The following packages will be installed: stringtie Fetching README... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done Fetching stringtie.SlackBuild... 0%100%100%100%100%100%Done Fetching stringtie.info... 0%100%100%100%100%100%Done stringtie-1.3.6/ stringtie-1.3.6/LICENSE stringtie-1.3.6/Makefile stringtie-1.3.6/README stringtie-1.3.6/README.md stringtie-1.3.6/gclib/ stringtie-1.3.6/gclib/GArgs.cpp stringtie-1.3.6/gclib/GArgs.h stringtie-1.3.6/gclib/GBam.cpp stringtie-1.3.6/gclib/GBam.h stringtie-1.3.6/gclib/GBase.cpp stringtie-1.3.6/gclib/GBase.h stringtie-1.3.6/gclib/GBitVec.h stringtie-1.3.6/gclib/GFaSeqGet.cpp stringtie-1.3.6/gclib/GFaSeqGet.h stringtie-1.3.6/gclib/GFastaIndex.cpp stringtie-1.3.6/gclib/GFastaIndex.h stringtie-1.3.6/gclib/GHash.hh stringtie-1.3.6/gclib/GIntHash.hh stringtie-1.3.6/gclib/GList.hh stringtie-1.3.6/gclib/GStr.cpp stringtie-1.3.6/gclib/GStr.h stringtie-1.3.6/gclib/GThreads.cpp stringtie-1.3.6/gclib/GThreads.h stringtie-1.3.6/gclib/GVec.hh stringtie-1.3.6/gclib/codons.cpp stringtie-1.3.6/gclib/codons.h stringtie-1.3.6/gclib/gdna.cpp stringtie-1.3.6/gclib/gdna.h stringtie-1.3.6/gclib/gff.cpp stringtie-1.3.6/gclib/gff.h stringtie-1.3.6/gclib/proc_mem.cpp stringtie-1.3.6/gclib/proc_mem.h stringtie-1.3.6/prepDE.py stringtie-1.3.6/prep_linux.sh stringtie-1.3.6/prep_mac.sh stringtie-1.3.6/prep_source.sh stringtie-1.3.6/rlink.cpp stringtie-1.3.6/rlink.h stringtie-1.3.6/samtools-0.1.18/ stringtie-1.3.6/samtools-0.1.18/AUTHORS stringtie-1.3.6/samtools-0.1.18/COPYING stringtie-1.3.6/samtools-0.1.18/ChangeLog stringtie-1.3.6/samtools-0.1.18/INSTALL stringtie-1.3.6/samtools-0.1.18/Makefile stringtie-1.3.6/samtools-0.1.18/NEWS stringtie-1.3.6/samtools-0.1.18/bam.c stringtie-1.3.6/samtools-0.1.18/bam.h stringtie-1.3.6/samtools-0.1.18/bam2bcf.c stringtie-1.3.6/samtools-0.1.18/bam2bcf.h stringtie-1.3.6/samtools-0.1.18/bam2bcf_indel.c stringtie-1.3.6/samtools-0.1.18/bam2depth.c stringtie-1.3.6/samtools-0.1.18/bam_aux.c stringtie-1.3.6/samtools-0.1.18/bam_cat.c stringtie-1.3.6/samtools-0.1.18/bam_color.c stringtie-1.3.6/samtools-0.1.18/bam_endian.h stringtie-1.3.6/samtools-0.1.18/bam_import.c stringtie-1.3.6/samtools-0.1.18/bam_index.c stringtie-1.3.6/samtools-0.1.18/bam_lpileup.c stringtie-1.3.6/samtools-0.1.18/bam_mate.c stringtie-1.3.6/samtools-0.1.18/bam_md.c stringtie-1.3.6/samtools-0.1.18/bam_pileup.c stringtie-1.3.6/samtools-0.1.18/bam_plcmd.c stringtie-1.3.6/samtools-0.1.18/bam_reheader.c stringtie-1.3.6/samtools-0.1.18/bam_rmdup.c stringtie-1.3.6/samtools-0.1.18/bam_rmdupse.c stringtie-1.3.6/samtools-0.1.18/bam_sort.c stringtie-1.3.6/samtools-0.1.18/bam_stat.c stringtie-1.3.6/samtools-0.1.18/bam_tview.c stringtie-1.3.6/samtools-0.1.18/bamtk.c stringtie-1.3.6/samtools-0.1.18/bedidx.c stringtie-1.3.6/samtools-0.1.18/bgzf.c stringtie-1.3.6/samtools-0.1.18/bgzf.h stringtie-1.3.6/samtools-0.1.18/bgzip.c stringtie-1.3.6/samtools-0.1.18/cut_target.c stringtie-1.3.6/samtools-0.1.18/errmod.c stringtie-1.3.6/samtools-0.1.18/errmod.h stringtie-1.3.6/samtools-0.1.18/faidx.c stringtie-1.3.6/samtools-0.1.18/faidx.h stringtie-1.3.6/samtools-0.1.18/kaln.c stringtie-1.3.6/samtools-0.1.18/kaln.h stringtie-1.3.6/samtools-0.1.18/khash.h stringtie-1.3.6/samtools-0.1.18/klist.h stringtie-1.3.6/samtools-0.1.18/knetfile.c stringtie-1.3.6/samtools-0.1.18/knetfile.h stringtie-1.3.6/samtools-0.1.18/kprobaln.c stringtie-1.3.6/samtools-0.1.18/kprobaln.h stringtie-1.3.6/samtools-0.1.18/kseq.h stringtie-1.3.6/samtools-0.1.18/ksort.h stringtie-1.3.6/samtools-0.1.18/kstring.c stringtie-1.3.6/samtools-0.1.18/kstring.h stringtie-1.3.6/samtools-0.1.18/phase.c stringtie-1.3.6/samtools-0.1.18/razf.c stringtie-1.3.6/samtools-0.1.18/razf.h stringtie-1.3.6/samtools-0.1.18/razip.c stringtie-1.3.6/samtools-0.1.18/sam.c stringtie-1.3.6/samtools-0.1.18/sam.h stringtie-1.3.6/samtools-0.1.18/sam_header.c stringtie-1.3.6/samtools-0.1.18/sam_header.h stringtie-1.3.6/samtools-0.1.18/sam_view.c stringtie-1.3.6/samtools-0.1.18/sample.c stringtie-1.3.6/samtools-0.1.18/sample.h stringtie-1.3.6/samtools-0.1.18/samtools.1 stringtie-1.3.6/stringtie.cpp stringtie-1.3.6/tablemaker.cpp stringtie-1.3.6/tablemaker.h stringtie-1.3.6/tag_git.sh stringtie-1.3.6/tmerge.cpp stringtie-1.3.6/tmerge.h cd ./samtools-0.1.18 && make lib make[1]: Entering directory '/usr/src/slapt-src/academic/stringtie/stringtie-1.3.6/samtools-0.1.18' gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam.c -o bam.o bam.c: In function ‘bam_header_write’: bam.c:116:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 116 | strncpy(buf, "BAM\001", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o bam_import.c: In function ‘append_text’: bam_import.c:179:55: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 179 | fprintf(stderr,"realloc failed to alloc %ld bytes\n", y); | ~~^ ~ | | | | long int size_t {aka unsigned int} | %d bam_import.c:186:46: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bam_import.c:186:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y); | ~~^ ~~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bam_import.c:186:58: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y); | ~~^ ~ | | | | long int size_t {aka unsigned int} | %d bam_import.c:186:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y); | ~~^ ~ | | | | long int size_t {aka unsigned int} | %d gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam.c -o sam.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o bam_index.c: In function ‘bam_index_core’: bam_index.c:173:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 173 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function ‘resolve_cigar2’: bam_pileup.c:75:16: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable] 75 | int k, is_head = 0; | ^~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o bam_md.c: In function ‘bam_prob_realn_core’: bam_md.c:209:35: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 209 | *(bq - 3) = 'Z'; | ~~~~~~~~~~^~~~~ bam_md.c:198:19: note: at offset -2 into destination object of size [0, 2147483647] allocated by ‘bam_aux_get’ 198 | if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; | ^~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. razf.c -o razf.o razf.c: In function ‘razf_open_w’: razf.c:178:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 178 | strncpy((char*)rz->header->extra, "RAZF", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o In file included from bam_sort.c:9: bam_sort.c:309:26: warning: ‘bam1_lt’ is static but used in inline function ‘__ks_insertsort_sort’ which is not static 309 | KSORT_INIT(sort, bam1_p, bam1_lt) | ^~~~~~~ ksort.h:148:46: note: in definition of macro ‘KSORT_INIT’ 148 | for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ | ^~~~~~~~~ bam_sort.c:53:27: warning: ‘heap_lt’ is static but used in inline function ‘__ks_insertsort_heap’ which is not static 53 | KSORT_INIT(heap, heap1_t, heap_lt) | ^~~~~~~ ksort.h:148:46: note: in definition of macro ‘KSORT_INIT’ 148 | for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ | ^~~~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function ‘bam_reheader’: bam_reheader.c:11:23: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] 11 | bam_header_t *old; | ^~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function ‘kpa_glocal’: kprobaln.c:78:28: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] 78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | ^~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[1]: Leaving directory '/usr/src/slapt-src/academic/stringtie/stringtie-1.3.6/samtools-0.1.18' g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/GBase.cpp -o gclib/GBase.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/GArgs.cpp -o gclib/GArgs.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/GStr.cpp -o gclib/GStr.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/GBam.cpp -o gclib/GBam.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/gdna.cpp -o gclib/gdna.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/codons.cpp -o gclib/codons.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/gff.cpp -o gclib/gff.o In file included from gclib/gff.cpp:1: gclib/gff.h: In copy constructor ‘GffExon::GffExon(const GffExon&)’: gclib/gff.h:655:19: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 655 | (*this)=ex; //use the default copy operator | ^~ gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ gclib/gff.cpp: In member function ‘void GffObj::getCDSegs(GVec&)’: gclib/gff.cpp:3170:37: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 3170 | cdseg=(*cdss->Get(i)); | ^ In file included from gclib/gff.cpp:1: gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ In file included from gclib/GList.hh:8, from gclib/GFastaIndex.h:12, from gclib/GFaSeqGet.h:3, from gclib/gff.h:9, from gclib/gff.cpp:1: gclib/GVec.hh: In instantiation of ‘void GVec::Reverse() [with OBJ = GffExon]’: gclib/gff.cpp:3198:17: required from here gclib/GVec.hh:330:7: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 330 | c=fArray[l];fArray[l]=fArray[r]; | ~^~~~~~~~ In file included from gclib/gff.cpp:1: gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ In file included from gclib/GList.hh:8, from gclib/GFastaIndex.h:12, from gclib/GFaSeqGet.h:3, from gclib/gff.h:9, from gclib/gff.cpp:1: gclib/GVec.hh:330:27: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 330 | c=fArray[l];fArray[l]=fArray[r]; | ~~~~~~~~~^~~~~~~~ In file included from gclib/gff.cpp:1: gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ In file included from gclib/GList.hh:8, from gclib/GFastaIndex.h:12, from gclib/GFaSeqGet.h:3, from gclib/gff.h:9, from gclib/gff.cpp:1: gclib/GVec.hh:331:15: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 331 | fArray[r]=c; | ~~~~~~~~~^~ In file included from gclib/gff.cpp:1: gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ In file included from gclib/GList.hh:8, from gclib/GFastaIndex.h:12, from gclib/GFaSeqGet.h:3, from gclib/gff.h:9, from gclib/gff.cpp:1: gclib/GVec.hh: In instantiation of ‘void GVec::setCapacity(int) [with OBJ = GffExon]’: gclib/GVec.hh:204:3: required from ‘GVec::GVec(int) [with OBJ = GffExon]’ gclib/gff.cpp:3135:16: required from here gclib/GVec.hh:297:21: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 297 | fArray[i] = oldArray[i]; | ~~~~~~~~~~^~~~~~~~~~~ In file included from gclib/gff.cpp:1: gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ In file included from gclib/GList.hh:8, from gclib/GFastaIndex.h:12, from gclib/GFaSeqGet.h:3, from gclib/gff.h:9, from gclib/gff.cpp:1: gclib/GVec.hh: In instantiation of ‘int GVec::Add(OBJ*) [with OBJ = GffExon]’: gclib/GVec.hh:76:36: required from ‘int GVec::Add(OBJ&) [with OBJ = GffExon]’ gclib/gff.cpp:3172:10: required from here gclib/GVec.hh:383:17: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 383 | fArray[fCount] = *item; //OBJ::operator= must copy OBJ properly! | ~~~~~~~~~~~~~~~^~~~~~~ In file included from gclib/gff.cpp:1: gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c gclib/GThreads.cpp -o gclib/GThreads.o g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c rlink.cpp -o rlink.o In file included from rlink.h:5, from rlink.cpp:1: ./gclib/gff.h: In copy constructor ‘GffExon::GffExon(const GffExon&)’: ./gclib/gff.h:655:19: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 655 | (*this)=ex; //use the default copy operator | ^~ ./gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c tablemaker.cpp -o tablemaker.o In file included from rlink.h:5, from tablemaker.cpp:2: ./gclib/gff.h: In copy constructor ‘GffExon::GffExon(const GffExon&)’: ./gclib/gff.h:655:19: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 655 | (*this)=ex; //use the default copy operator | ^~ ./gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c tmerge.cpp -o tmerge.o In file included from rlink.h:5, from tmerge.h:5, from tmerge.cpp:1: ./gclib/gff.h: In copy constructor ‘GffExon::GffExon(const GffExon&)’: ./gclib/gff.h:655:19: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 655 | (*this)=ex; //use the default copy operator | ^~ ./gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ g++ -O2 -march=i586 -mtune=i686 -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -c stringtie.cpp -o stringtie.o In file included from rlink.h:5, from stringtie.cpp:2: ./gclib/gff.h: In copy constructor ‘GffExon::GffExon(const GffExon&)’: ./gclib/gff.h:655:19: warning: implicitly-declared ‘GffExon& GffExon::operator=(const GffExon&)’ is deprecated [-Wdeprecated-copy] 655 | (*this)=ex; //use the default copy operator | ^~ ./gclib/gff.h:654:3: note: because ‘GffExon’ has user-provided ‘GffExon::GffExon(const GffExon&)’ 654 | GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor | ^~~~~~~ g++ -g -L./samtools-0.1.18 -o stringtie gclib/GBase.o gclib/GArgs.o gclib/GStr.o gclib/GBam.o gclib/gdna.o gclib/codons.o gclib/GFastaIndex.o gclib/GFaSeqGet.o gclib/gff.o gclib/GThreads.o rlink.o tablemaker.o tmerge.o stringtie.o -lbam -lz -lpthread Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/stringtie/stringtie-1.3.6-i586-1salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/stringtie usr/doc/ usr/doc/stringtie-1.3.6/ usr/doc/stringtie-1.3.6/LICENSE usr/doc/stringtie-1.3.6/README.md usr/doc/stringtie-1.3.6/stringtie.SlackBuild Slackware package /usr/src/slapt-src/academic/stringtie/stringtie-1.3.6-i586-1salix15.0.txz created. Installing package stringtie-1.3.6-i586-1salix15.0... | stringtie (Assembler of RNA-Seq alignments) | | StringTie is a fast and highly efficient assembler of RNA-Seq | alignments into potential transcripts. It uses a novel network | flow algorithm as well as an optional de novo assembly step to | assemble and quantitate full-length transcripts representing | multiple splice variants for each gene locus. | | Home: http://ccb.jhu.edu/software/stringtie/ | | | |