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NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier
Package 87/238HostnameOSArchBUILDCHECKBUILD BIN

GeneticsPed

1.1.0

Gregor Gorjanc
Last Changed Date: 2007-04-24 11:31:42 -0700
Last Changed Rev: 24217
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
churchill Solaris 2.9 sparc  OK  OK 
lemming Windows Server 2003 (32-bit) x64  OK [ OK ]skipped
Package: GeneticsPed
Version: 1.1.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check GeneticsPed_1.1.0.tar.gz
RetCode: 0
Time: 58.2 seconds
Status: OK
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneticsPed' version '1.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneticsPed' 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 whether the name space 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
check.Pedigree: no visible global function definition for 'checkSex'
check.Pedigree: no visible global function definition for
  'checkDtBirth'
checkId: no visible global function definition for 'subjectNA'
codeUnit: no visible binding for global variable 'mapFactor'
* 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 ... OK
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating GeneticsPed-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/GeneticsPed.Rcheck/tests'
  Running 'doRUnit.R'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/GeneticsPed.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneticsPed-manual.tex ... OK
* checking GeneticsPed-manual.tex ... OK

GeneticsPed.Rcheck/00install.out:

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


---------- 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   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function `sargolzaei':
sargolzaei.c:62: warning: statement with no effect
sargolzaei.c:19: warning: 'S' might be used uninitialized in this function
sargolzaei.c:19: warning: 'MIP' might be used uninitialized in this function
sargolzaei.c:19: warning: 'N' might be used uninitialized in this function
g77 -O3 -Wall   -c ggmatmult.f -o ggmatmult.o
g77 -O3 -Wall   -c gpi.f -o gpi.o
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c ainverse.cc -o ainverse.o
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c eibd.cc -o eibd.o
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_tree.h: In member function `typename std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Link_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_copy(const std::_Rb_tree_node<_Val>*, std::_Rb_tree_node<_Val>*) [with _Key = unsigned int, _Val = std::pair<const unsigned int, EIBDMember>, _KeyOfValue = std::_Select1st<std::pair<const unsigned int, EIBDMember> >, _Compare = std::less<unsigned int>, _Alloc = std::allocator<std::pair<const unsigned int, EIBDMember> >]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_tree.h:1029: warning: '__top' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_tree.h:365: warning: '__tmp' might be used uninitialized in this function
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c inbreed.cc -o inbreed.o
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c inverseAdditive.cc -o inverseAdditive.o
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c meuwissen.cc -o meuwissen.o
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c pedSort.cc -o pedSort.o
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c pedtemplate.cc -o pedtemplate.o
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c register.cc -o register.o
g++   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O2   -c sortped.cc -o sortped.o
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h: In member function `void std::vector<_Tp, _Alloc>::_M_fill_insert(__gnu_cxx::__normal_iterator<typename _Alloc::pointer, std::vector<_Tp, _Alloc> >, size_t, const _Tp&) [with _Tp = std::string, _Alloc = std::allocator<std::string>]':
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/c++/3.4.5/bits/stl_uninitialized.h:82: warning: '__cur' might be used uninitialized in this function
windres -I d:/biocbld/bbs-2.1-bioc/R/include  -i GeneticsPed_res.rc -o GeneticsPed_res.o
g++  -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  -Ld:/biocbld/bbs-2.1-bioc/R/bin   -lg2c -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'GeneticsPed'
     Formats: text html latex example chm 
  Mrode                             text    html    latex   example chm
  TDT                               text    html    latex   example chm
  check                             text    html    latex   example chm
  codeUnit                          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
  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
  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 d:\biocbld\bbs-2.1-bioc\meat\GeneticsPed.Rcheck\00_pkg_src\GeneticsPed\chm\GeneticsPed.chm


Compile time: 0 minutes, 0 seconds
21	Topics
91	Local links
12	Internet links
1	Graphic


Created d:\biocbld\bbs-2.1-bioc\meat\GeneticsPed.Rcheck\00_pkg_src\GeneticsPed\chm\GeneticsPed.chm, 51,376 bytes
Compression decreased file by 40,580 bytes.
  preparing package GeneticsPed for lazy loading
Loading required package: gdata
Loading required package: MASS
  adding MD5 sums

* DONE (GeneticsPed)