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Package 269/294HostnameOS / ArchBUILDCHECKBUILD BIN
snpMatrix 1.6.1
David Clayton
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/snpMatrix
Last Changed Rev: 34836 / Revision: 38965
Last Changed Date: 2008-10-22 08:29:57 -0700 (Wed, 22 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64 [ OK ] WARNINGS  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  WARNINGS  OK 
Package: snpMatrix
Version: 1.6.1
Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD build snpMatrix
StartedAt: 2009-04-18 17:29:08 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 17:31:08 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 120.6 seconds
RetCode: 0
Status: OK
PackageFile: snpMatrix_1.6.1.tar.gz
PackageFileSize: 7.426 MiB

Command output

* checking for file 'snpMatrix/DESCRIPTION' ... OK
* preparing 'snpMatrix':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.3-bioc/tmpdir/Rinst451645065


---------- Making package snpMatrix ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making adler32.d from adler32.c
making bind.d from bind.c
making compress.d from compress.c
making covwin.d from covwin.c
making crc32.d from crc32.c
making deflate.d from deflate.c
making force_hom.d from force_hom.c
making glm_test.d from glm_test.c
making glm_test_R.d from glm_test_R.c
making gzio.d from gzio.c
making hash_index.d from hash_index.c
making ibs.d from ibs.c
making imputation.d from imputation.c
making in.d from in.c
making infback.d from infback.c
making inffast.d from inffast.c
making inflate.d from inflate.c
making inftrees.d from inftrees.c
making input.d from input.c
making inputNew.d from inputNew.c
making input_unsorted.d from input_unsorted.c
making invert.d from invert.c
making ld_graphic_eps.d from ld_graphic_eps.c
making ld_with.d from ld_with.c
making mla.d from mla.c
making outdata.d from outdata.c
making pairwise_linkage.d from pairwise_linkage.c
making read_chiamo.d from read_chiamo.c
making read_hapmap.d from read_hapmap.c
making read_pedfile.d from read_pedfile.c
making read_signals.d from read_signals.c
making readbed.d from readbed.c
making readped.d from readped.c
making sdfpw.d from sdfpw.c
making single_snp_tests.d from single_snp_tests.c
making snp_summary.d from snp_summary.c
making snpmpy.d from snpmpy.c
making solve_cubic.d from solve_cubic.c
making solve_quadratic.d from solve_quadratic.c
making structure.d from structure.c
making switch.d from switch.c
making tdt.d from tdt.c
making trees.d from trees.c
making uncompr.d from uncompr.c
making zutil.d from zutil.c
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c adler32.c -o adler32.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c bind.c -o bind.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c compress.c -o compress.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c covwin.c -o covwin.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c crc32.c -o crc32.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c deflate.c -o deflate.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c force_hom.c -o force_hom.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_score_test':
glm_test.c:326: warning: unused variable 'test'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:672: warning: unused variable 'err'
glm_test_R.c: In function 'pool2_glm':
glm_test_R.c:867: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:867: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RV' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RU' may be used uninitialized in this function
glm_test_R.c: In function 'snp_lhs_score':
glm_test_R.c:175: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:175: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:285: warning: 'i' may be used uninitialized in this function
glm_test_R.c:205: warning: 'V' may be used uninitialized in this function
glm_test_R.c:205: warning: 'U' may be used uninitialized in this function
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:468: warning: 'Rule_names' may be used uninitialized in this function
glm_test_R.c:592: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:592: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:592: warning: 'TestNames' may be used uninitialized in this function
glm_test_R.c:674: warning: 'len' may be used uninitialized in this function
glm_test_R.c:651: warning: 'Snames' may be used uninitialized in this function
glm_test_R.c:651: warning: 'V' may be used uninitialized in this function
glm_test_R.c:651: warning: 'U' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c gzio.c -o gzio.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c hash_index.c -o hash_index.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c ibs.c -o ibs.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c imputation.c -o imputation.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c in.c -o in.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c infback.c -o infback.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c inffast.c -o inffast.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c inflate.c -o inflate.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c inftrees.c -o inftrees.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c input.c -o input.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c inputNew.c -o inputNew.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c input_unsorted.c -o input_unsorted.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c invert.c -o invert.o
invert.c: In function 'syminv':
invert.c:63: warning: unused variable 'nn'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c ld_with.c -o ld_with.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c mla.c -o mla.o
mla.c: In function 'wsum':
mla.c:154: warning: unused variable 'i'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c outdata.c -o outdata.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c pairwise_linkage.c -o pairwise_linkage.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c read_chiamo.c -o read_chiamo.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c read_hapmap.c -o read_hapmap.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c read_pedfile.c -o read_pedfile.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c read_signals.c -o read_signals.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c readbed.c -o readbed.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c readped.c -o readped.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c sdfpw.c -o sdfpw.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c single_snp_tests.c -o single_snp_tests.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c snp_summary.c -o snp_summary.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c snpmpy.c -o snpmpy.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c solve_cubic.c -o solve_cubic.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c solve_quadratic.c -o solve_quadratic.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c structure.c -o structure.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c switch.c -o switch.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c tdt.c -o tdt.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c trees.c -o trees.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c uncompr.c -o uncompr.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c zutil.c -o zutil.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include  -i snpMatrix_res.rc -o snpMatrix_res.o
gcc  -std=gnu99  -shared -s  -o snpMatrix.dll snpMatrix.def adler32.o bind.o compress.o covwin.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o invert.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readbed.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o switch.o tdt.o trees.o uncompr.o zutil.o snpMatrix_res.o  -Le:/biocbld/bbs-2.3-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package snpMatrix for lazy loading
Loading required package: survival
Loading required package: splines
Creating a new generic function for "plot" in "snpMatrix"
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'snpMatrix'
     Formats: text html latex example chm 
  X.snp-class                       text    html    latex   example chm
  X.snp.matrix-class                text    html    latex   example chm
  chi.squared                       text    html    latex   example chm
  epsout.ld.snp                     text    html    latex   example chm
  families                          text    html    latex   example chm
  filter.rules                      text    html    latex   example chm
  for.exercise                      text    html    latex   example chm
  glm.test.control                  text    html    latex           chm
Note: removing empty section \references in file 'ibs.stats.Rd'
Note: removing empty section \seealso in file 'ibs.stats.Rd'
Note: removing empty section \references in file 'ibs.stats.Rd'
Note: removing empty section \seealso in file 'ibs.stats.Rd'
  ibs.stats                         text    html    latex   example chm
  ibsCount                          text    html    latex   example chm
  ibsDist                           text    html    latex   example chm
  imputation.maf                    text    html    latex   example chm
  impute.snps                       text    html    latex   example chm
  ld.snp                            text    html    latex   example chm
  ld.with                           text    html    latex   example chm
  misinherits                       text    html    latex   example chm
  pair.result.ld.snp                text    html    latex   example chm
  plot.snp.dprime                   text    html    latex   example chm
  pool                              text    html    latex   example chm
  pool2                             text    html    latex           chm
  qq.chisq                          text    html    latex   example chm
  read.HapMap.data                  text    html    latex   example chm
Note: removing empty section \examples in file 'read.pedfile.info.Rd'
Note: removing empty section \examples in file 'read.pedfile.info.Rd'
  read.pedfile.info                 text    html    latex           chm
Note: removing empty section \examples in file 'read.pedfile.map.Rd'
Note: removing empty section \examples in file 'read.pedfile.map.Rd'
  read.pedfile.map                  text    html    latex           chm
  read.plink                        text    html    latex           chm
Note: removing empty section \note in file 'read.snps.chiamo.Rd'
Note: removing empty section \note in file 'read.snps.chiamo.Rd'
  read.snps.chiamo                  text    html    latex   example chm
  read.snps.long                    text    html    latex           chm
  read.snps.long.old                text    html    latex           chm
  read.snps.pedfile                 text    html    latex           chm
Note: removing empty section \seealso in file 'read.wtccc.signals.Rd'
Note: removing empty section \seealso in file 'read.wtccc.signals.Rd'
  read.wtccc.signals                text    html    latex   example chm
  row.summary                       text    html    latex   example chm
WARNING: \code inside code block in file 'single.snp.tests.Rd'
WARNING: \code inside code block in file 'single.snp.tests.Rd'
  single.snp.tests                  text    html    latex   example chm
  snp-class                         text    html    latex   example chm
  snp.cbind                         text    html    latex   example chm
  snp.cor                           text    html    latex   example chm
  snp.dprime-class                  text    html    latex   example chm
  snp.imputation                    text    html    latex   example chm
  snp.lhs.tests                     text    html    latex   example chm
  snp.matrix-class                  text    html    latex   example chm
  snp.pre                           text    html    latex   example chm
  snp.reg.imputation-class          text    html    latex   example chm
  snp.rhs.tests                     text    html    latex   example chm
  snp.tests.glm-class               text    html    latex   example chm
  snp.tests.single-class            text    html    latex   example chm
  snpMatrix-internal                text    html    latex           chm
  snpMatrix-package                 text    html    latex           chm
  switch.alleles                    text    html    latex   example chm
  tdt.snp                           text    html    latex   example chm
  test.allele.switch                text    html    latex   example chm
  testdata                          text    html    latex   example chm
  write.snp.matrix                  text    html    latex           chm
Note: removing empty section \note in file 'wtccc.sample.list.Rd'
Note: removing empty section \examples in file 'wtccc.sample.list.Rd'
Note: removing empty section \note in file 'wtccc.sample.list.Rd'
Note: removing empty section \examples in file 'wtccc.sample.list.Rd'
  wtccc.sample.list                 text    html    latex           chm
  xxt                               text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.3-bioc\meat\snpMatrix\chm\snpMatrix.chm





Compile time: 0 minutes, 1 second

54	Topics

394	Local links

27	Internet links

1	Graphic





Created e:\biocbld\bbs-2.3-bioc\meat\snpMatrix\chm\snpMatrix.chm, 122,886 bytes

Compression decreased file by 144,784 bytes.

  adding MD5 sums

* DONE (snpMatrix)
* 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 'snpMatrix_1.6.1.tar.gz'