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BUILD BIN report for LEA on celaya2

This page was generated on 2020-01-16 13:41:34 -0500 (Thu, 16 Jan 2020).

Package 895/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LEA 2.9.0
Eric Frichot , Olivier Francois
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/LEA
Branch: master
Last Commit: d70849d
Last Changed Date: 2019-10-29 13:39:05 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: LEA
Version: 2.9.0
Command: rm -rf LEA.buildbin-libdir && mkdir LEA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh LEA_2.9.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R LEA.buildbin-libdir
StartedAt: 2020-01-16 11:11:26 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 11:11:54 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 27.8 seconds
RetCode: 0
Status:  OK 
PackageFile: LEA_2.9.0.tgz
PackageFileSize: 682.1 KiB

Command output

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###
### Running command:
###
###   rm -rf LEA.buildbin-libdir && mkdir LEA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh LEA_2.9.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R LEA.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=LEA.buildbin-libdir LEA_2.9.0.tar.gz'
>>>>>>> 

* installing *source* package ‘LEA’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_LFMM.c -o R_LFMM.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_crossEntropy.c -o R_crossEntropy.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_createDataSet.c -o R_createDataSet.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_sNMF.c -o R_sNMF.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_geno2lfmm.c -o R_geno2lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_lfmm2geno.c -o R_lfmm2geno.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_pca.c -o R_pca.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ped2geno.c -o R_ped2geno.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ped2lfmm.c -o R_ped2lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_vcf2geno.c -o R_vcf2geno.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_tracyWidom.c -o R_tracyWidom.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_LEA.c -o R_init_LEA.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/bituint.c -o bituint/bituint.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/calc_bituint.c -o bituint/calc_bituint.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/slice_bituint.c -o bituint/slice_bituint.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/thread_bituint.c -o bituint/thread_bituint.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/ancestrymap.c -o convert/ancestrymap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/geno.c -o convert/geno.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/ped.c -o convert/ped.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/vcf2geno.c -o convert/vcf2geno.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/geno2lfmm.c -o convert/geno2lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/lfmm2geno.c -o convert/lfmm2geno.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/register_convert.c -o convert/register_convert.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c createDataSet/error_cds.c -o createDataSet/error_cds.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c createDataSet/print_cds.c -o createDataSet/print_cds.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c createDataSet/register_cds.c -o createDataSet/register_cds.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_data_double.c -o io/io_data_double.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_data_float.c -o io/io_data_float.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_data_int.c -o io/io_data_int.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_error.c -o io/io_error.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_tools.c -o io/io_tools.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/print_bar.c -o io/print_bar.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/beta.c -o LFMM/beta.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/U.c -o LFMM/U.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/beta_k0.c -o LFMM/beta_k0.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/V.c -o LFMM/V.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/LFMM.c -o LFMM/LFMM.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/thread_var.c -o LFMM/thread_var.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/cholesky.c -o matrix/cholesky.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/error_matrix.c -o matrix/error_matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/normalize.c -o matrix/normalize.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/slice_matrix.c -o matrix/slice_matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/data.c -o matrix/data.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/inverse.c -o matrix/inverse.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/rand.c -o matrix/rand.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/sylvester.c -o matrix/sylvester.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/diagonalize.c -o matrix/diagonalize.o
matrix/diagonalize.c:61:35: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
                if (val[k] < 0 && abs(val[k]) < 1e-10)
                                  ^
matrix/diagonalize.c:61:35: note: use function 'fabs' instead
                if (val[k] < 0 && abs(val[k]) < 1e-10)
                                  ^~~
                                  fabs
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/matrix.c -o matrix/matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/random_projection.c -o matrix/random_projection.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/thread_matrix.c -o matrix/thread_matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c nnlsm/sort.c -o nnlsm/sort.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/calc_cov.c -o pca/calc_cov.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/error_pca.c -o pca/error_pca.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/pca.c -o pca/pca.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/print_pca.c -o pca/print_pca.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/register_pca.c -o pca/register_pca.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/als.c -o sNMF/als.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/als_k1.c -o sNMF/als_k1.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/criteria.c -o sNMF/criteria.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/print_snmf.c -o sNMF/print_snmf.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/sNMF.c -o sNMF/sNMF.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/thread_Q.c -o sNMF/thread_Q.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/als_F.c -o sNMF/als_F.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/als_Q.c -o sNMF/als_Q.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/error_snmf.c -o sNMF/error_snmf.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/register_snmf.c -o sNMF/register_snmf.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/thread_F.c -o sNMF/thread_F.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/beta_distribution.c -o stats/beta_distribution.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/gamma_density.c -o stats/gamma_density.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/ln_beta_function.c -o stats/ln_beta_function.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/beta_function.c -o stats/beta_function.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/gamma_distribution.c -o stats/gamma_distribution.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -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.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/student_t_distribution.c -o stats/student_t_distribution.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/factorial.c -o stats/factorial.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/gamma_function.c -o stats/gamma_function.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -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/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/LEA.buildbin-libdir/00LOCK-LEA/00new/LEA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LEA)


>>>>>>> 
>>>>>>> FIXING LINKS FOR LEA.buildbin-libdir/LEA/libs//LEA.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "LEA.buildbin-libdir/LEA/libs//LEA.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "LEA.buildbin-libdir/LEA/libs//LEA.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "LEA.buildbin-libdir/LEA/libs//LEA.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "LEA.buildbin-libdir/LEA/libs//LEA.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "LEA.buildbin-libdir/LEA/libs//LEA.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "LEA.buildbin-libdir/LEA/libs//LEA.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "LEA.buildbin-libdir/LEA/libs//LEA.so"