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ctSkennerton / crass

The CRISPR assembler
http://ctskennerton.github.io/crass
GNU General Public License v3.0
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Crass make failure #'Utils.h' file not found #72

Closed fmoyaflores closed 9 years ago

fmoyaflores commented 9 years ago

Hi ctSkennerton,

I've been trying to install crass on my computer during the past days, and I came across some posts in github with the same issues I've been dealing with. I've tested the newest version of the software (v0.3.11) just now. I see some things working this time (the libcrispr error doesn't appear anymore), but I'm still unable to get it to work. Here's the log info, with the errors appearing at the end:

dyn-72-33-149-176:crass-0.3.11 Francisco$ ./autogen.sh Preparing the crass build system...please wait

Found GNU Autoconf version 2.69 Found GNU Automake version 1.15 Found GNU Libtool version 2.4

Automatically preparing build ... done

The crass build system is now prepared. To build here, run: ./configure make

dyn-72-33-149-176:crass-0.3.11 Francisco$ sudo ./configure Password: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... build/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-apple-darwin14.1.0 checking host system type... x86_64-apple-darwin14.1.0 checking how to print strings... printf checking for style of include used by make... GNU 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 whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin14.1.0 file names to x86_64-apple-darwin14.1.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin14.1.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin14.1.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin14.1.0 dyld checking how to hardcode library paths into programs... immediate checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) gcc3 checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... -D_THREAD_SAFE checking for PTHREAD_PRIO_INHERIT... yes checking for Xerces C++ Parser headers in /usr/local/include and /usr/local/include/xercesc... found checking for Xerces C++ Parser libraries... found checking for Xerces C++ Parser... yes checking for velvetg... no checking for cap3... no checking for gzread in -lz... yes checking for ANSI C header files... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for memset... yes checking for pow... yes checking for strchr... yes checking for strspn... yes checking for pdflatex... no configure: WARNING: Unable to create PDF version of the user manual. checking for cap3... no checking for velvetg... no checking for velveth... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/crass/Makefile config.status: creating man/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands

dyn-72-33-149-176:crass-0.3.11 Francisco$ sudo make Password: /Library/Developer/CommandLineTools/usr/bin/make all-recursive Making all in src Making all in crass g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT PatternMatcher.o -MD -MP -MF .deps/PatternMatcher.Tpo -c -o PatternMatcher.o PatternMatcher.cpp mv -f .deps/PatternMatcher.Tpo .deps/PatternMatcher.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT Rainbow.o -MD -MP -MF .deps/Rainbow.Tpo -c -o Rainbow.o Rainbow.cpp mv -f .deps/Rainbow.Tpo .deps/Rainbow.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT crass.o -MD -MP -MF .deps/crass.Tpo -c -o crass.o crass.cpp In file included from crass.cpp:53: In file included from ./crass.h:47: ./kseq.h:76:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

In file included from crass.cpp:53: In file included from ./crass.h:49: In file included from ./WorkHorse.h:50: In file included from ./NodeManager.h:61: In file included from ./writer.h:37: ./base.h:412:8: warning: no newline at end of file [-Wnewline-eof]

endif

   ^

In file included from crass.cpp:53: In file included from ./crass.h:49: In file included from ./WorkHorse.h:50: In file included from ./NodeManager.h:61: ./writer.h:275:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

In file included from crass.cpp:53: In file included from ./crass.h:49: In file included from ./WorkHorse.h:58: In file included from ./Aligner.h:42: ./ksw.h:72:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

4 warnings generated. mv -f .deps/crass.Tpo .deps/crass.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT WuManber.o -MD -MP -MF .deps/WuManber.Tpo -c -o WuManber.o WuManber.cpp mv -f .deps/WuManber.Tpo .deps/WuManber.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT LoggerSimp.o -MD -MP -MF .deps/LoggerSimp.Tpo -c -o LoggerSimp.o LoggerSimp.cpp mv -f .deps/LoggerSimp.Tpo .deps/LoggerSimp.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT SeqUtils.o -MD -MP -MF .deps/SeqUtils.Tpo -c -o SeqUtils.o SeqUtils.cpp mv -f .deps/SeqUtils.Tpo .deps/SeqUtils.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT CrisprNode.o -MD -MP -MF .deps/CrisprNode.Tpo -c -o CrisprNode.o CrisprNode.cpp In file included from CrisprNode.cpp:44: In file included from ./CrisprNode.h:50: In file included from ./libcrispr.h:53: ./kseq.h:76:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

1 warning generated. mv -f .deps/CrisprNode.Tpo .deps/CrisprNode.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT NodeManager.o -MD -MP -MF .deps/NodeManager.Tpo -c -o NodeManager.o NodeManager.cpp In file included from NodeManager.cpp:48: In file included from ./NodeManager.h:54: In file included from ./CrisprNode.h:50: In file included from ./libcrispr.h:53: ./kseq.h:76:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

In file included from NodeManager.cpp:48: In file included from ./NodeManager.h:61: In file included from ./writer.h:37: ./base.h:412:8: warning: no newline at end of file [-Wnewline-eof]

endif

   ^

In file included from NodeManager.cpp:48: In file included from ./NodeManager.h:61: ./writer.h:275:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

3 warnings generated. mv -f .deps/NodeManager.Tpo .deps/NodeManager.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT libcrispr.o -MD -MP -MF .deps/libcrispr.Tpo -c -o libcrispr.o libcrispr.cpp In file included from libcrispr.cpp:54: In file included from ./libcrispr.h:53: ./kseq.h:76:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

1 warning generated. mv -f .deps/libcrispr.Tpo .deps/libcrispr.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT WorkHorse.o -MD -MP -MF .deps/WorkHorse.Tpo -c -o WorkHorse.o WorkHorse.cpp In file included from WorkHorse.cpp:55: In file included from ./WorkHorse.h:49: In file included from ./libcrispr.h:53: ./kseq.h:76:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

In file included from WorkHorse.cpp:55: In file included from ./WorkHorse.h:50: In file included from ./NodeManager.h:61: In file included from ./writer.h:37: ./base.h:412:8: warning: no newline at end of file [-Wnewline-eof]

endif

   ^

In file included from WorkHorse.cpp:55: In file included from ./WorkHorse.h:50: In file included from ./NodeManager.h:61: ./writer.h:275:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

In file included from WorkHorse.cpp:55: In file included from ./WorkHorse.h:58: In file included from ./Aligner.h:42: ./ksw.h:72:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

4 warnings generated. mv -f .deps/WorkHorse.Tpo .deps/WorkHorse.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT SpacerInstance.o -MD -MP -MF .deps/SpacerInstance.Tpo -c -o SpacerInstance.o SpacerInstance.cpp In file included from SpacerInstance.cpp:41: In file included from ./SpacerInstance.h:48: In file included from ./CrisprNode.h:50: In file included from ./libcrispr.h:53: ./kseq.h:76:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

1 warning generated. mv -f .deps/SpacerInstance.Tpo .deps/SpacerInstance.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT ReadHolder.o -MD -MP -MF .deps/ReadHolder.Tpo -c -o ReadHolder.o ReadHolder.cpp mv -f .deps/ReadHolder.Tpo .deps/ReadHolder.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT SmithWaterman.o -MD -MP -MF .deps/SmithWaterman.Tpo -c -o SmithWaterman.o SmithWaterman.cpp mv -f .deps/SmithWaterman.Tpo .deps/SmithWaterman.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT StringCheck.o -MD -MP -MF .deps/StringCheck.Tpo -c -o StringCheck.o StringCheck.cpp mv -f .deps/StringCheck.Tpo .deps/StringCheck.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT kseq.o -MD -MP -MF .deps/kseq.Tpo -c -o kseq.o kseq.cpp In file included from kseq.cpp:36: ./kseq.h:76:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

kseq.cpp:226:2: warning: no newline at end of file [-Wnewline-eof] } ^ 2 warnings generated. mv -f .deps/kseq.Tpo .deps/kseq.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT SearchChecker.o -MD -MP -MF .deps/SearchChecker.Tpo -c -o SearchChecker.o SearchChecker.cpp SearchChecker.cpp:65:2: warning: no newline at end of file [-Wnewline-eof] } ^ 1 warning generated. mv -f .deps/SearchChecker.Tpo .deps/SearchChecker.Po gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT ksw.o -MD -MP -MF .deps/ksw.Tpo -c -o ksw.o ksw.c mv -f .deps/ksw.Tpo .deps/ksw.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT Aligner.o -MD -MP -MF .deps/Aligner.Tpo -c -o Aligner.o Aligner.cpp In file included from Aligner.cpp:37: In file included from ./Aligner.h:42: ./ksw.h:72:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

1 warning generated. mv -f .deps/Aligner.Tpo .deps/Aligner.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT base.o -MD -MP -MF .deps/base.Tpo -c -o base.o base.cpp In file included from base.cpp:35: ./base.h:412:8: warning: no newline at end of file [-Wnewline-eof]

endif

   ^

1 warning generated. mv -f .deps/base.Tpo .deps/base.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT parser.o -MD -MP -MF .deps/parser.Tpo -c -o parser.o parser.cpp In file included from parser.cpp:35: In file included from ./parser.h:37: In file included from ./reader.h:37: ./base.h:412:8: warning: no newline at end of file [-Wnewline-eof]

endif

   ^

In file included from parser.cpp:35: In file included from ./parser.h:37: ./reader.h:63:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

In file included from parser.cpp:35: In file included from ./parser.h:38: ./writer.h:275:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

In file included from parser.cpp:35: ./parser.h:50:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

parser.cpp:40:3: warning: no newline at end of file [-Wnewline-eof] {} ^ 5 warnings generated. mv -f .deps/parser.Tpo .deps/parser.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT reader.o -MD -MP -MF .deps/reader.Tpo -c -o reader.o reader.cpp In file included from reader.cpp:35: In file included from ./reader.h:37: ./base.h:412:8: warning: no newline at end of file [-Wnewline-eof]

endif

   ^

In file included from reader.cpp:35: ./reader.h:63:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

2 warnings generated. mv -f .deps/reader.Tpo .deps/reader.Po g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT writer.o -MD -MP -MF .deps/writer.Tpo -c -o writer.o writer.cpp In file included from writer.cpp:35: In file included from ./writer.h:37: ./base.h:412:8: warning: no newline at end of file [-Wnewline-eof]

endif

   ^

In file included from writer.cpp:35: ./writer.h:275:7: warning: no newline at end of file [-Wnewline-eof]

endif

  ^

./writer.h:45:17: warning: private field 'XW_CurrentSourceId' is not used [-Wunused-private-field] int XW_CurrentSourceId; ^ 3 warnings generated. mv -f .deps/writer.Tpo .deps/writer.Po /bin/sh ../../libtool --tag=CXX --mode=link g++ -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -L/usr/local/lib -lz -lxerces-c -o crass PatternMatcher.o Rainbow.o crass.o WuManber.o LoggerSimp.o SeqUtils.o CrisprNode.o NodeManager.o libcrispr.o WorkHorse.o SpacerInstance.o ReadHolder.o SmithWaterman.o StringCheck.o kseq.o SearchChecker.o ksw.o Aligner.o base.o parser.o reader.o writer.o
libtool: link: g++ -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -o crass PatternMatcher.o Rainbow.o crass.o WuManber.o LoggerSimp.o SeqUtils.o CrisprNode.o NodeManager.o libcrispr.o WorkHorse.o SpacerInstance.o ReadHolder.o SmithWaterman.o StringCheck.o kseq.o SearchChecker.o ksw.o Aligner.o base.o parser.o reader.o writer.o -Wl,-bind_at_load -L/usr/local/lib -lz -lxerces-c g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include -I/usr/local/include/xercesc -pedantic -Wall -g -O2 -MT crisprtools.o -MD -MP -MF .deps/crisprtools.Tpo -c -o crisprtools.o crisprtools.cpp crisprtools.cpp:25:10: fatal error: 'Utils.h' file not found

include "Utils.h"

     ^

1 error generated. make[3]: * [crisprtools.o] Error 1 make[2]: * [all-recursive] Error 1 make[1]: * [all-recursive] Error 1 make: * [all] Error 2

I also tried sudo ./configure --with-xerces=/usr/local/opt/xerces-c with the same results. I hope you can help me solve this issue.

Thanks! Francisco

ctSkennerton commented 9 years ago

Oops, forgot to add in a file to that latest release. Try now with v0.3.12

fmoyaflores commented 9 years ago

Yes it worked! Thanks!