BioC 3.2: CHECK report for LEA on perceval

Package: LEA

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LEA_1.1.0.tar.gz

StartedAt: 2015-08-24 02:08:36 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:12:28 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 232.0 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_1.1.0.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 (2015-08-14 r69078)
* 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 ‘1.1.0’
* 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 ... [11s/12s] 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 ... [169s/192s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
main_LFMM     90.124  0.100  90.262
main_sNMF     23.021  3.729  30.221
mlog10pvalues 14.320  0.059  22.307
pvalues       14.298  0.079  21.894
zscores       14.261  0.046  16.078
readZscore     7.130  0.025   8.731
* 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	0.240	0.018	0.259
Q	0.176	0.021	0.197
ancestrymap2geno	0.005	0.001	0.007
ancestrymap2lfmm	0.005	0.001	0.007
crossEntropy	0.151	0.012	0.164
geno2lfmm	0.030	0.002	0.033
lfmm2geno	0.031	0.003	0.034
main_LFMM	90.124	0.100	90.262
main_createDataSet	0.025	0.001	0.027
main_crossEntropyEstimation	0.083	0.006	0.089
main_pca	0.066	0.008	0.074
main_sNMF	23.021	3.729	30.221
main_tracyWidom	0.041	0.006	0.105
mlog10pvalues	14.320	0.059	22.307
ped2geno	0.005	0.002	0.011
ped2lfmm	0.005	0.001	0.006
pvalues	14.298	0.079	21.894
readEnv	0.005	0.001	0.005
readGeno	0.039	0.002	0.067
readLfmm	0.071	0.003	0.137
readZscore	7.130	0.025	8.731
vcf2geno	0.005	0.002	0.017
vcf2lfmm	0.005	0.001	0.007
writeEnv	0.002	0.000	0.002
writeGeno	0.040	0.001	0.042
writeLFMM	0.079	0.001	0.086
zscores	14.261	0.046	16.078