############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ShortRead ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c alphabet.c -o alphabet.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c count.c -o count.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c io.c -o io.o io.c: In function ‘read_prb_as_character’: io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] 227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0))); | ~^ | | | double | %s io.c: In function ‘_read_solexa_export_file’: io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 658 | error("invalid 'strand' field '%s', %s:%d", | ~^ | | | char * | %d 659 | *elt[13], fname, lineno); | ~~~~~~~~ | | | int io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 676 | error("invalid 'filtering' field '%s', %s:%d", | ~^ | | | char * | %d 677 | *elt[21], fname, lineno); | ~~~~~~~~ | | | int gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c io_bowtie.c -o io_bowtie.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c io_soap.c -o io_soap.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -DR_NO_REMAP -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++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -DR_NO_REMAP -c read_maq_map.cc -o read_maq_map.o In file included from read_maq_map.cc:13: maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c sampler.c -o sampler.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c trim.c -o trim.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c util.c -o util.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -c xsnap.c -o xsnap.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-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)