BioC 3.4: CHECK report for LEA on malbec1

Package: LEA

Version: 1.6.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings LEA_1.6.0.tar.gz

StartedAt: 2017-04-14 23:28:06 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:31:17 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 190.9 seconds

RetCode: 0

Status:  OK

CheckDir: LEA.Rcheck

Warnings: 0

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###
### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings LEA_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/LEA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LEA/DESCRIPTION’ ... OK
* this is package ‘LEA’ version ‘1.6.0’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
main_LFMM        82.428  0.024  82.512
main_sNMF        14.816  1.056  15.958
mlog10pvalues    13.344  0.004  13.355
pvalues          13.168  0.008  13.179
adjusted_pvalues 13.080  0.000  13.086
zscores          13.044  0.000  13.049
readZscore        6.820  0.000   6.823
* 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
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_LFMM.c -o R_LFMM.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_crossEntropy.c -o R_crossEntropy.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_createDataSet.c -o R_createDataSet.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_sNMF.c -o R_sNMF.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_geno2lfmm.c -o R_geno2lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_lfmm2geno.c -o R_lfmm2geno.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_pca.c -o R_pca.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_ped2geno.c -o R_ped2geno.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_ped2lfmm.c -o R_ped2lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_vcf2geno.c -o R_vcf2geno.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_tracyWidom.c -o R_tracyWidom.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_LEA.c -o R_init_LEA.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c bituint/bituint.c -o bituint/bituint.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c bituint/calc_bituint.c -o bituint/calc_bituint.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c bituint/slice_bituint.c -o bituint/slice_bituint.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c bituint/thread_bituint.c -o bituint/thread_bituint.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c convert/ancestrymap.c -o convert/ancestrymap.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c convert/geno.c -o convert/geno.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c convert/ped.c -o convert/ped.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c convert/vcf2geno.c -o convert/vcf2geno.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c convert/geno2lfmm.c -o convert/geno2lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c convert/lfmm2geno.c -o convert/lfmm2geno.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c convert/register_convert.c -o convert/register_convert.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c createDataSet/error_cds.c -o createDataSet/error_cds.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c createDataSet/print_cds.c -o createDataSet/print_cds.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c createDataSet/register_cds.c -o createDataSet/register_cds.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c io/io_data_double.c -o io/io_data_double.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c io/io_data_float.c -o io/io_data_float.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c io/io_data_int.c -o io/io_data_int.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c io/io_error.c -o io/io_error.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c io/io_tools.c -o io/io_tools.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c io/print_bar.c -o io/print_bar.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/beta.c -o LFMM/beta.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/U.c -o LFMM/U.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/beta_k0.c -o LFMM/beta_k0.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/V.c -o LFMM/V.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/LFMM.c -o LFMM/LFMM.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c LFMM/thread_var.c -o LFMM/thread_var.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/cholesky.c -o matrix/cholesky.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/error_matrix.c -o matrix/error_matrix.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/normalize.c -o matrix/normalize.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/slice_matrix.c -o matrix/slice_matrix.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/data.c -o matrix/data.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/inverse.c -o matrix/inverse.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/rand.c -o matrix/rand.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/sylvester.c -o matrix/sylvester.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/diagonalize.c -o matrix/diagonalize.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/matrix.c -o matrix/matrix.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/random_projection.c -o matrix/random_projection.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix/thread_matrix.c -o matrix/thread_matrix.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c nnlsm/sort.c -o nnlsm/sort.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c pca/calc_cov.c -o pca/calc_cov.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c pca/error_pca.c -o pca/error_pca.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c pca/pca.c -o pca/pca.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c pca/print_pca.c -o pca/print_pca.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c pca/register_pca.c -o pca/register_pca.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/als.c -o sNMF/als.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/als_k1.c -o sNMF/als_k1.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/criteria.c -o sNMF/criteria.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/print_snmf.c -o sNMF/print_snmf.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/sNMF.c -o sNMF/sNMF.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/thread_Q.c -o sNMF/thread_Q.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/als_F.c -o sNMF/als_F.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/als_Q.c -o sNMF/als_Q.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/error_snmf.c -o sNMF/error_snmf.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/register_snmf.c -o sNMF/register_snmf.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/thread_F.c -o sNMF/thread_F.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/beta_distribution.c -o stats/beta_distribution.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/gamma_density.c -o stats/gamma_density.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/ln_beta_function.c -o stats/ln_beta_function.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/beta_function.c -o stats/beta_function.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/gamma_distribution.c -o stats/gamma_distribution.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/student_t_distribution.c -o stats/student_t_distribution.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/factorial.c -o stats/factorial.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c stats/gamma_function.c -o stats/gamma_function.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -Wall -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/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/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/LEA.Rcheck/LEA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LEA)

name	user	system	elapsed
G	0.216	0.008	0.223
Q	0.116	0.004	0.121
adjusted_pvalues	13.080	0.000	13.086
ancestrymap2geno	0.000	0.000	0.003
ancestrymap2lfmm	0.000	0.000	0.002
crossEntropy	0.108	0.004	0.110
geno2lfmm	0.024	0.000	0.026
lfmm2geno	0.028	0.000	0.028
main_LFMM	82.428	0.024	82.512
main_createDataSet	0.036	0.004	0.043
main_crossEntropyEstimation	0.100	0.008	0.109
main_pca	0.148	0.012	0.163
main_sNMF	14.816	1.056	15.958
main_tracyWidom	0.028	0.000	0.029
mlog10pvalues	13.344	0.004	13.355
ped2geno	0.004	0.000	0.004
ped2lfmm	0.004	0.000	0.004
pvalues	13.168	0.008	13.179
readEnv	0.000	0.000	0.002
readGeno	0.028	0.000	0.028
readLfmm	0.064	0.012	0.078
readZscore	6.820	0.000	6.823
vcf2geno	0.004	0.000	0.007
vcf2lfmm	0.004	0.000	0.005
writeEnv	0.000	0.000	0.001
writeGeno	0.024	0.000	0.027
writeLFMM	0.080	0.000	0.079
zscores	13.044	0.000	13.049