BioC 3.2: CHECK report for LEA on perceval

Package: LEA

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LEA_1.2.0.tar.gz

StartedAt: 2015-11-10 06:22:09 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 06:26:45 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 275.7 seconds

RetCode: 0

Status:  OK

CheckDir: LEA.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LEA_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/LEA.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LEA/DESCRIPTION’ ... OK
* this is package ‘LEA’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘LEA’ can be installed ... [10s/10s] 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [233s/238s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
main_LFMM     117.987  0.105 118.163
main_sNMF      31.336  3.625  37.974
pvalues        24.729  0.043  25.436
mlog10pvalues  21.014  0.038  21.952
zscores        17.308  0.021  17.335
readZscore     14.201  0.030  15.407
* 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: OK

* installing *source* package ‘LEA’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_LFMM.c -o R_LFMM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_crossEntropy.c -o R_crossEntropy.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_createDataSet.c -o R_createDataSet.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_sNMF.c -o R_sNMF.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_geno2lfmm.c -o R_geno2lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_lfmm2geno.c -o R_lfmm2geno.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_pca.c -o R_pca.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_ped2geno.c -o R_ped2geno.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_ped2lfmm.c -o R_ped2lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_vcf2geno.c -o R_vcf2geno.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_tracyWidom.c -o R_tracyWidom.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_LEA.c -o R_init_LEA.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bituint/bituint.c -o bituint/bituint.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bituint/calc_bituint.c -o bituint/calc_bituint.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bituint/slice_bituint.c -o bituint/slice_bituint.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bituint/thread_bituint.c -o bituint/thread_bituint.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c convert/ancestrymap.c -o convert/ancestrymap.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c convert/geno.c -o convert/geno.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c convert/ped.c -o convert/ped.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c convert/vcf2geno.c -o convert/vcf2geno.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c convert/geno2lfmm.c -o convert/geno2lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c convert/lfmm2geno.c -o convert/lfmm2geno.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c convert/register_convert.c -o convert/register_convert.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c createDataSet/error_cds.c -o createDataSet/error_cds.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c createDataSet/print_cds.c -o createDataSet/print_cds.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c createDataSet/register_cds.c -o createDataSet/register_cds.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c io/io_data_double.c -o io/io_data_double.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c io/io_data_float.c -o io/io_data_float.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c io/io_data_int.c -o io/io_data_int.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c io/io_error.c -o io/io_error.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c io/io_tools.c -o io/io_tools.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c io/print_bar.c -o io/print_bar.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/beta.c -o LFMM/beta.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/U.c -o LFMM/U.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/beta_k0.c -o LFMM/beta_k0.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/V.c -o LFMM/V.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/LFMM.c -o LFMM/LFMM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LFMM/thread_var.c -o LFMM/thread_var.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/cholesky.c -o matrix/cholesky.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/error_matrix.c -o matrix/error_matrix.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/normalize.c -o matrix/normalize.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/slice_matrix.c -o matrix/slice_matrix.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/data.c -o matrix/data.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/inverse.c -o matrix/inverse.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/rand.c -o matrix/rand.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/sylvester.c -o matrix/sylvester.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/diagonalize.c -o matrix/diagonalize.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/matrix.c -o matrix/matrix.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/random_projection.c -o matrix/random_projection.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix/thread_matrix.c -o matrix/thread_matrix.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c nnlsm/sort.c -o nnlsm/sort.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pca/calc_cov.c -o pca/calc_cov.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pca/error_pca.c -o pca/error_pca.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pca/pca.c -o pca/pca.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pca/print_pca.c -o pca/print_pca.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pca/register_pca.c -o pca/register_pca.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/als.c -o sNMF/als.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/als_k1.c -o sNMF/als_k1.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/criteria.c -o sNMF/criteria.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/print_snmf.c -o sNMF/print_snmf.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/sNMF.c -o sNMF/sNMF.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/thread_Q.c -o sNMF/thread_Q.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/als_F.c -o sNMF/als_F.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/als_Q.c -o sNMF/als_Q.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/error_snmf.c -o sNMF/error_snmf.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/register_snmf.c -o sNMF/register_snmf.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/thread_F.c -o sNMF/thread_F.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/beta_distribution.c -o stats/beta_distribution.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/gamma_density.c -o stats/gamma_density.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/ln_beta_function.c -o stats/ln_beta_function.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/beta_function.c -o stats/beta_function.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/gamma_distribution.c -o stats/gamma_distribution.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/student_t_distribution.c -o stats/student_t_distribution.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/factorial.c -o stats/factorial.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c stats/gamma_function.c -o stats/gamma_function.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o LEA.so 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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/LEA.Rcheck/LEA/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘LEA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LEA)

name	user	system	elapsed
G	0.247	0.013	0.261
Q	0.192	0.015	0.207
ancestrymap2geno	0.006	0.001	0.007
ancestrymap2lfmm	0.004	0.002	0.006
crossEntropy	0.165	0.010	0.176
geno2lfmm	0.033	0.002	0.035
lfmm2geno	0.031	0.002	0.033
main_LFMM	117.987	0.105	118.163
main_createDataSet	0.045	0.001	0.046
main_crossEntropyEstimation	0.134	0.008	0.143
main_pca	0.100	0.009	0.110
main_sNMF	31.336	3.625	37.974
main_tracyWidom	0.063	0.006	0.069
mlog10pvalues	21.014	0.038	21.952
ped2geno	0.005	0.001	0.006
ped2lfmm	0.005	0.001	0.006
pvalues	24.729	0.043	25.436
readEnv	0.003	0.000	0.004
readGeno	0.065	0.002	0.070
readLfmm	0.117	0.005	0.143
readZscore	14.201	0.030	15.407
vcf2geno	0.009	0.002	0.011
vcf2lfmm	0.009	0.002	0.012
writeEnv	0.004	0.001	0.004
writeGeno	0.068	0.003	0.071
writeLFMM	0.118	0.002	0.119
zscores	17.308	0.021	17.335