LEA 1.7.0
Eric Frichot
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LEA | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LEA_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LEA/DESCRIPTION’ ... OK
* this is package ‘LEA’ version ‘1.7.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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 73.229 0.100 76.505
main_sNMF 17.914 2.527 21.157
pvalues 11.168 0.018 11.188
adjusted_pvalues 10.755 0.018 12.625
mlog10pvalues 10.647 0.019 10.712
zscores 10.195 0.015 10.211
readZscore 5.502 0.011 5.716
* 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_LFMM.c -o R_LFMM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_crossEntropy.c -o R_crossEntropy.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_createDataSet.c -o R_createDataSet.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_sNMF.c -o R_sNMF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_geno2lfmm.c -o R_geno2lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_lfmm2geno.c -o R_lfmm2geno.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_pca.c -o R_pca.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_ped2geno.c -o R_ped2geno.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_ped2lfmm.c -o R_ped2lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_vcf2geno.c -o R_vcf2geno.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_tracyWidom.c -o R_tracyWidom.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_init_LEA.c -o R_init_LEA.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bituint/bituint.c -o bituint/bituint.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bituint/calc_bituint.c -o bituint/calc_bituint.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bituint/slice_bituint.c -o bituint/slice_bituint.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bituint/thread_bituint.c -o bituint/thread_bituint.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c convert/ancestrymap.c -o convert/ancestrymap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c convert/geno.c -o convert/geno.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c convert/ped.c -o convert/ped.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c convert/vcf2geno.c -o convert/vcf2geno.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c convert/geno2lfmm.c -o convert/geno2lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c convert/lfmm2geno.c -o convert/lfmm2geno.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c convert/register_convert.c -o convert/register_convert.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c createDataSet/error_cds.c -o createDataSet/error_cds.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c createDataSet/print_cds.c -o createDataSet/print_cds.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c createDataSet/register_cds.c -o createDataSet/register_cds.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c io/io_data_double.c -o io/io_data_double.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c io/io_data_float.c -o io/io_data_float.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c io/io_data_int.c -o io/io_data_int.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c io/io_error.c -o io/io_error.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c io/io_tools.c -o io/io_tools.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c io/print_bar.c -o io/print_bar.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/beta.c -o LFMM/beta.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/U.c -o LFMM/U.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/beta_k0.c -o LFMM/beta_k0.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/V.c -o LFMM/V.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/LFMM.c -o LFMM/LFMM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c LFMM/thread_var.c -o LFMM/thread_var.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/cholesky.c -o matrix/cholesky.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/error_matrix.c -o matrix/error_matrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/normalize.c -o matrix/normalize.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/slice_matrix.c -o matrix/slice_matrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/data.c -o matrix/data.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/inverse.c -o matrix/inverse.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/rand.c -o matrix/rand.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/sylvester.c -o matrix/sylvester.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/diagonalize.c -o matrix/diagonalize.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/matrix.c -o matrix/matrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/random_projection.c -o matrix/random_projection.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrix/thread_matrix.c -o matrix/thread_matrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c nnlsm/sort.c -o nnlsm/sort.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pca/calc_cov.c -o pca/calc_cov.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pca/error_pca.c -o pca/error_pca.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pca/pca.c -o pca/pca.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pca/print_pca.c -o pca/print_pca.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pca/register_pca.c -o pca/register_pca.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/als.c -o sNMF/als.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/als_k1.c -o sNMF/als_k1.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/criteria.c -o sNMF/criteria.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/print_snmf.c -o sNMF/print_snmf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/sNMF.c -o sNMF/sNMF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/thread_Q.c -o sNMF/thread_Q.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/als_F.c -o sNMF/als_F.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/als_Q.c -o sNMF/als_Q.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/error_snmf.c -o sNMF/error_snmf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/register_snmf.c -o sNMF/register_snmf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/thread_F.c -o sNMF/thread_F.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/beta_distribution.c -o stats/beta_distribution.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/gamma_density.c -o stats/gamma_density.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/ln_beta_function.c -o stats/ln_beta_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/beta_function.c -o stats/beta_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/gamma_distribution.c -o stats/gamma_distribution.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/student_t_distribution.c -o stats/student_t_distribution.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/factorial.c -o stats/factorial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stats/gamma_function.c -o stats/gamma_function.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o
clang -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 -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/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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)