 'char*'
eibd.cc:93: warning: deprecated conversion from string constant to 'char*'
eibd.cc:97: warning: deprecated conversion from string constant to 'char*'
eibd.cc:99: warning: deprecated conversion from string constant to 'char*'
eibd.cc: In member function 'void EIBDMat::Show()':
eibd.cc:289: warning: deprecated conversion from string constant to 'char*'
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c inbreed.cc -o inbreed.o
In file included from ../include/inbreed.h:21,
                 from inbreed.cc:10:
../include/math_utilities.h: In function 'double dabs(double)':
../include/math_utilities.h:86: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double erfinv(double)':
../include/math_utilities.h:104: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double incomplete_beta(double, double, double)':
../include/math_utilities.h:170: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double betacf(double, double, double)':
../include/math_utilities.h:243: warning: deprecated conversion from string constant to 'char*'
inbreed.cc: In member function 'void AmatRow::Show()':
inbreed.cc:125: warning: deprecated conversion from string constant to 'char*'
inbreed.cc:128: warning: deprecated conversion from string constant to 'char*'
inbreed.cc:131: warning: deprecated conversion from string constant to 'char*'
inbreed.cc: In member function 'void Amat::Show()':
inbreed.cc:193: warning: deprecated conversion from string constant to 'char*'
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c inverseAdditive.cc -o inverseAdditive.o
In file included from ../include/inbreed.h:21,
                 from ../include/ainverse.h:23,
                 from inverseAdditive.cc:8:
../include/math_utilities.h: In function 'double dabs(double)':
../include/math_utilities.h:86: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double erfinv(double)':
../include/math_utilities.h:104: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double incomplete_beta(double, double, double)':
../include/math_utilities.h:170: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double betacf(double, double, double)':
../include/math_utilities.h:243: warning: deprecated conversion from string constant to 'char*'
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c meuwissen.cc -o meuwissen.o
In file included from ../include/inbreed.h:21,
                 from meuwissen.cc:5:
../include/math_utilities.h: In function 'double dabs(double)':
../include/math_utilities.h:86: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double erfinv(double)':
../include/math_utilities.h:104: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double incomplete_beta(double, double, double)':
../include/math_utilities.h:170: warning: deprecated conversion from string constant to 'char*'
../include/math_utilities.h: In function 'double betacf(double, double, double)':
../include/math_utilities.h:243: warning: deprecated conversion from string constant to 'char*'
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c pedSort.cc -o pedSort.o
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c pedtemplate.cc -o pedtemplate.o
pedtemplate.cc: In member function 'void TPed::ShowPed()':
pedtemplate.cc:428: warning: deprecated conversion from string constant to 'char*'
pedtemplate.cc:431: warning: deprecated conversion from string constant to 'char*'
pedtemplate.cc:437: warning: deprecated conversion from string constant to 'char*'
pedtemplate.cc:441: warning: deprecated conversion from string constant to 'char*'
pedtemplate.cc:445: warning: deprecated conversion from string constant to 'char*'
pedtemplate.cc:449: warning: deprecated conversion from string constant to 'char*'
pedtemplate.cc:454: warning: deprecated conversion from string constant to 'char*'
pedtemplate.cc: In member function 'void Pedigree::ShowPed()':
pedtemplate.cc:478: warning: deprecated conversion from string constant to 'char*'
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c register.cc -o register.o
In file included from ../include/../include/inbreed.h:21,
                 from ../include/meuwissen.h:9,
                 from register.cc:8:
../include/../include/math_utilities.h: In function 'double dabs(double)':
../include/../include/math_utilities.h:86: warning: deprecated conversion from string constant to 'char*'
../include/../include/math_utilities.h: In function 'double erfinv(double)':
../include/../include/math_utilities.h:104: warning: deprecated conversion from string constant to 'char*'
../include/../include/math_utilities.h: In function 'double incomplete_beta(double, double, double)':
../include/../include/math_utilities.h:170: warning: deprecated conversion from string constant to 'char*'
../include/../include/math_utilities.h: In function 'double betacf(double, double, double)':
../include/../include/math_utilities.h:243: warning: deprecated conversion from string constant to 'char*'
g++-sjlj   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c sortped.cc -o sortped.o
sortped.cc: In function 'void SortPed(Pedigree&, TPedVec&)':
sortped.cc:24: warning: deprecated conversion from string constant to 'char*'
sortped.cc:29: warning: deprecated conversion from string constant to 'char*'
sortped.cc:39: warning: deprecated conversion from string constant to 'char*'
sortped.cc:44: warning: deprecated conversion from string constant to 'char*'
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include  -i GeneticsPed_res.rc -o GeneticsPed_res.o
g++-sjlj   -shared -s  -o GeneticsPed.dll GeneticsPed.def sargolzaei.o ggmatmult.o gpi.o ainverse.o eibd.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sortped.o GeneticsPed_res.o  -Le:/biocbld/bbs-2.2-bioc/R/bin   -lgfortran -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package GeneticsPed for lazy loading
Loading required package: gdata
Loading required package: genetics
Loading required package: combinat

Attaching package: 'combinat'


	The following object(s) are masked from package:utils :

	 combn 

Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm

Attaching package: 'genetics'


	The following object(s) are masked from package:base :

	 %in%,
	 as.factor,
	 order 

  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'GeneticsPed'
     Formats: text html latex example chm 
  TDT                               text    html    latex   example chm
  check                             text    html    latex   example chm
  datasets                          text    html    latex   example chm
  extend                            text    html    latex   example chm
  family                            text    html    latex   example chm
  founder                           text    html    latex   example chm
  geneContribution                  text    html    latex   example chm
  generatePedigree                  text    html    latex   example chm
  generation                        text    html    latex   example chm
  gpi                               text    html    latex   example chm
  gpiUtil                           text    html    latex   example chm
  inbreeding                        text    html    latex   example chm
  model.matrix                      text    html    latex   example chm
  nIndividual                       text    html    latex   example chm
  pedigree                          text    html    latex   example chm
  prune                             text    html    latex   example chm
  relationshipAdditive              text    html    latex   example chm
  removeIndividual                  text    html    latex   example chm
  sort.pedigree                     text    html    latex   example chm
  summary.pedigree                  text    html    latex   example chm
  undocumented                      text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.2-bioc\meat\GeneticsPed\chm\GeneticsPed.chm





Compile time: 0 minutes, 0 seconds

22	Topics

103	Local links

13	Internet links

1	Graphic





Created e:\biocbld\bbs-2.2-bioc\meat\GeneticsPed\chm\GeneticsPed.chm, 55,366 bytes

Compression decreased file by 47,005 bytes.

  adding MD5 sums

* DONE (GeneticsPed)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'GeneticsPed_1.1.0.tar.gz'