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o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rgraphviz/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (Rgraphviz)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘png’ ...
** package ‘png’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   `libpng-config --cflags` -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read.c -o read.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   `libpng-config --cflags` -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c write.c -o write.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o png.so read.o write.o -lpng12 -lz -lm -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/png/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (png)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘FNN’ ...
** package ‘FNN’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ANN.cpp -o ANN.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c KNN_ANN.cpp -o KNN_ANN.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c KNN_correlation_distance.cpp -o KNN_correlation_distance.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c KNN_cover_test.cpp -o KNN_cover_test.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c KNN_cover_tree.cpp -o KNN_cover_tree.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c KNN_mutual_information.cpp -o KNN_mutual_information.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bd_fix_rad_search.cpp -o bd_fix_rad_search.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bd_pr_search.cpp -o bd_pr_search.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bd_search.cpp -o bd_search.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bd_tree.cpp -o bd_tree.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c brute.cpp -o brute.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kd_dump.cpp -o kd_dump.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kd_fix_rad_search.cpp -o kd_fix_rad_search.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kd_pr_search.cpp -o kd_pr_search.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kd_search.cpp -o kd_search.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kd_split.cpp -o kd_split.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kd_tree.cpp -o kd_tree.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kd_util.cpp -o kd_util.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c label_point.cpp -o label_point.o
g++  -I/usr/local/lib/R/include -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c perf.cpp -o perf.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o FNN.so ANN.o KNN_ANN.o KNN_correlation_distance.o KNN_cover_test.o KNN_cover_tree.o KNN_mutual_information.o bd_fix_rad_search.o bd_pr_search.o bd_search.o bd_tree.o brute.o kd_dump.o kd_fix_rad_search.o kd_pr_search.o kd_search.o kd_split.o kd_tree.o kd_util.o label_point.o perf.o -L/usr/local/lib/R/lib -lR
rm -f *.o core
installing to /usr/local/lib/R/site-library/FNN/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (FNN)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘minpack.lm’ ...
** package ‘minpack.lm’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -g -O2  -c chkder.f -o chkder.o
gfortran   -fpic  -g -O2  -c dogleg.f -o dogleg.o
gfortran   -fpic  -g -O2  -c dpmpar.f -o dpmpar.o
gfortran   -fpic  -g -O2  -c enorm.f -o enorm.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fcn_lmder.c -o fcn_lmder.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fcn_lmdif.c -o fcn_lmdif.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fcn_message.c -o fcn_message.o
gfortran   -fpic  -g -O2  -c fdjac2.f -o fdjac2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c get_element.c -o get_element.o
gfortran   -fpic  -g -O2  -c lmder.f -o lmder.o
gfortran   -fpic  -g -O2  -c lmdif.f -o lmdif.o
gfortran   -fpic  -g -O2  -c lmpar.f -o lmpar.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nls_lm.c -o nls_lm.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c prod.c -o prod.o
gfortran   -fpic  -g -O2  -c qform.f -o qform.o
gfortran   -fpic  -g -O2  -c qrfac.f -o qrfac.o
gfortran   -fpic  -g -O2  -c qrsolv.f -o qrsolv.o
gfortran   -fpic  -g -O2  -c r1mpyq.f -o r1mpyq.o
gfortran   -fpic  -g -O2  -c r1updt.f -o r1updt.o
gfortran   -fpic  -g -O2  -c rwupdt.f -o rwupdt.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c transpose.c -o transpose.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vector.c -o vector.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o minpack.lm.so chkder.o dogleg.o dpmpar.o enorm.o fcn_lmder.o fcn_lmdif.o fcn_message.o fdjac2.o get_element.o lmder.o lmdif.o lmpar.o nls_lm.o prod.o qform.o qrfac.o qrsolv.o r1mpyq.o r1updt.o rwupdt.o transpose.o vector.o -L/usr/local/lib/R/lib -lRlapack -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/minpack.lm/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (minpack.lm)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gmp’ ...
** package ‘gmp’ successfully unpacked and MD5 sums checked
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c apply.cc -o apply.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c biginteger.cc -o biginteger.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bigintegerR.cc -o bigintegerR.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bigmod.cc -o bigmod.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bigrational.cc -o bigrational.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bigrationalR.cc -o bigrationalR.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bigvec.cc -o bigvec.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bigvec_q.cc -o bigvec_q.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c extract_matrix.cc -o extract_matrix.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c factor.cc -o factor.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c factorize.cc -o factorize.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cc -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrix.cc -o matrix.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrixq.cc -o matrixq.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include/    -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c solve.cc -o solve.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o gmp.so apply.o biginteger.o bigintegerR.o bigmod.o bigrational.o bigrationalR.o bigvec.o bigvec_q.o extract_matrix.o factor.o factorize.o init.o matrix.o matrixq.o solve.o -L/usr/local/lib/ -lgmp -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/gmp/libs
** R
** data
** preparing package for lazy loading
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘gmp’
Creating a generic function for ‘which.min’ from package ‘base’ in package ‘gmp’
** help
*** installing help indices
** building package indices

Attaching package: ‘gmp’

The following objects are masked from ‘package:base’:

    %*%, apply, crossprod, matrix, tcrossprod

** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gmp)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking whether g++ version is sufficient... (4.9.2) yes
checking LAPACK_LIBS... fallback LAPACK from R 3.3.0 or later used
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloLapack.h
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppArmadillo.cpp -o RcppArmadillo.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastLm.cpp -o fastLm.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o init.o -L/usr/local/lib/R/lib -lRlapack -lopenblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (RcppArmadillo)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gtable’ ...
** package ‘gtable’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gtable)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ropls’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ropls)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘prettyunits’ ...
** package ‘prettyunits’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (prettyunits)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘pkgmaker’ ...
** package ‘pkgmaker’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Creating meta registry in package 'pkgmaker' ... OK
Creating registry 'extra_handler' in package 'pkgmaker' ... OK
Creating registry 'extra_action' in package 'pkgmaker' ... OK
Registering extra handler 'install.packages' [function] ... OK
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (pkgmaker)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘munsell’ ...
** package ‘munsell’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (munsell)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘shiny’ ...
** package ‘shiny’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (shiny)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘affy’ ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma2.c -o rma2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (affy)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘pcaMethods’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nipals.cpp -o nipals.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o pcaMethods.so RcppExports.o nipals.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/pcaMethods/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘loadings’ in package ‘pcaMethods’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (pcaMethods)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘class’ ...
** package ‘class’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c class.c -o class.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o class.so class.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (class)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c NCList.c -o NCList.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ranges_class.c -o Ranges_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coverage_methods.c -o coverage_methods.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inter_range_methods.c -o inter_range_methods.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (IRanges)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘foreach’ ...
** package ‘foreach’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (foreach)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gdata’ ...
** package ‘gdata’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gdata)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘reshape2’ ...
** package ‘reshape2’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c melt.cpp -o melt.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o reshape2.so RcppExports.o melt.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/reshape2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (reshape2)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘tibble’ ...
** package ‘tibble’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrixToDataFrame.cpp -o matrixToDataFrame.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o tibble.so RcppExports.o matrixToDataFrame.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/tibble/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (tibble)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘multtest’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rpack.c -o Rpack.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c VScount.c -o VScount.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c block_sampling_fixed.c -o block_sampling_fixed.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bootloop.c -o bootloop.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mt.c -o mt.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pairt_sampling.c -o pairt_sampling.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c random.c -o random.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sampling.c -o sampling.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sampling_fixed.c -o sampling_fixed.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stat_func.c -o stat_func.o
stat_func.c: In function ‘read_infile’:
stat_func.c:703:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fh, "%s", pdata->name);
   ^
stat_func.c:705:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fh, "%d", pdata->L+j);
     ^
stat_func.c:710:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fh, "%s", pdata->id[i]);
     ^
stat_func.c:714:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
       fscanf(fh, "%lg",&ftemp);
       ^
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stat_order.c -o stat_order.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/multtest/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
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (multtest)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘MassSpecWavelet’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c convolve2.c -o convolve2.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o MassSpecWavelet.so convolve2.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/MassSpecWavelet/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
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (MassSpecWavelet)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘sandwich’ ...
** package ‘sandwich’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (sandwich)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘kohonen’ ...
** package ‘kohonen’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c batch-supersom.cpp -o batch-supersom.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c distance-functions.cpp -o distance-functions.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kohonen_init.c -o kohonen_init.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c map.cpp -o map.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c neighbourhood-functions.cpp -o neighbourhood-functions.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pbatch-supersom.cpp -o pbatch-supersom.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c supersom.cpp -o supersom.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o kohonen.so RcppExports.o batch-supersom.o distance-functions.o kohonen_init.o map.o neighbourhood-functions.o pbatch-supersom.o supersom.o -fopenmp -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/kohonen/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (kohonen)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘RSQLite’ ...
** package ‘RSQLite’ successfully unpacked and MD5 sums checked
** libs
Makevars:21: Makevars.local: No such file or directory
touch "Makevars.local"
g++  -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteConnection.cpp -o SqliteConnection.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteDataFrame.cpp -o SqliteDataFrame.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteResult.cpp -o SqliteResult.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteResultImpl.cpp -o SqliteResultImpl.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c affinity.c -o affinity.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c connection.cpp -o connection.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c import-file.c -o import-file.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c result.cpp -o result.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rsqlite.cpp -o rsqlite.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sqlite3/extension-functions.c -o sqlite3/extension-functions.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sqlite3/sqlite3.c -o sqlite3/sqlite3.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RSQLite.so RcppExports.o SqliteConnection.o SqliteDataFrame.o SqliteResult.o SqliteResultImpl.o affinity.o connection.o import-file.o result.o rsqlite.o sqlite3/extension-functions.o sqlite3/sqlite3.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/RSQLite/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (RSQLite)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘edgeR’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_add_prior_count.cpp -o R_add_prior_count.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_add_repeat_matrices.cpp -o R_add_repeat_matrices.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_calculate_cpm.cpp -o R_calculate_cpm.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_check_counts.cpp -o R_check_counts.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_compute_apl.cpp -o R_compute_apl.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_levenberg.cpp -o R_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_loess_by_col.cpp -o R_loess_by_col.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_one_group.cpp -o R_one_group.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c add_prior.cpp -o add_prior.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c adj_coxreid.cpp -o adj_coxreid.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fmm_spline.c -o fmm_spline.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glm_levenberg.cpp -o glm_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glm_one_group.cpp -o glm_one_group.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c interpolator.cpp -o interpolator.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matvec_check.cpp -o matvec_check.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nbdev.cpp -o nbdev.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_add_repeat_matrices.o R_ave_log_cpm.o R_calculate_cpm.o R_check_counts.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_get_one_way_fitted.o R_initialize_levenberg.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/usr/local/lib/R/lib -lRlapack -lopenblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/edgeR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (edgeR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘HTMLUtils’ ...
** package ‘HTMLUtils’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (HTMLUtils)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘pracma’ ...
** package ‘pracma’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (pracma)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘Rmpfr’ ...
** package ‘Rmpfr’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mpfr.h usability... yes
checking mpfr.h presence... yes
checking for mpfr.h... yes
checking gmp.h usability... yes
checking gmp.h presence... yes
checking for gmp.h... yes
checking for __gmpz_init in -lgmp... yes
checking for mpfr_init in -lmpfr... yes
checking for mpfr_digamma in -lmpfr... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ops.c -o Ops.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Summary.c -o Summary.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c convert.c -o convert.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Rmpfr.so Ops.o Summary.o convert.o init.o utils.o -lmpfr -lgmp -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rmpfr/libs
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘factorial’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Rmpfr’
Creating a new generic function for ‘cbind’ in package ‘Rmpfr’
Creating a new generic function for ‘rbind’ in package ‘Rmpfr’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘norm’ from package ‘base’ in package ‘Rmpfr’
in method for ‘show’ with signature ‘"integrateR"’: no definition for class “integrateR”
Creating a new generic function for ‘pmin’ in package ‘Rmpfr’
Creating a new generic function for ‘pmax’ in package ‘Rmpfr’
Creating a generic function for ‘atan2’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘beta’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘lbeta’ from package ‘base’ in package ‘Rmpfr’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (Rmpfr)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ALS’ ...
** package ‘ALS’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ALS)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘signal’ ...
** package ‘signal’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -g -O2  -c dpchim.f -o dpchim.o
gfortran   -fpic  -g -O2  -c dpchst.f -o dpchst.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c remez.c -o remez.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o signal.so dpchim.o dpchst.o remez.o -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/signal/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (signal)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gridExtra’ ...
** package ‘gridExtra’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gridExtra)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘progress’ ...
** package ‘progress’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (progress)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘doParallel’ ...
** package ‘doParallel’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (doParallel)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘rngtools’ ...
** package ‘rngtools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (rngtools)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c address.cpp -o address.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c api.cpp -o api.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c arrange.cpp -o arrange.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c between.cpp -o between.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bind.cpp -o bind.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c combine_variables.cpp -o combine_variables.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c distinct.cpp -o distinct.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dplyr.cpp -o dplyr.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c filter.cpp -o filter.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c group_indices.cpp -o group_indices.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c join.cpp -o join.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nth.cpp -o nth.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c select.cpp -o select.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strings_addresses.cpp -o strings_addresses.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c summarise.cpp -o summarise.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c test.cpp -o test.o
g++  -I/usr/local/lib/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c window.cpp -o window.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o dplyr.so RcppExports.o address.o api.o arrange.o between.o bind.o combine_variables.o distinct.o dplyr.o filter.o group_indices.o init.o join.o nth.o select.o strings_addresses.o summarise.o test.o window.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (dplyr)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘shinydashboard’ ...
** package ‘shinydashboard’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (shinydashboard)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘XVector’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_XVector.c -o R_init_XVector.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedDouble_class.c -o SharedDouble_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedInteger_class.c -o SharedInteger_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedRaw_class.c -o SharedRaw_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XRawList_comparison.c -o XRawList_comparison.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVectorList_class.c -o XVectorList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_utils.c -o io_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c slice_methods.c -o slice_methods.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c view_summarization_methods.c -o view_summarization_methods.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/XVector/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (XVector)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘scales’ ...
** package ‘scales’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c colors.cpp -o colors.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o scales.so RcppExports.o colors.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/scales/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (scales)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘e1071’ ...
** package ‘e1071’ successfully unpacked and MD5 sums checked
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rsvm.c -o Rsvm.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cmeans.c -o cmeans.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cshell.c -o cshell.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c floyd.c -o floyd.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c svm.cpp -o svm.o
svm.cpp: In function ‘svm_model* svm_load_model(const char*)’:
svm.cpp:2788:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp,"%80s",cmd);
                        ^
svm.cpp:2792:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%80s",cmd);
                         ^
svm.cpp:2817:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%80s",cmd);
                         ^
svm.cpp:2841:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&param.degree);
                                 ^
svm.cpp:2843:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%lf",&param.gamma);
                                 ^
svm.cpp:2845:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%lf",&param.coef0);
                                 ^
svm.cpp:2847:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&model->nr_class);
                                    ^
svm.cpp:2849:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&model->l);
                             ^
svm.cpp:2855:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->rho[i]);
                                    ^
svm.cpp:2862:37: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%d",&model->label[i]);
                                     ^
svm.cpp:2869:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->probA[i]);
                                      ^
svm.cpp:2876:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->probB[i]);
                                      ^
svm.cpp:2883:35: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%d",&model->nSV[i]);
                                   ^
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o init.o svm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/e1071/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (e1071)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
in method for ‘initialize’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘toString’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘show’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘rev’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (AnnotationDbi)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gplots’ ...
** package ‘gplots’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gplots)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘maxLik’ ...
** package ‘maxLik’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (maxLik)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ChemometricsWithR’ ...
** package ‘ChemometricsWithR’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ChemometricsWithR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘RankProd’ ...
** R
** data
** inst
** preparing package for lazy loading
[1] "this is the new version of the RankProd package"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (RankProd)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘biomaRt’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomaRt)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘mzID’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (mzID)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘GO.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (GO.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘doRNG’ ...
** package ‘doRNG’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (doRNG)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘KEGG.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (KEGG.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (annotate)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c MIndex_class.c -o MIndex_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSetList_class.c -o XStringSetList_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSet_io.c -o XStringSet_io.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_utils.c -o align_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict.c -o match_pdict.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_utils.c -o match_pdict_utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replaceAt.c -o replaceAt.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strutils.c -o strutils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c translate.c -o translate.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xscat.c -o xscat.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (Biostrings)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ggplot2)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘safe’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (safe)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘org.Hs.eg.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (org.Hs.eg.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘org.Mm.eg.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (org.Mm.eg.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘org.Rn.eg.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (org.Rn.eg.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘biosigner’ ...
** R
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** help
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** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (biosigner)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘tofsims’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c LapackEigen.cpp -o LapackEigen.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c c_importer.cpp -o c_importer.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nn.cpp -o nn.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c readRawPhi.cpp -o readRawPhi.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tofsims_init.c -o tofsims_init.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.cpp -o utilities.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o tofsims.so LapackEigen.o RcppExports.o c_importer.o nn.o readRawPhi.o tofsims_init.o utilities.o -llapack -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/tofsims/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (tofsims)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ggbeeswarm’ ...
** package ‘ggbeeswarm’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ggbeeswarm)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘viridis’ ...
** package ‘viridis’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (viridis)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘vsn’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vsn.c -o vsn.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vsn2.c -o vsn2.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o vsn.so init.o vsn.o vsn2.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/vsn/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
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (vsn)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘hgu133plus2.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (hgu133plus2.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘hgu133a.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (hgu133a.db)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘GSEABase’ ...
** R
** inst
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** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (GSEABase)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘ChemmineR’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DisjointSets.cpp -o DisjointSets.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cluster.cc -o cluster.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cstrsplit.cc -o cstrsplit.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c desc.cc -o desc.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fingerprints.cc -o fingerprints.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c formats.cc -o formats.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c molecule.cc -o molecule.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c r_wrap.cc -o r_wrap.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c script.cc -o script.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c similarity.cc -o similarity.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/ChemmineR/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
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (ChemmineR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘topGO’ ...
** R
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** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (topGO)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘globaltest’ ...
** R
** inst
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** help
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** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (globaltest)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘KEGGREST’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (KEGGREST)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘scater’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c calc_exprs.cpp -o calc_exprs.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrix_info.cpp -o matrix_info.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.cpp -o utils.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o scater.so calc_exprs.o init.o matrix_info.o utils.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for ‘mutate’ in package ‘scater’
Creating a new generic function for ‘filter’ in package ‘scater’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (scater)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘MSnbase’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Spectrum1_class.c -o Spectrum1_class.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Spectrum2_class.c -o Spectrum2_class.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (MSnbase)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘gage’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (gage)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘PADOG’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (PADOG)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘GSVA’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kernel_estimation.c -o kernel_estimation.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ks_test.c -o ks_test.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c register_cmethods.c -o register_cmethods.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/GSVA/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (GSVA)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘organism’ in package ‘bioassayR’
Creating a new generic function for ‘organism<-’ in package ‘bioassayR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (bioassayR)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘pathview’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (pathview)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘Glimma’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (Glimma)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘xcms’ ...
** libs
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
In file included from massifquant/SegProc.h:4:0,
                 from massifquant/SegProc.cpp:10:
massifquant/SegProc.cpp: In member function ‘double SegProc::Rf_pt(double, double, int, int)’:
massifquant/nmath.h:77:26: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
 #define _(String) (String)
                          ^
massifquant/nmath.h:125:21: note: in expansion of macro ‘_’
         char *msg = _(""); \
                     ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:128:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                             msg = _("argument out of domain in '%s'\n"); \
                                 ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:131:32: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                            msg = _("value out of range in '%s'\n"); \
                                ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:134:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                             msg = _("convergence failed in '%s'\n"); \
                                 ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:137:36: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                                msg = _("full precision may not have been achieved in '%s'\n"); \
                                    ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
massifquant/nmath.h:140:36: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
                                msg = _("underflow occurred in '%s'\n"); \
                                    ^
massifquant/nmath.h:117:29: note: in expansion of macro ‘ML_ERROR’
 #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; }
                             ^
massifquant/SegProc.cpp:361:19: note: in expansion of macro ‘ML_ERR_return_NAN’
     if (n <= 0.0) ML_ERR_return_NAN;
                   ^
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/mat.cpp -o obiwarp/mat.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/vec.cpp -o obiwarp/vec.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mzClust_hclust.c -o mzClust_hclust.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mzROI.c -o mzROI.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c util.c -o util.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xcms.c -o xcms.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c binners.c -o binners.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/xcms/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘sigma’ in package ‘xcms’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (xcms)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘EGSEA’ ...
** R
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (EGSEA)
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* installing *source* package ‘proFIA’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c UtilFunc.c -o UtilFunc.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatchPpm.c -o fastMatchPpm.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/proFIA/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
* DONE (proFIA)

The downloaded source packages are in
	‘/tmp/RtmpymWdyo/downloaded_packages’
> 
> # just in case there were warnings, we want to see them
> # without having to scroll up:
> warnings()
NULL
> 
> if (!is.null(warnings()))
+ {
+     w <- capture.output(warnings())
+     if (length(grep("is not available|had non-zero exit status", w)))
+         quit("no", 1L)
+ }
> 
> suppressWarnings(BiocInstaller::biocValid(fix=TRUE, ask=FALSE))
[1] TRUE
> 
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Removing intermediate container c1e28e51f12d
Successfully built 42dfde5613f1
[container-bioc_devel_protmetcore] $ docker tag 42dfde5613f1 docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:latest
[container-bioc_devel_protmetcore] $ docker inspect 42dfde5613f1
[container-bioc_devel_protmetcore] $ docker push docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:devel
The push refers to a repository [docker-registry-v2.local:30750/bioconductor/devel_protmetcore2]
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[container-bioc_devel_protmetcore] $ docker push docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:latest
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Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Triggering a new build of container-bioc_devel_metabolomics
Finished: SUCCESS