Installing MEME using cygwin on Windows Probems Configuring

[Cameron Gable]

It seems that when using the command:

./configure --prefix=$HOME/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt

I get quite a few errors.

checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.exe checking for suffix of executables... .exe 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 for style of include used by make... GNU checking dependency style of gcc... gcc3 checking whether gcc and cc understand -c and -o together... yes checking build system type... x86_64-unknown-cygwin checking host system type... x86_64-unknown-cygwin checking how to print strings... printf 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... /usr/x86_64-pc-cygwin/bin/ld.exe checking if the linker (/usr/x86_64-pc-cygwin/bin/ld.exe) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 8192 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-cygwin file names to x86_64-unknown-cygwin format... func_convert_file_noop checking how to convert x86_64-unknown-cygwin file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-cygwin/bin/ld.exe option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... file_magic ^x86 archive import|^x86 DLL checking for dlltool... dlltool checking how to associate runtime and link libraries... func_cygming_dll_for_implib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no 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... no checking for gcc option to produce PIC... -DDLL_EXPORT -DPIC checking if gcc PIC flag -DDLL_EXPORT -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/x86_64-pc-cygwin/bin/ld.exe) supports shared libraries... yes checking whether -lc should be explicitly linked in... yes checking dynamic linker characteristics... Win32 ld.exe 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 whether make sets $(MAKE)... (cached) yes checking for ld... /usr/x86_64-pc-cygwin/bin/ld.exe checking for sed... (cached) /usr/bin/sed checking for sendmail... /usr/sbin/sendmail checking for perl... /usr/bin/perl checking for python... /usr/bin/python checking for convert... /usr/bin/convert checking for gs... /usr/bin/gs checking for xml2-config... /usr/bin/xml2-config checking for xslt-config... /usr/bin/xslt-config checking for ant... no checking for isnan, sqrt, log, exp, fabs, pow, floor, ceil in -lm... yes checking for compress in -lz... yes checking for ANSI C header files... (cached) yes checking for sys/wait.h that is POSIX.1 compatible... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... 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 netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for pid_t... yes checking for size_t... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) 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 return type of signal handlers... void checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for floor... yes checking for getcwd... yes checking for gethostbyname... yes checking for isascii... yes checking for memset... yes checking for pow... yes checking for rint... yes checking for socket... yes checking for sqrt... yes checking for strchr... yes checking for strcspn... yes checking for strdup... yes checking for strspn... yes checking for strstr... yes checking for strlcpy... yes getconf: Unrecognized variable `LFS_CFLAGS' checking for mpicc... /usr/bin/mpicc checking for mpirun... /usr/bin/mpirun checking for MPI_Comm_rank in -lmpi... yes checking for perl... (cached) /usr/bin/perl checking for python... (cached) /usr/bin/python checking for convert... (cached) /usr/bin/convert checking for gs... (cached) /usr/bin/gs checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/css/Makefile config.status: creating doc/examples/Makefile config.status: creating doc/examples/compute_prior_dist_example_output_files/Makefile config.status: creating doc/examples/sample_opal_scripts/Makefile config.status: creating doc/images/Makefile config.status: creating doc/js/Makefile config.status: creating etc/Makefile config.status: creating src/filters/Makefile config.status: creating src/filters/purge/Makefile config.status: creating src/filters/dust/Makefile config.status: creating scripts/Makefile config.status: creating src/Makefile config.status: creating src/libxml2/Makefile config.status: creating src/libxml2/include/Makefile config.status: creating src/libxml2/include/libxml/Makefile config.status: creating src/libxslt/Makefile config.status: creating src/libexslt/Makefile config.status: creating src/parallel/Makefile config.status: creating src/wiggle/Makefile config.status: creating tests/Makefile config.status: creating tests/ame/Makefile config.status: creating tests/centrimo/Makefile config.status: creating tests/clustalw2fasta/Makefile config.status: creating tests/common/Makefile config.status: creating tests/create-priors/Makefile config.status: creating tests/draw-mhmm/Makefile config.status: creating tests/dreme/Makefile config.status: creating tests/fasta-center/Makefile config.status: creating tests/fimo/Makefile config.status: creating tests/glam2/Makefile config.status: creating tests/glam2scan/Makefile config.status: creating tests/gomo/Makefile config.status: creating tests/mast/Makefile config.status: creating tests/mcast/Makefile config.status: creating tests/meme/Makefile config.status: creating tests/mhmm/Makefile config.status: creating tests/mhmms/Makefile config.status: creating tests/mhmmscan/Makefile config.status: creating tests/motiph/Makefile config.status: creating tests/psp-gen/Makefile config.status: creating tests/qvalue/Makefile config.status: creating tests/scaffold/Makefile config.status: creating tests/spamo/Makefile config.status: creating tests/scripts/Makefile config.status: creating tests/tomtom/Makefile config.status: creating tests/web/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: Checking Required Perl Modules: HTML::Template missing. XML::Compile::SOAP11 missing. Used for downloading sequence databases from RSAT XML::Compile::WSDL11 missing. Used for downloading sequence databases from RSAT XML::Compile::Transport::SOAPHTTP missing. Used for downloading sequence databases from RSAT Checking Optional Modules: Math::CDF missing. Only required for fasta-enriched-center script (which is not called by the web scripts). ======================== Configuration parameters ======================== Install path: /home/camer_000/meme Install UID: Version: 4.10.1 C compiler: gcc C compiler flags: -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -Wl,--stack,9000000 -O3 Linker: /usr/x86_64-pc-cygwin/bin/ld.exe Special Libs: -lmpi -lz -lm MPICC /usr/bin/mpicc MPIRUN /usr/bin/mpirun MPI_CMD /usr/bin/mpirun -np MPIINC -DMPI -I/usr/include MPILIBDIR /usr/lib MPIFLAGS -DPARALLEL MEME URL: http://meme-suite.org PREVIOUS VERSION URL: SERVER CONTACT: DEVELOPER CONTACT: meme-...@uw.edu GO-SERVER URL: http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID PERL: /usr/bin/perl PYTHON: /usr/bin/python CONVERT: /usr/bin/convert GHOSTSCRIPT: /usr/bin/gs BUILD LIBXML2: yes LIBXML2 compiler flags: -I${top_srcdir}/src/libxml2/include LIBXML2 libs: ${top_builddir}/src/libxml2/libxml2.la BUILD LIBXSLT: yes LIBXSLT compiler flags: -I${top_srcdir}/src/ LIBXSLT libs: ${top_builddir}/src/libxslt/libxslt.la MEME DB: ${prefix}/db MEME LOGS: ${prefix}/LOGS MEME TEMP FILES: OPAL URL: no OPAL DEPLOY DIRECTORY: Run the following commands to compile, test and install meme: make make test make install  

For example, I have downloaded Perl but MEME can't seem to find the modules it is looking for.  Because I am using cygwin, it is having trouble find the prerequisite programs?

[cegrant]

There are several distributions of Perl, and the exact set of modules included varies from distribution to distribution. It looks like your distribution is missing a few. These can be downloaded from CPAN (http://www.cpan.org).

HTML::Template is only needed if you are setting up a MEME Suite web server. The other missing modules are only used if you are using ‘updatedb’ to download a set of sequence databases. If you are just using the command line utilities the missing modules shouldn’t be a problem. Try running ‘make’ and ‘make check’.