############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ShortRead ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘ShortRead’ ... ** using staged installation checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/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 size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c alphabet.c -o alphabet.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c count.c -o count.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io.c -o io.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io_bowtie.c -o io_bowtie.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io_soap.c -o io_soap.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’: readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 35 | (void) fread( seq_name, sizeof(char), name_len, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 37 | (void) fread( &seq_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -c read_maq_map.cc -o read_maq_map.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sampler.c -o sampler.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c trim.c -o trim.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c util.c -o util.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c xsnap.c -o xsnap.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ShortRead/00new/ShortRead/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ShortRead)