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BioC 2.13: CHECK report for snpStats on moscato1

This page was generated on 2014-04-05 09:49:39 -0700 (Sat, 05 Apr 2014).

Package 672/750HostnameOS / ArchBUILDCHECKBUILD BIN
snpStats 1.12.0
David Clayton
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/snpStats
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: snpStats
Version: 1.12.0
Command: rm -rf snpStats.buildbin-libdir && mkdir snpStats.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=snpStats.buildbin-libdir snpStats_1.12.0.tar.gz >snpStats-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=snpStats.buildbin-libdir --install="check:snpStats-install.out" --force-multiarch --no-vignettes --timings snpStats_1.12.0.tar.gz && mv snpStats.buildbin-libdir/* snpStats.Rcheck/ && rmdir snpStats.buildbin-libdir
StartedAt: 2014-04-05 06:51:02 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 06:54:48 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 225.7 seconds
RetCode: 0
Status:  OK  
CheckDir: snpStats.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/snpStats.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snpStats/DESCRIPTION' ... OK
* this is package 'snpStats' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'snpStats' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    2.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'survival' 'Matrix'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
Package in Depends field not imported from: 'Matrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .Last.lib will not be used unless it is exported
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.13-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/i386/snpStats.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/x64/snpStats.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/i386/snpStats.dll':
  Found non-API call to R: 'R_data_class'
File 'D:/biocbld/bbs-2.13-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/x64/snpStats.dll':
  Found non-API call to R: 'R_data_class'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'data-input-vignette.Rnw', 'differences.Rnw',
  'imputation-vignette.Rnw', 'ld-vignette.Rnw', 'pca-vignette.Rnw',
  'snpStats-vignette.Rnw', 'tdt-vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [20s] OK
** running examples for arch 'x64' ... [17s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 6 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/snpStats.Rcheck/00check.log'
for details.

snpStats.Rcheck/00install.out:


install for i386

* installing *source* package 'snpStats' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Runcertain.c -o Runcertain.o
Runcertain.c: In function 'Rpost2g':
Runcertain.c:80:38: warning: operation on 'pij' may be undefined [-Wsequence-point]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c adler32.c -o adler32.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bind.c -o bind.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c compress.c -o compress.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c count_gt.c -o count_gt.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c covwin.c -o covwin.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crc32.c -o crc32.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c deflate.c -o deflate.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c force_hom.c -o force_hom.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c fst.c -o fst.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_fit':
glm_test.c:261:26: warning: 'dfr' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:370:8: warning: variable 'testname' set but not used [-Wunused-but-set-variable]
glm_test_R.c: In function 'snp_rhs_estimate':
glm_test_R.c:1520:11: warning: variable 'Uc' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c gzclose.c -o gzclose.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c gzlib.c -o gzlib.o
gzlib.c: In function 'gz_error':
gzlib.c:518:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c gzread.c -o gzread.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c gzwrite.c -o gzwrite.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c hash_index.c -o hash_index.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c hphase.c -o hphase.o
hphase.c: In function 'emhap':
hphase.c:261:9: warning: variable 'ipfault' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c imputation.c -o imputation.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c in.c -o in.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c infback.c -o infback.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c inffast.c -o inffast.o
inffast.c: In function 'inflate_fast':
inffast.c:324:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c inflate.c -o inflate.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c inftrees.c -o inftrees.o
inftrees.c: In function 'inflate_table':
inftrees.c:330:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c input.c -o input.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c invert.c -o invert.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ipf.c -o ipf.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ld.c -o ld.o
ld.c: In function 'set_arrays':
ld.c:334:10: warning: unused variable 'OR' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c misc.c -o misc.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mla.c -o mla.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mvphenotype.c -o mvphenotype.o
mvphenotype.c: In function 'mvphen':
mvphenotype.c:190:7: warning: variable 'ifX' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c outdata.c -o outdata.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c plink.c -o plink.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_uncertain.c -o read_uncertain.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c readped.c -o readped.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c single_snp_tests.c -o single_snp_tests.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c snp_summary.c -o snp_summary.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c snpmpy.c -o snpmpy.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c solve_cubic.c -o solve_cubic.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c structure.c -o structure.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c switch.c -o switch.o
switch.c: In function 'test_switch':
switch.c:52:10: warning: variable 'fg' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c tdt.c -o tdt.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c trees.c -o trees.o
trees.c: In function '_tr_init':
trees.c:410:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_stored_block':
trees.c:883:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_align':
trees.c:919:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_flush_block':
trees.c:1020:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_tally':
trees.c:1071:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: At top level:
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c uncertain.c -o uncertain.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c uncompr.c -o uncompr.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c zutil.c -o zutil.o
zutil.c: In function 'zcalloc':
zutil.c:308:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
zutil.c: In function 'zcfree':
zutil.c:316:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m32 -shared -s -static-libgcc -o snpStats.dll tmp.def Runcertain.o adler32.o bind.o compress.o count_gt.o covwin.o crc32.o deflate.o force_hom.o fst.o glm_test.o glm_test_R.o gzclose.o gzlib.o gzread.o gzwrite.o hash_index.o hphase.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o switch.o tdt.o trees.o uncertain.o uncompr.o zutil.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'snpStats'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'snpStats' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Runcertain.c -o Runcertain.o
Runcertain.c: In function 'Rpost2g':
Runcertain.c:80:38: warning: operation on 'pij' may be undefined [-Wsequence-point]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c adler32.c -o adler32.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bind.c -o bind.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c compress.c -o compress.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c count_gt.c -o count_gt.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c covwin.c -o covwin.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crc32.c -o crc32.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c deflate.c -o deflate.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c force_hom.c -o force_hom.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c fst.c -o fst.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_fit':
glm_test.c:261:26: warning: 'dfr' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:370:8: warning: variable 'testname' set but not used [-Wunused-but-set-variable]
glm_test_R.c: In function 'snp_rhs_estimate':
glm_test_R.c:1520:11: warning: variable 'Uc' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c gzclose.c -o gzclose.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c gzlib.c -o gzlib.o
gzlib.c: In function 'gz_error':
gzlib.c:518:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c gzread.c -o gzread.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c gzwrite.c -o gzwrite.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c hash_index.c -o hash_index.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c hphase.c -o hphase.o
hphase.c: In function 'emhap':
hphase.c:261:9: warning: variable 'ipfault' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c imputation.c -o imputation.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c in.c -o in.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c infback.c -o infback.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c inffast.c -o inffast.o
inffast.c: In function 'inflate_fast':
inffast.c:324:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c inflate.c -o inflate.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c inftrees.c -o inftrees.o
inftrees.c: In function 'inflate_table':
inftrees.c:330:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c input.c -o input.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c invert.c -o invert.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ipf.c -o ipf.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ld.c -o ld.o
ld.c: In function 'set_arrays':
ld.c:334:10: warning: unused variable 'OR' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c misc.c -o misc.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mla.c -o mla.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mvphenotype.c -o mvphenotype.o
mvphenotype.c: In function 'mvphen':
mvphenotype.c:190:7: warning: variable 'ifX' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c outdata.c -o outdata.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c plink.c -o plink.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_uncertain.c -o read_uncertain.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c readped.c -o readped.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c single_snp_tests.c -o single_snp_tests.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c snp_summary.c -o snp_summary.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c snpmpy.c -o snpmpy.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c solve_cubic.c -o solve_cubic.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c structure.c -o structure.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c switch.c -o switch.o
switch.c: In function 'test_switch':
switch.c:52:10: warning: variable 'fg' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c tdt.c -o tdt.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c trees.c -o trees.o
trees.c: In function '_tr_init':
trees.c:410:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_stored_block':
trees.c:883:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_align':
trees.c:919:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_flush_block':
trees.c:1020:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_tally':
trees.c:1071:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: At top level:
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c uncertain.c -o uncertain.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c uncompr.c -o uncompr.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c zutil.c -o zutil.o
zutil.c: In function 'zcalloc':
zutil.c:308:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
zutil.c: In function 'zcfree':
zutil.c:316:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m64 -shared -s -static-libgcc -o snpStats.dll tmp.def Runcertain.o adler32.o bind.o compress.o count_gt.o covwin.o crc32.o deflate.o force_hom.o fst.o glm_test.o glm_test_R.o gzclose.o gzlib.o gzread.o gzwrite.o hash_index.o hphase.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o switch.o tdt.o trees.o uncertain.o uncompr.o zutil.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snpStats' as snpStats_1.12.0.zip
* DONE (snpStats)

snpStats.Rcheck/examples_i386/snpStats-Ex.timings:

nameusersystemelapsed
Fst1.090.051.14
GlmEstimates-class0.000.020.02
GlmTests-class000
ImputationRules-class0.020.000.01
SingleSnpTests-class000
SnpMatrix-class0.350.010.38
XSnpMatrix-class0.170.000.17
chi.squared0.170.000.30
families0.070.000.06
filter.rules000
for.exercise1.890.021.90
ibsCount0.760.000.76
ibsDist0.450.000.45
imputation.maf000
impute.snps2.320.082.40
ld0.350.010.36
mean2g0.170.000.17
misinherits0.070.010.09
mvtests000
plotUncertainty000
pool0.380.000.37
pp0.360.000.36
qq.chisq000
read.beagle0.010.000.02
read.impute000
read.long000
read.mach000
read.pedfile000
row.summary0.250.000.25
single.snp.tests0.170.000.19
sm.compare000
snp.cor0.860.000.86
snp.imputation1.760.051.81
snp.lhs.estimates0.590.010.60
snp.lhs.tests0.140.000.14
snp.pre.multiply0.140.000.14
snp.rhs.estimates0.140.030.17
snp.rhs.tests0.110.020.13
switch.alleles0.120.000.12
tdt.snp0.040.000.03
test.allele.switch0.230.000.24
testdata0.20.00.2
write.plink0.280.000.30
xxt0.720.010.73

snpStats.Rcheck/examples_x64/snpStats-Ex.timings:

nameusersystemelapsed
Fst0.780.030.81
GlmEstimates-class0.010.000.01
GlmTests-class000
ImputationRules-class000
SingleSnpTests-class0.020.000.02
SnpMatrix-class0.230.000.23
XSnpMatrix-class0.110.020.12
chi.squared0.110.000.11
families0.030.000.03
filter.rules000
for.exercise1.590.001.60
ibsCount1.030.021.04
ibsDist0.360.000.36
imputation.maf000
impute.snps1.840.061.90
ld0.240.010.26
mean2g0.100.020.11
misinherits0.080.000.08
mvtests000
plotUncertainty0.010.000.02
pool0.220.010.23
pp0.20.00.2
qq.chisq000
read.beagle000
read.impute000
read.long0.020.000.02
read.mach000
read.pedfile000
row.summary0.170.000.17
single.snp.tests0.110.020.13
sm.compare000
snp.cor0.720.000.71
snp.imputation1.810.091.91
snp.lhs.estimates0.500.040.53
snp.lhs.tests0.110.010.12
snp.pre.multiply0.140.000.14
snp.rhs.estimates0.150.000.16
snp.rhs.tests0.130.000.12
switch.alleles0.120.000.13
tdt.snp0.030.000.03
test.allele.switch0.220.020.23
testdata0.20.00.2
write.plink0.250.000.27
xxt0.730.010.75