GitLab

marques@marques:~/Documents/Plastome-assembly/org-asm$ sudo python3 setup.py --serenity install [sudo] password for marques: ['/home/marques/Documents/Plastome-assembly/org-asm', '/usr/lib/python35.zip', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-x86_64-linux-gnu', '/usr/lib/python3.5/lib-dynload', '/usr/local/lib/python3.5/dist-packages', '/usr/lib/python3/dist-packages', '/home/marques/Documents/Plastome-assembly/org-asm/distutils.ext', '/home/marques/Documents/Plastome-assembly/org-asm/python'] Installing ORG.asm (1.0.00-alpha3) in serenity mode You are running the good python Restarting installation within the ORG.asm-1.0.00-alpha3 virtualenv Install script restarting... ['/home/marques/Documents/Plastome-assembly/org-asm', '/usr/lib/python35.zip', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-x86_64-linux-gnu', '/usr/lib/python3.5/lib-dynload', '/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages', '/home/marques/Documents/Plastome-assembly/org-asm/distutils.ext', '/home/marques/Documents/Plastome-assembly/org-asm/python'] Installing ORG.asm (1.0.00-alpha3) in serenity mode You are running the good python ORG.asm will be installed with python : /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/python Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (>=0.24) : ok version 0.25.2 installed Look for package Sphinx (>=1.3) : ok version 1.5.1 installed You are running the good python Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (>=0.24) : ok version 0.25.2 installed Look for package Sphinx (>=1.3) : ok version 1.5.1 installed Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (>=0.24) : ok version 0.25.2 installed Look for package Sphinx (>=1.3) : ok version 1.5.1 installed Cython module : ['src/_sse.h', 'src/buffer.c', 'src/buildindex.c', '@code16bits.c', '@codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/debug.h', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/orgasm.h', 'src/sort.c', 'src/fgetln.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h'] Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/orgasm.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h', '@expand8bits.c'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h'] Cython module : [] Cython module : [] running install running build running littlebigman building 'littlebigman' program x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c distutils.ext/src/littlebigman.c -o build/temp.linux-x86_64-3.5/distutils.ext/src/littlebigman.o -msse2 x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/distutils.ext/src/littlebigman.o -o build/temp.linux-x86_64-3.5/littlebigman Your CPU is in mode : -DLITTLE_END running build_py running build_ext Look for CPU architecture... [('LITTLE_END', None)] running build_files running build_ctools building 'buildcomplement' program x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildcomplement.c -o build/temp.linux-x86_64-3.5/src/buildcomplement.o -msse2 x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildcomplement.o -o build/temp.linux-x86_64-3.5/buildcomplement building 'buildcode' program x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildcode.c -o build/temp.linux-x86_64-3.5/src/buildcode.o -msse2 src/buildcode.c: In function ‘main’: src/buildcode.c:44:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] fprintf(stdout," INT64_C(0x%16llX), // %04X --> %8s \n", ((uint64_t)nu ^ src/buildcode.c:44:19: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] fprintf(stdout," INT64_C(0x%16llX), // %04X --> %8s \n", ((uint64_t)nu ^ src/buildcode.c:46:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] fprintf(stdout," INT64_C(0x%16llX) // %04X --> %8s \n", ((uint64_t)nu ^ src/buildcode.c:46:19: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] fprintf(stdout," INT64_C(0x%16llX) // %04X --> %8s \n", ((uint64_t)nu ^ x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildcode.o -o build/temp.linux-x86_64-3.5/buildcode building 'buildexpand8bits' program x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildexpand8bits.c -o build/temp.linux-x86_64-3.5/src/buildexpand8bits.o -msse2 src/buildexpand8bits.c: In function ‘main’: src/buildexpand8bits.c:40:1: warning: multi-line comment [-Wcomment] // ((uint32_t)nuc) = ((uint32_t)nuc) >> 24 |
^ src/buildexpand8bits.c:47:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] fprintf(stdout," 0x%08XUL, // %04X\n", ((uint32_t)nuc),code); ^ src/buildexpand8bits.c:49:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] fprintf(stdout," 0x%08XUL // %04X\n", ((uint32_t)nuc),code); ^ x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/buildexpand8bits.o -o build/temp.linux-x86_64-3.5/buildexpand8bits Building file : codecomp.c --> build/temp.linux-x86_64-3.5/buildcomplement > build/temp.linux-x86_64-3.5/codecomp.c Done.

Building file : code16bits.c --> build/temp.linux-x86_64-3.5/buildcode > build/temp.linux-x86_64-3.5/code16bits.c Done.

Building file : expand8bits.c --> build/temp.linux-x86_64-3.5/buildexpand8bits > build/temp.linux-x86_64-3.5/expand8bits.c Done.

running build_cexe Look for CPU architecture... [('LITTLE_END', None)] orgasmi :-> src/orgasmi.c ok orgasmi :-> src/buffer.c ok orgasmi :-> src/buildindex.c ok orgasmi :-> @code16bits.c changed to build/temp.linux-x86_64-3.5/code16bits.c orgasmi :-> @codecomp.c changed to build/temp.linux-x86_64-3.5/codecomp.c orgasmi :-> src/compsort.c ok orgasmi :-> src/debug.c ok orgasmi :-> src/decode.c ok orgasmi :-> src/encode.c ok orgasmi :-> src/fastq.c ok orgasmi :-> src/indexinput.c ok orgasmi :-> src/indexoutput.c ok orgasmi :-> src/load.c ok orgasmi :-> src/lookfor.c ok orgasmi :-> src/malloc.c ok orgasmi :-> src/fgetln.c ok orgasmi :-> src/sort.c ok building 'orgasmi' program x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/orgasmi.c -o build/temp.linux-x86_64-3.5/src/orgasmi.o -msse2 src/orgasmi.c:27:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static void PrintHelp() ^ src/orgasmi.c:62:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static void ExitUsage(stat) ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buffer.c -o build/temp.linux-x86_64-3.5/src/buffer.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildindex.c -o build/temp.linux-x86_64-3.5/src/buildindex.o -msse2 src/buildindex.c: In function ‘buildIndex’: src/buildindex.c:44:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration] asprintf(&indexFileName,"%s.ofx",indexname); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.5/code16bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.5/codecomp.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/compsort.c -o build/temp.linux-x86_64-3.5/src/compsort.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/debug.c -o build/temp.linux-x86_64-3.5/src/debug.o -msse2 src/debug.c: In function ‘int2bin’: src/debug.c:23:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] u = *(unsigned *)&i; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/decode.c -o build/temp.linux-x86_64-3.5/src/decode.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/encode.c -o build/temp.linux-x86_64-3.5/src/encode.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/fastq.c -o build/temp.linux-x86_64-3.5/src/fastq.o -msse2 src/fastq.c: In function ‘readFastq’: src/fastq.c:42:11: warning: implicit declaration of function ‘fgetln’ [-Wimplicit-function-declaration] buffer = fgetln(in,&lseq); ^ src/fastq.c:42:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion] buffer = fgetln(in,&lseq); ^ src/fastq.c:45:10: warning: assignment makes pointer from integer without a cast [-Wint-conversion] buffer = fgetln(in,&lseq); ^ src/fastq.c:59:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion] buffer = fgetln(in,&lseq); ^ src/fastq.c:60:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion] buffer = fgetln(in,&lseq); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/indexinput.c -o build/temp.linux-x86_64-3.5/src/indexinput.o -msse2 src/indexinput.c: In function ‘loadGeneralData’: src/indexinput.c:57:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,1,sizeof(buffer_t),input); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/indexoutput.c -o build/temp.linux-x86_64-3.5/src/indexoutput.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/load.c -o build/temp.linux-x86_64-3.5/src/load.o -msse2 src/load.c: In function ‘loadIndexedReads’: src/load.c:34:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration] asprintf(&indexFileName,"%s.ogx",indexname); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/lookfor.c -o build/temp.linux-x86_64-3.5/src/lookfor.o -msse2 src/lookfor.c: In function ‘shiftKey’: src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable] uint8_t rmask; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/malloc.c -o build/temp.linux-x86_64-3.5/src/malloc.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/fgetln.c -o build/temp.linux-x86_64-3.5/src/fgetln.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/sort.c -o build/temp.linux-x86_64-3.5/src/sort.o -msse2 x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/src/orgasmi.o build/temp.linux-x86_64-3.5/src/buffer.o build/temp.linux-x86_64-3.5/src/buildindex.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o build/temp.linux-x86_64-3.5/src/compsort.o build/temp.linux-x86_64-3.5/src/debug.o build/temp.linux-x86_64-3.5/src/decode.o build/temp.linux-x86_64-3.5/src/encode.o build/temp.linux-x86_64-3.5/src/fastq.o build/temp.linux-x86_64-3.5/src/indexinput.o build/temp.linux-x86_64-3.5/src/indexoutput.o build/temp.linux-x86_64-3.5/src/load.o build/temp.linux-x86_64-3.5/src/lookfor.o build/temp.linux-x86_64-3.5/src/malloc.o build/temp.linux-x86_64-3.5/src/fgetln.o build/temp.linux-x86_64-3.5/src/sort.o -o build/scripts-3.5/orgasmi orgasm.indexer._orgasm :-> python/orgasm/indexer/_orgasm.pyx ok orgasm.indexer._orgasm :-> src/buffer.c ok orgasm.indexer._orgasm :-> src/buildindex.c ok orgasm.indexer._orgasm :-> @code16bits.c changed to build/temp.linux-x86_64-3.5/code16bits.c orgasm.indexer._orgasm :-> @codecomp.c changed to build/temp.linux-x86_64-3.5/codecomp.c orgasm.indexer._orgasm :-> src/compsort.c ok orgasm.indexer._orgasm :-> src/debug.c ok orgasm.indexer._orgasm :-> src/decode.c ok orgasm.indexer._orgasm :-> src/encode.c ok orgasm.indexer._orgasm :-> src/fastq.c ok orgasm.indexer._orgasm :-> src/indexinput.c ok orgasm.indexer._orgasm :-> src/indexoutput.c ok orgasm.indexer._orgasm :-> src/load.c ok orgasm.indexer._orgasm :-> src/lookfor.c ok orgasm.indexer._orgasm :-> src/malloc.c ok orgasm.indexer._orgasm :-> src/sort.c ok orgasm.indexer._orgasm :-> src/fgetln.c ok orgasm.indexer.fakereads :-> python/orgasm/indexer/fakereads.pyx ok orgasm.apps.command :-> python/orgasm/apps/command.pyx ok orgasm.apps.progress :-> python/orgasm/apps/progress.pyx ok orgasm.apps.config :-> python/orgasm/apps/config.pyx ok orgasm.apps.logging :-> python/orgasm/apps/logging.pyx ok orgasm.apps.counter :-> python/orgasm/apps/counter.pyx ok orgasm.apps.arguments :-> python/orgasm/apps/arguments.pyx ok orgasm.graph._graphmultiedge :-> python/orgasm/graph/_graphmultiedge.pyx ok orgasm.graph._fibointheap :-> python/orgasm/graph/_fibointheap.pyx ok orgasm.graph._fibointheap :-> fiboheap/fibo.c ok orgasm.graph._fibominintheap :-> python/orgasm/graph/_fibominintheap.pyx ok orgasm.graph._fibominintheap :-> fiboheap/fibo.c ok orgasm.graph._fibomaxintheap :-> python/orgasm/graph/_fibomaxintheap.pyx ok orgasm.graph._fibomaxintheap :-> fiboheap/fibo.c ok orgasm.graph._graph :-> python/orgasm/graph/_graph.pyx ok orgasm.assembler._assembler :-> python/orgasm/assembler/_assembler.pyx ok orgasm.assembler._asmbgraph :-> python/orgasm/assembler/_asmbgraph.pyx ok orgasm.assembler._tango :-> python/orgasm/assembler/_tango.pyx ok orgasm.utils._progress :-> python/orgasm/utils/_progress.pyx ok orgasm.utils.dna :-> python/orgasm/utils/dna.pyx ok orgasm.multialign._dynamic :-> python/orgasm/multialign/_dynamic.pyx ok orgasm.multialign._multi :-> python/orgasm/multialign/_multi.pyx ok orgasm.backtranslate._bitvector :-> python/orgasm/backtranslate/_bitvector.pyx ok orgasm.backtranslate._ahocorasick :-> python/orgasm/backtranslate/_ahocorasick.pyx ok orgasm.backtranslate._ahocorasick :-> @expand8bits.c changed to build/temp.linux-x86_64-3.5/expand8bits.c orgasm.fiboheap._fiboheap :-> python/orgasm/fiboheap/_fiboheap.pyx ok orgasm.fiboheap._fiboheap :-> fiboheap/fibo.c ok orgasm.reads._sequences :-> python/orgasm/reads/_sequences.pyx ok orgasm.reads._fastq :-> python/orgasm/reads/_fastq.pyx ok orgasm.reads._fasta :-> python/orgasm/reads/_fasta.pyx ok orgasm.files.uncompress :-> python/orgasm/files/uncompress.pyx ok orgasm.files.universalopener :-> python/orgasm/files/universalopener.pyx ok orgasm.files.linebuffer :-> python/orgasm/files/linebuffer.pyx ok orgasm.indexer._orgasm :-> ['python/orgasm/indexer/_orgasm.pyx', 'src/buffer.c', 'src/buildindex.c', 'build/temp.linux-x86_64-3.5/code16bits.c', 'build/temp.linux-x86_64-3.5/codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/sort.c', 'src/fgetln.c'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c' Cython extension (up-to-date) building 'orgasm.indexer._orgasm' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c: In function ‘__pyx_f_6orgasm_7indexer_7_orgasm_5Index_getIds’: build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c:289:40: warning: ‘__pyx_v_t’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^ build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.c:8981:7: note: ‘__pyx_v_t’ was declared here int __pyx_v_t; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/buffer.c -o build/temp.linux-x86_64-3.5/src/buffer.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/buildindex.c -o build/temp.linux-x86_64-3.5/src/buildindex.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/buildindex.c: In function ‘buildIndex’: src/buildindex.c:44:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration] asprintf(&indexFileName,"%s.ofx",indexname); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/code16bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/codecomp.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/compsort.c -o build/temp.linux-x86_64-3.5/src/compsort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/debug.c -o build/temp.linux-x86_64-3.5/src/debug.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/debug.c: In function ‘int2bin’: src/debug.c:23:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] u = *(unsigned *)&i; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/decode.c -o build/temp.linux-x86_64-3.5/src/decode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/encode.c -o build/temp.linux-x86_64-3.5/src/encode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/fastq.c -o build/temp.linux-x86_64-3.5/src/fastq.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/fastq.c: In function ‘readFastq’: src/fastq.c:42:11: warning: implicit declaration of function ‘fgetln’ [-Wimplicit-function-declaration] buffer = fgetln(in,&lseq); ^ src/fastq.c:42:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion] buffer = fgetln(in,&lseq); ^ src/fastq.c:45:10: warning: assignment makes pointer from integer without a cast [-Wint-conversion] buffer = fgetln(in,&lseq); ^ src/fastq.c:59:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion] buffer = fgetln(in,&lseq); ^ src/fastq.c:60:9: warning: assignment makes pointer from integer without a cast [-Wint-conversion] buffer = fgetln(in,&lseq); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/indexinput.c -o build/temp.linux-x86_64-3.5/src/indexinput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/indexinput.c: In function ‘loadGeneralData’: src/indexinput.c:57:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,1,sizeof(buffer_t),input); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/indexoutput.c -o build/temp.linux-x86_64-3.5/src/indexoutput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/load.c -o build/temp.linux-x86_64-3.5/src/load.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/load.c: In function ‘loadIndexedReads’: src/load.c:34:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration] asprintf(&indexFileName,"%s.ogx",indexname); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/lookfor.c -o build/temp.linux-x86_64-3.5/src/lookfor.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/lookfor.c: In function ‘shiftKey’: src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable] uint8_t rmask; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/malloc.c -o build/temp.linux-x86_64-3.5/src/malloc.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/sort.c -o build/temp.linux-x86_64-3.5/src/sort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c src/fgetln.c -o build/temp.linux-x86_64-3.5/src/fgetln.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/_orgasm.o build/temp.linux-x86_64-3.5/src/buffer.o build/temp.linux-x86_64-3.5/src/buildindex.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/code16bits.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/codecomp.o build/temp.linux-x86_64-3.5/src/compsort.o build/temp.linux-x86_64-3.5/src/debug.o build/temp.linux-x86_64-3.5/src/decode.o build/temp.linux-x86_64-3.5/src/encode.o build/temp.linux-x86_64-3.5/src/fastq.o build/temp.linux-x86_64-3.5/src/indexinput.o build/temp.linux-x86_64-3.5/src/indexoutput.o build/temp.linux-x86_64-3.5/src/load.o build/temp.linux-x86_64-3.5/src/lookfor.o build/temp.linux-x86_64-3.5/src/malloc.o build/temp.linux-x86_64-3.5/src/sort.o build/temp.linux-x86_64-3.5/src/fgetln.o -o build/lib.linux-x86_64-3.5/orgasm/indexer/_orgasm.cpython-35m-x86_64-linux-gnu.so orgasm.indexer.fakereads :-> ['python/orgasm/indexer/fakereads.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/indexer/fakereads.c' Cython extension (up-to-date) orgasm.apps.command :-> ['python/orgasm/apps/command.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/command.c' Cython extension (up-to-date) orgasm.apps.progress :-> ['python/orgasm/apps/progress.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/progress.c' Cython extension (up-to-date) orgasm.apps.config :-> ['python/orgasm/apps/config.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/config.c' Cython extension (up-to-date) orgasm.apps.logging :-> ['python/orgasm/apps/logging.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/logging.c' Cython extension (up-to-date) orgasm.apps.counter :-> ['python/orgasm/apps/counter.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/counter.c' Cython extension (up-to-date) orgasm.apps.arguments :-> ['python/orgasm/apps/arguments.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/apps/arguments.c' Cython extension (up-to-date) orgasm.graph._graphmultiedge :-> ['python/orgasm/graph/_graphmultiedge.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graphmultiedge.c' Cython extension (up-to-date) orgasm.graph._fibointheap :-> ['python/orgasm/graph/_fibointheap.pyx', 'fiboheap/fibo.c'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibointheap.c' Cython extension (up-to-date) orgasm.graph._fibominintheap :-> ['python/orgasm/graph/_fibominintheap.pyx', 'fiboheap/fibo.c'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibominintheap.c' Cython extension (up-to-date) orgasm.graph._fibomaxintheap :-> ['python/orgasm/graph/_fibomaxintheap.pyx', 'fiboheap/fibo.c'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_fibomaxintheap.c' Cython extension (up-to-date) orgasm.graph._graph :-> ['python/orgasm/graph/_graph.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/graph/_graph.c' Cython extension (up-to-date) orgasm.assembler._assembler :-> ['python/orgasm/assembler/_assembler.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_assembler.c' Cython extension (up-to-date) orgasm.assembler._asmbgraph :-> ['python/orgasm/assembler/_asmbgraph.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_asmbgraph.c' Cython extension (up-to-date) orgasm.assembler._tango :-> ['python/orgasm/assembler/_tango.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/assembler/_tango.c' Cython extension (up-to-date) orgasm.utils._progress :-> ['python/orgasm/utils/_progress.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/utils/_progress.c' Cython extension (up-to-date) orgasm.utils.dna :-> ['python/orgasm/utils/dna.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/utils/dna.c' Cython extension (up-to-date) orgasm.multialign._dynamic :-> ['python/orgasm/multialign/_dynamic.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/multialign/_dynamic.c' Cython extension (up-to-date) orgasm.multialign._multi :-> ['python/orgasm/multialign/_multi.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/multialign/_multi.c' Cython extension (up-to-date) orgasm.backtranslate._bitvector :-> ['python/orgasm/backtranslate/_bitvector.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_bitvector.c' Cython extension (up-to-date) orgasm.backtranslate._ahocorasick :-> ['python/orgasm/backtranslate/_ahocorasick.pyx', 'build/temp.linux-x86_64-3.5/expand8bits.c'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c' Cython extension (up-to-date) building 'orgasm.backtranslate._ahocorasick' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_11AhoCorasick_simpleMatch’: build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:6063:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] __pyx_v_nextstate = (__pyx_v_table[__pyx_v_letter]); ^ build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_addSequence’: build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:8959:8: warning: variable ‘__pyx_v_letter’ set but not used [-Wunused-but-set-variable] char __pyx_v_letter[2]; ^ build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_scanIndex’: build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:289:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^ build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:9993:7: note: ‘__pyx_v_locmax’ was declared here int __pyx_v_locmax; ^ build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_14NucAhoCorasick_scanIndex’: build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:289:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^ build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:12390:7: note: ‘__pyx_v_locmax’ was declared here int __pyx_v_locmax; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/include -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/expand8bits.c -o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/expand8bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/pyrex/orgasm/backtranslate/_ahocorasick.o build/temp.linux-x86_64-3.5/build/temp.linux-x86_64-3.5/expand8bits.o -o build/lib.linux-x86_64-3.5/orgasm/backtranslate/_ahocorasick.cpython-35m-x86_64-linux-gnu.so orgasm.fiboheap._fiboheap :-> ['python/orgasm/fiboheap/_fiboheap.pyx', 'fiboheap/fibo.c'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/fiboheap/_fiboheap.c' Cython extension (up-to-date) orgasm.reads._sequences :-> ['python/orgasm/reads/_sequences.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_sequences.c' Cython extension (up-to-date) orgasm.reads._fastq :-> ['python/orgasm/reads/_fastq.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_fastq.c' Cython extension (up-to-date) orgasm.reads._fasta :-> ['python/orgasm/reads/_fasta.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/reads/_fasta.c' Cython extension (up-to-date) orgasm.files.uncompress :-> ['python/orgasm/files/uncompress.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/uncompress.c' Cython extension (up-to-date) orgasm.files.universalopener :-> ['python/orgasm/files/universalopener.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/universalopener.c' Cython extension (up-to-date) orgasm.files.linebuffer :-> ['python/orgasm/files/linebuffer.pyx'] skipping 'build/temp.linux-x86_64-3.5/pyrex/orgasm/files/linebuffer.c' Cython extension (up-to-date) running build_scripts running build_sphinx Running Sphinx v1.5.1 WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead. loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 0 source files that are out of date updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler". /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised: Traceback (most recent call last): File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object import(self.modname) File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in from orgasm.assembler import tango, getusedreads # @UnresolvedImport ImportError: cannot import name 'getusedreads' looking for now-outdated files... none found pickling environment... done checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree done preparing documents... done writing output... [100%] userapi
generating indices... genindex py-modindex highlighting module code... [100%] orgasm.assembler._assembler
writing additional pages... search copying downloadable files... [100%] ../../samples/butterfly.mito.intermediate.gml copying static files... WARNING: html_static_path entry '/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 8 warnings. Running Sphinx v1.5.1 WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todolist' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todo_node' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.graphviz']: node class 'graphviz' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.inheritance_diagram']: node class 'inheritance_diagram' is already registered, its visitors will be overridden WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead. WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'displaymath' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'eqref' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'numfig']: node class 'page_ref' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'numfig']: node class 'num_ref' is already registered, its visitors will be overridden loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [epub]: targets for 0 source files that are out of date updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler". /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised: Traceback (most recent call last): File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object import(self.modname) File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in from orgasm.assembler import tango, getusedreads # @UnresolvedImport ImportError: cannot import name 'getusedreads' looking for now-outdated files... none found pickling environment... done checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree done preparing documents... done writing output... [100%] userapi
generating indices... genindex py-modindex highlighting module code... [100%] orgasm.assembler._assembler
writing additional pages... copying static files... WARNING: html_static_path entry '/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/_static' does not exist done copying extra files... done writing mimetype file... writing META-INF/container.xml file... writing content.opf file... writing nav.xhtml file... writing toc.ncx file... writing OrganelleAssembler.epub file... build succeeded, 16 warnings. Running Sphinx v1.5.1 WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todolist' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todo_node' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.graphviz']: node class 'graphviz' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.inheritance_diagram']: node class 'inheritance_diagram' is already registered, its visitors will be overridden WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead. WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'displaymath' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'eqref' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'numfig']: node class 'page_ref' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'numfig']: node class 'num_ref' is already registered, its visitors will be overridden loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [man]: all manpages updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] userapi
/home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler". /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:10: WARNING: autodoc: failed to import module 'orgasm.tango'; the following exception was raised: Traceback (most recent call last): File "/home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object import(self.modname) File "/home/marques/Documents/Plastome-assembly/org-asm/build/lib.linux-x86_64-3.5/orgasm/tango.py", line 26, in from orgasm.assembler import tango, getusedreads # @UnresolvedImport ImportError: cannot import name 'getusedreads' looking for now-outdated files... none found pickling environment... done checking consistency... /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree done writing... organelleassembler.1 { install oa preparing commands/index assembling commands/seeds commands/buildgraph finishing commands/fillgaps commands/cutlow unfolding commands/unfold commands/unfoldrdna commands/path commands/fasta utilities commands/list commands/compact fasta fastq embl mitochondrion algorithms algorithms/seedselection algorithms/graphextension algorithms/graphcleanning algorithms/gapfilling algorithms/graphunfolding } /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --length ### /home/marques/Documents/Plastome-assembly/org-asm/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --estimate-length #.##

build succeeded, 17 warnings. running install_lib copying build/lib.linux-x86_64-3.5/orgasm/indexer/_orgasm.cpython-35m-x86_64-linux-gnu.so -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/orgasm/indexer copying build/lib.linux-x86_64-3.5/orgasm/backtranslate/_ahocorasick.cpython-35m-x86_64-linux-gnu.so -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/orgasm/backtranslate running install_scripts copying build/scripts-3.5/orgasmi -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin changing mode of /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/orgasmi to 755 changing mode of /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/oa to 755 exporting file /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/orgasmi -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/bin/orgasmi exporting file /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/bin/oa -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/bin/oa running install_egg_info Removing /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/ORG.asm-1.0.00_alpha3.egg-info Writing /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/lib/python3.5/site-packages/ORG.asm-1.0.00_alpha3.egg-info running install_sphinx copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/index.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/genindex.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/py-modindex.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/searchindex.js -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/.buildinfo -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/search.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/basic.css -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/pygments.css -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/searchtools.js -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/doctools.js -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_static/nature.css -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_static copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/userapi.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/objects.inv -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/html/_modules/index.html -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/html/_modules copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/man/organelleassembler.1 -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share/man/man1 copying /home/marques/Documents/Plastome-assembly/org-asm/build/sphinx/epub/OrganelleAssembler.epub -> /home/marques/Documents/Plastome-assembly/org-asm/ORG.asm-1.0.00-alpha3/export/share marques@marques:~/Documents/Plastome-assembly/org-asm$

It seems that there is something wrong with sphinx installation, but I cannot figure out the problem.