############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL rhdf5 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5.c -o H5.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5A.c -o H5A.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5D.c -o H5D.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5E.c -o H5E.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5F.c -o H5F.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5G.c -o H5G.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5I.c -o H5I.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5L.c -o H5L.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5O.c -o H5O.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5P.c -o H5P.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5PL.c -o H5PL.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5R.c -o H5R.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5S.c -o H5S.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5S_extras.c -o H5S_extras.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5T.c -o H5T.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5T_extras.c -o H5T_extras.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5Z.c -o H5Z.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c H5constants.c -o H5constants.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c HandleList.cpp -o HandleList.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bit64conversion.c -o bit64conversion.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c external_filters.c -o external_filters.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c h5dump.c -o h5dump.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c h5ls.c -o h5ls.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c h5testLock.c -o h5testLock.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c printdatatype.c -o printdatatype.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c wrap.c -o wrap.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5PL.o H5R.o H5S.o H5S_extras.o H5T.o H5T_extras.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-rhdf5/00new/rhdf5/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5)