BioC 3.5: CHECK report for LEA on tokay2

Package: LEA

Version: 1.8.1

Command: rm -rf LEA.buildbin-libdir LEA.Rcheck && mkdir LEA.buildbin-libdir LEA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LEA.buildbin-libdir LEA_1.8.1.tar.gz >LEA.Rcheck\00install.out 2>&1 && cp LEA.Rcheck\00install.out LEA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=LEA.buildbin-libdir --install="check:LEA-install.out" --force-multiarch --no-vignettes --timings LEA_1.8.1.tar.gz

StartedAt: 2017-10-18 00:53:58 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:01:54 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 475.9 seconds

RetCode: 0

Status:  OK

CheckDir: LEA.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf LEA.buildbin-libdir LEA.Rcheck && mkdir LEA.buildbin-libdir LEA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LEA.buildbin-libdir LEA_1.8.1.tar.gz >LEA.Rcheck\00install.out 2>&1 && cp LEA.Rcheck\00install.out LEA-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=LEA.buildbin-libdir --install="check:LEA-install.out" --force-multiarch --no-vignettes --timings LEA_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LEA/DESCRIPTION' ... OK
* this is package 'LEA' version '1.8.1'
* 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 'LEA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking 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 ... OK
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions 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 'C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.buildbin-libdir/LEA/libs/i386/LEA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
main_LFMM        97.28   0.05   97.53
main_sNMF        18.69   5.27   27.54
zscores          16.31   0.02   16.36
adjusted_pvalues 15.07   0.01   15.41
pvalues          14.86   0.02   14.89
mlog10pvalues    14.11   0.01   14.12
readZscore        7.14   0.02    7.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
main_LFMM        71.38   0.04   74.40
main_sNMF        19.91   5.84   57.82
adjusted_pvalues 12.42   0.02   12.44
pvalues          11.64   0.00   11.64
zscores          11.47   0.00   11.46
mlog10pvalues    11.32   0.01   11.34
readZscore        5.88   0.03    5.91
* 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
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'LEA' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_LFMM.c -o R_LFMM.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_crossEntropy.c -o R_crossEntropy.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_createDataSet.c -o R_createDataSet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_sNMF.c -o R_sNMF.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_geno2lfmm.c -o R_geno2lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_lfmm2geno.c -o R_lfmm2geno.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_pca.c -o R_pca.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_ped2geno.c -o R_ped2geno.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_ped2lfmm.c -o R_ped2lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_vcf2geno.c -o R_vcf2geno.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_tracyWidom.c -o R_tracyWidom.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_LEA.c -o R_init_LEA.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bituint/bituint.c -o bituint/bituint.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bituint/calc_bituint.c -o bituint/calc_bituint.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bituint/slice_bituint.c -o bituint/slice_bituint.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bituint/thread_bituint.c -o bituint/thread_bituint.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c convert/ancestrymap.c -o convert/ancestrymap.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c convert/geno.c -o convert/geno.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c convert/ped.c -o convert/ped.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c convert/vcf2geno.c -o convert/vcf2geno.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c convert/geno2lfmm.c -o convert/geno2lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c convert/lfmm2geno.c -o convert/lfmm2geno.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c convert/register_convert.c -o convert/register_convert.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c createDataSet/error_cds.c -o createDataSet/error_cds.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c createDataSet/print_cds.c -o createDataSet/print_cds.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c createDataSet/register_cds.c -o createDataSet/register_cds.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io/io_data_double.c -o io/io_data_double.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io/io_data_float.c -o io/io_data_float.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io/io_data_int.c -o io/io_data_int.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io/io_error.c -o io/io_error.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io/io_tools.c -o io/io_tools.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io/print_bar.c -o io/print_bar.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/beta.c -o LFMM/beta.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/U.c -o LFMM/U.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/beta_k0.c -o LFMM/beta_k0.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/V.c -o LFMM/V.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/LFMM.c -o LFMM/LFMM.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c LFMM/thread_var.c -o LFMM/thread_var.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/cholesky.c -o matrix/cholesky.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/error_matrix.c -o matrix/error_matrix.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/normalize.c -o matrix/normalize.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/slice_matrix.c -o matrix/slice_matrix.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/data.c -o matrix/data.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/inverse.c -o matrix/inverse.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/rand.c -o matrix/rand.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/sylvester.c -o matrix/sylvester.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/diagonalize.c -o matrix/diagonalize.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/matrix.c -o matrix/matrix.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/random_projection.c -o matrix/random_projection.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix/thread_matrix.c -o matrix/thread_matrix.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nnlsm/sort.c -o nnlsm/sort.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pca/calc_cov.c -o pca/calc_cov.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pca/error_pca.c -o pca/error_pca.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pca/pca.c -o pca/pca.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pca/print_pca.c -o pca/print_pca.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pca/register_pca.c -o pca/register_pca.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/als.c -o sNMF/als.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/als_k1.c -o sNMF/als_k1.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/criteria.c -o sNMF/criteria.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/print_snmf.c -o sNMF/print_snmf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/sNMF.c -o sNMF/sNMF.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/thread_Q.c -o sNMF/thread_Q.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/als_F.c -o sNMF/als_F.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/als_Q.c -o sNMF/als_Q.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/error_snmf.c -o sNMF/error_snmf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/register_snmf.c -o sNMF/register_snmf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/thread_F.c -o sNMF/thread_F.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/beta_distribution.c -o stats/beta_distribution.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/gamma_density.c -o stats/gamma_density.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/ln_beta_function.c -o stats/ln_beta_function.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/beta_function.c -o stats/beta_function.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/gamma_distribution.c -o stats/gamma_distribution.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/student_t_distribution.c -o stats/student_t_distribution.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/factorial.c -o stats/factorial.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats/gamma_function.c -o stats/gamma_function.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o LEA.dll tmp.def R_LFMM.o R_crossEntropy.o R_createDataSet.o R_sNMF.o R_ancestrymap2geno.o R_ancestrymap2lfmm.o R_geno2lfmm.o R_lfmm2geno.o R_pca.o R_ped2geno.o R_ped2lfmm.o R_vcf2geno.o R_tracyWidom.o R_init_LEA.o bituint/bituint.o bituint/calc_bituint.o bituint/io_geno_bituint.o bituint/slice_bituint.o bituint/thread_bituint.o convert/ancestrymap.o convert/geno.o convert/ped.o convert/vcf2geno.o convert/geno2lfmm.o convert/lfmm2geno.o convert/register_convert.o createDataSet/createDataSet.o createDataSet/error_cds.o createDataSet/print_cds.o createDataSet/register_cds.o crossEntropy/crossEntropy.o crossEntropy/error_ce.o crossEntropy/print_ce.o crossEntropy/register_ce.o io/io_data_double.o io/io_data_float.o io/io_data_int.o io/io_error.o io/io_tools.o io/print_bar.o LFMM/beta.o LFMM/error_lfmm.o LFMM/lfmm_k0.o LFMM/slice_lfmm.o LFMM/U.o LFMM/beta_k0.o LFMM/lfmm_algo.o LFMM/print_lfmm.o LFMM/thread_lfmm.o LFMM/V.o LFMM/data_lfmm.o LFMM/LFMM.o LFMM/register_lfmm.o LFMM/thread_var.o matrix/cholesky.o matrix/error_matrix.o matrix/normalize.o matrix/slice_matrix.o matrix/data.o matrix/inverse.o matrix/rand.o matrix/sylvester.o matrix/diagonalize.o matrix/matrix.o matrix/random_projection.o matrix/thread_matrix.o nnlsm/blockpivot.o nnlsm/nnlsm.o nnlsm/solvenormaleqcomb.o nnlsm/sort.o pca/calc_cov.o pca/error_pca.o pca/pca.o pca/print_pca.o pca/register_pca.o sNMF/als.o sNMF/als_k1.o sNMF/criteria.o sNMF/print_snmf.o sNMF/sNMF.o sNMF/thread_Q.o sNMF/als_F.o sNMF/als_Q.o sNMF/error_snmf.o sNMF/register_snmf.o sNMF/thread_F.o sNMF/thread_snmf.o stats/beta_distribution.o stats/gamma_density.o stats/ln_beta_function.o stats/beta_function.o stats/gamma_distribution.o stats/ln_gamma_function.o stats/entire_incomplete_gamma_function.o stats/gamma_dist_tables.o stats/student_t_distribution.o stats/factorial.o stats/gamma_function.o tracyWidom/error_tracyWidom.o tracyWidom/register_tracyWidom.o tracyWidom/print_tracyWidom.o tracyWidom/tracyWidom.o -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.buildbin-libdir/LEA/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'LEA' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_LFMM.c -o R_LFMM.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_crossEntropy.c -o R_crossEntropy.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_createDataSet.c -o R_createDataSet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_sNMF.c -o R_sNMF.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_geno2lfmm.c -o R_geno2lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_lfmm2geno.c -o R_lfmm2geno.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_pca.c -o R_pca.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_ped2geno.c -o R_ped2geno.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_ped2lfmm.c -o R_ped2lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_vcf2geno.c -o R_vcf2geno.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_tracyWidom.c -o R_tracyWidom.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_LEA.c -o R_init_LEA.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bituint/bituint.c -o bituint/bituint.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bituint/calc_bituint.c -o bituint/calc_bituint.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bituint/slice_bituint.c -o bituint/slice_bituint.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bituint/thread_bituint.c -o bituint/thread_bituint.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c convert/ancestrymap.c -o convert/ancestrymap.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c convert/geno.c -o convert/geno.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c convert/ped.c -o convert/ped.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c convert/vcf2geno.c -o convert/vcf2geno.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c convert/geno2lfmm.c -o convert/geno2lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c convert/lfmm2geno.c -o convert/lfmm2geno.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c convert/register_convert.c -o convert/register_convert.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c createDataSet/error_cds.c -o createDataSet/error_cds.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c createDataSet/print_cds.c -o createDataSet/print_cds.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c createDataSet/register_cds.c -o createDataSet/register_cds.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io/io_data_double.c -o io/io_data_double.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io/io_data_float.c -o io/io_data_float.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io/io_data_int.c -o io/io_data_int.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io/io_error.c -o io/io_error.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io/io_tools.c -o io/io_tools.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io/print_bar.c -o io/print_bar.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/beta.c -o LFMM/beta.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/U.c -o LFMM/U.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/beta_k0.c -o LFMM/beta_k0.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/V.c -o LFMM/V.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/LFMM.c -o LFMM/LFMM.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c LFMM/thread_var.c -o LFMM/thread_var.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/cholesky.c -o matrix/cholesky.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/error_matrix.c -o matrix/error_matrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/normalize.c -o matrix/normalize.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/slice_matrix.c -o matrix/slice_matrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/data.c -o matrix/data.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/inverse.c -o matrix/inverse.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/rand.c -o matrix/rand.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/sylvester.c -o matrix/sylvester.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/diagonalize.c -o matrix/diagonalize.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/matrix.c -o matrix/matrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/random_projection.c -o matrix/random_projection.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix/thread_matrix.c -o matrix/thread_matrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nnlsm/sort.c -o nnlsm/sort.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pca/calc_cov.c -o pca/calc_cov.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pca/error_pca.c -o pca/error_pca.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pca/pca.c -o pca/pca.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pca/print_pca.c -o pca/print_pca.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pca/register_pca.c -o pca/register_pca.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/als.c -o sNMF/als.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/als_k1.c -o sNMF/als_k1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/criteria.c -o sNMF/criteria.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/print_snmf.c -o sNMF/print_snmf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/sNMF.c -o sNMF/sNMF.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/thread_Q.c -o sNMF/thread_Q.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/als_F.c -o sNMF/als_F.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/als_Q.c -o sNMF/als_Q.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/error_snmf.c -o sNMF/error_snmf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/register_snmf.c -o sNMF/register_snmf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/thread_F.c -o sNMF/thread_F.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/beta_distribution.c -o stats/beta_distribution.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/gamma_density.c -o stats/gamma_density.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/ln_beta_function.c -o stats/ln_beta_function.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/beta_function.c -o stats/beta_function.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/gamma_distribution.c -o stats/gamma_distribution.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/student_t_distribution.c -o stats/student_t_distribution.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/factorial.c -o stats/factorial.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats/gamma_function.c -o stats/gamma_function.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I.    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o LEA.dll tmp.def R_LFMM.o R_crossEntropy.o R_createDataSet.o R_sNMF.o R_ancestrymap2geno.o R_ancestrymap2lfmm.o R_geno2lfmm.o R_lfmm2geno.o R_pca.o R_ped2geno.o R_ped2lfmm.o R_vcf2geno.o R_tracyWidom.o R_init_LEA.o bituint/bituint.o bituint/calc_bituint.o bituint/io_geno_bituint.o bituint/slice_bituint.o bituint/thread_bituint.o convert/ancestrymap.o convert/geno.o convert/ped.o convert/vcf2geno.o convert/geno2lfmm.o convert/lfmm2geno.o convert/register_convert.o createDataSet/createDataSet.o createDataSet/error_cds.o createDataSet/print_cds.o createDataSet/register_cds.o crossEntropy/crossEntropy.o crossEntropy/error_ce.o crossEntropy/print_ce.o crossEntropy/register_ce.o io/io_data_double.o io/io_data_float.o io/io_data_int.o io/io_error.o io/io_tools.o io/print_bar.o LFMM/beta.o LFMM/error_lfmm.o LFMM/lfmm_k0.o LFMM/slice_lfmm.o LFMM/U.o LFMM/beta_k0.o LFMM/lfmm_algo.o LFMM/print_lfmm.o LFMM/thread_lfmm.o LFMM/V.o LFMM/data_lfmm.o LFMM/LFMM.o LFMM/register_lfmm.o LFMM/thread_var.o matrix/cholesky.o matrix/error_matrix.o matrix/normalize.o matrix/slice_matrix.o matrix/data.o matrix/inverse.o matrix/rand.o matrix/sylvester.o matrix/diagonalize.o matrix/matrix.o matrix/random_projection.o matrix/thread_matrix.o nnlsm/blockpivot.o nnlsm/nnlsm.o nnlsm/solvenormaleqcomb.o nnlsm/sort.o pca/calc_cov.o pca/error_pca.o pca/pca.o pca/print_pca.o pca/register_pca.o sNMF/als.o sNMF/als_k1.o sNMF/criteria.o sNMF/print_snmf.o sNMF/sNMF.o sNMF/thread_Q.o sNMF/als_F.o sNMF/als_Q.o sNMF/error_snmf.o sNMF/register_snmf.o sNMF/thread_F.o sNMF/thread_snmf.o stats/beta_distribution.o stats/gamma_density.o stats/ln_beta_function.o stats/beta_function.o stats/gamma_distribution.o stats/ln_gamma_function.o stats/entire_incomplete_gamma_function.o stats/gamma_dist_tables.o stats/student_t_distribution.o stats/factorial.o stats/gamma_function.o tracyWidom/error_tracyWidom.o tracyWidom/register_tracyWidom.o tracyWidom/print_tracyWidom.o tracyWidom/tracyWidom.o -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.buildbin-libdir/LEA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LEA' as LEA_1.8.1.zip
* DONE (LEA)

name	user	system	elapsed
G	0.17	0.03	0.20
Q	0.31	0.03	0.35
adjusted_pvalues	15.07	0.01	15.41
ancestrymap2geno	0.00	0.02	0.02
ancestrymap2lfmm	0	0	0
crossEntropy	0.21	0.00	0.20
geno2lfmm	0.04	0.00	0.05
lfmm2geno	0.05	0.00	0.04
main_LFMM	97.28	0.05	97.53
main_createDataSet	0.08	0.00	0.08
main_crossEntropyEstimation	0.17	0.00	0.17
main_pca	0.12	0.01	0.33
main_sNMF	18.69	5.27	27.54
main_tracyWidom	0.14	0.00	0.14
mlog10pvalues	14.11	0.01	14.12
ped2geno	0.00	0.02	0.02
ped2lfmm	0	0	0
pvalues	14.86	0.02	14.89
readEnv	0	0	0
readGeno	0.04	0.00	0.05
readLfmm	0.05	0.01	0.06
readZscore	7.14	0.02	7.16
vcf2geno	0.00	0.01	0.01
vcf2lfmm	0	0	0
writeEnv	0	0	0
writeGeno	0.05	0.00	0.05
writeLFMM	0.06	0.00	0.06
zscores	16.31	0.02	16.36

name	user	system	elapsed
G	0.20	0.01	0.22
Q	0.27	0.00	0.27
adjusted_pvalues	12.42	0.02	12.44
ancestrymap2geno	0	0	0
ancestrymap2lfmm	0.02	0.00	0.01
crossEntropy	0.25	0.00	0.25
geno2lfmm	0.05	0.00	0.05
lfmm2geno	0.04	0.00	0.05
main_LFMM	71.38	0.04	74.40
main_createDataSet	0.08	0.00	0.08
main_crossEntropyEstimation	0.14	0.02	0.16
main_pca	0.12	0.02	0.29
main_sNMF	19.91	5.84	57.82
main_tracyWidom	0.11	0.02	0.12
mlog10pvalues	11.32	0.01	11.34
ped2geno	0	0	0
ped2lfmm	0.02	0.00	0.02
pvalues	11.64	0.00	11.64
readEnv	0.02	0.00	0.02
readGeno	0.03	0.00	0.03
readLfmm	0.04	0.00	0.04
readZscore	5.88	0.03	5.91
vcf2geno	0	0	0
vcf2lfmm	0	0	0
writeEnv	0	0	0
writeGeno	0.04	0.00	0.04
writeLFMM	0.06	0.00	0.07
zscores	11.47	0.00	11.46