Code:
martijn@MartijnDesktop:~$ tar -xjvf tacg-4.1.0-src.tar.bz2
tacg-4.1.0-src/
tacg-4.1.0-src/Data/
tacg-4.1.0-src/Data/rebase.dam+dcm.data
tacg-4.1.0-src/Data/regex.data
tacg-4.1.0-src/Data/rebase.dam.data
tacg-4.1.0-src/Data/rules.data
tacg-4.1.0-src/Data/matrix.data
tacg-4.1.0-src/Data/rebase.data
tacg-4.1.0-src/Data/rebase.dcm.data
tacg-4.1.0-src/Data/codon.data
tacg-4.1.0-src/Docs/
tacg-4.1.0-src/Docs/tacg4.man.html
tacg-4.1.0-src/Docs/tacg4.help.html
tacg-4.1.0-src/Docs/nedit.macros
tacg-4.1.0-src/Docs/tacg.1
tacg-4.1.0-src/Docs/tacg4.xman.html
tacg-4.1.0-src/Docs/tacg4.0.main.html
tacg-4.1.0-src/NEWS
tacg-4.1.0-src/Seqs/
tacg-4.1.0-src/Seqs/hsp.cluster.1000.fasta
tacg-4.1.0-src/Seqs/humanprlreceptor.gb
tacg-4.1.0-src/Seqs/humprlrec.pep.fasta
tacg-4.1.0-src/Seqs/test.gcg
tacg-4.1.0-src/Seqs/test.pir
tacg-4.1.0-src/Seqs/test.m-embl
tacg-4.1.0-src/Seqs/test.m-ig-b
tacg-4.1.0-src/Seqs/test.m-nbrf
tacg-4.1.0-src/Seqs/test.m-paup
tacg-4.1.0-src/Seqs/test.fasta
tacg-4.1.0-src/Seqs/test.fitch
tacg-4.1.0-src/Seqs/test.gb
tacg-4.1.0-src/Seqs/test.ig
tacg-4.1.0-src/Seqs/test.m-msf
tacg-4.1.0-src/Seqs/test.m-pir
tacg-4.1.0-src/Seqs/humanprlreceptor.gcg
tacg-4.1.0-src/Seqs/test.strider
tacg-4.1.0-src/Seqs/test.embl
tacg-4.1.0-src/Seqs/test.m-gb
tacg-4.1.0-src/Seqs/test.m-ig
tacg-4.1.0-src/Seqs/test.ig-b
tacg-4.1.0-src/Seqs/test.nbrf
tacg-4.1.0-src/Seqs/hlef.seq
tacg-4.1.0-src/Seqs/test.m-fasta
tacg-4.1.0-src/test/
tacg-4.1.0-src/test/testtacg.pl
tacg-4.1.0-src/control
tacg-4.1.0-src/SeqFuncs.c
tacg-4.1.0-src/Proximity.c
tacg-4.1.0-src/ORF.c
tacg-4.1.0-src/MatrixMatch.c
tacg-4.1.0-src/README
tacg-4.1.0-src/configure
tacg-4.1.0-src/seqio.c
tacg-4.1.0-src/seqio.h
tacg-4.1.0-src/configure.in
tacg-4.1.0-src/config.guess
tacg-4.1.0-src/install-sh
tacg-4.1.0-src/ReadMatrix.c
tacg-4.1.0-src/config.sub
tacg-4.1.0-src/missing
tacg-4.1.0-src/mkinstalldirs
tacg-4.1.0-src/SlidWin.c
tacg-4.1.0-src/getopt.c
tacg-4.1.0-src/getopt.h
tacg-4.1.0-src/Makefile.am
tacg-4.1.0-src/Makefile.in
tacg-4.1.0-src/getopt1.c
tacg-4.1.0-src/GelLadSumFrgSits.c
tacg-4.1.0-src/Cutting.c
tacg-4.1.0-src/tacg.c
tacg-4.1.0-src/tacg.h
tacg-4.1.0-src/tacgi4/
tacg-4.1.0-src/tacgi4/tacg_Map.pdf
tacg-4.1.0-src/tacgi4/form4.html.in
tacg-4.1.0-src/tacgi4/tacgi4-cgi.pl.in
tacg-4.1.0-src/tacgi4/tacg_web_install.pl
tacg-4.1.0-src/tacgi4/microplasmid.gif
tacg-4.1.0-src/tacgi4/index.html.in
tacg-4.1.0-src/tacgi4/tacg-4.1-banner.gif
tacg-4.1.0-src/tacgi4/nedit.macros
tacg-4.1.0-src/tacgi4/tacgi4.pl.in
tacg-4.1.0-src/AUTHORS
tacg-4.1.0-src/SetFlags.c
tacg-4.1.0-src/RecentFuncs.c
tacg-4.1.0-src/INSTALL
tacg-4.1.0-src/ReadEnzFile.c
tacg-4.1.0-src/ReadRegex.c
tacg-4.1.0-src/ChangeLog
tacg-4.1.0-src/COPYING
tacg-4.1.0-src/strsep.c
tacg-4.1.0-src/strsep.h
tacg-4.1.0-src/COPYRIGHT
martijn@MartijnDesktop:~$ cd tacg-4.1.0-src/
martijn@MartijnDesktop:~/tacg-4.1.0-src$ dir
AUTHORS configure COPYRIGHT GelLadSumFrgSits.c INSTALL MatrixMatch.c ORF.c README seqio.c SlidWin.c tacg.h
ChangeLog configure.in Cutting.c getopt1.c install-sh missing Proximity.c ReadRegex.c seqio.h strsep.c tacgi4
config.guess control Data getopt.c Makefile.am mkinstalldirs ReadEnzFile.c RecentFuncs.c Seqs strsep.h test
config.sub COPYING Docs getopt.h Makefile.in NEWS ReadMatrix.c SeqFuncs.c SetFlags.c tacg.c
martijn@MartijnDesktop:~/tacg-4.1.0-src$ ./configure
creating cache ./config.cache
checking for a BSD compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking whether make sets ${MAKE}... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking for working makeinfo... missing
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler (gcc ) works... yes
checking whether the C compiler (gcc ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... yes
checking for a BSD compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking for strerror in -lcposix... no
checking for st_blksize in struct stat... yes
checking for sin in -lm... yes
checking for pcre_exec in -lpcre... yes
checking for dirent.h that defines DIR... yes
checking for opendir in -ldir... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for fcntl.h... yes
checking for unistd.h... yes
checking for working const... yes
checking for pid_t... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for uid_t in sys/types.h... yes
checking for 8-bit clean memcmp... yes
checking for unistd.h... (cached) yes
checking for getpagesize... yes
checking for working mmap... yes
checking for strftime... yes
checking for vprintf... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for putenv... yes
checking for strsep... yes
checking for strdup... yes
checking for strspn... yes
checking for strstr... yes
checking for uname... yes
updating cache ./config.cache
creating ./config.status
creating Makefile
martijn@MartijnDesktop:~/tacg-4.1.0-src$ make
gcc -DPACKAGE=\"tacg\" -DVERSION=\"4.1.0\" -DHAVE_ST_BLKSIZE=1 -DHAVE_LIBM=1 -DHAVE_LIBPCRE=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_UNISTD_H=1 -DHAVE_GETPAGESIZE=1 -DHAVE_MMAP=1 -DHAVE_STRFTIME=1 -DHAVE_VPRINTF=1 -DHAVE_ALLOCA_H=1 -DHAVE_ALLOCA=1 -DHAVE_PUTENV=1 -DHAVE_STRSEP=1 -DHAVE_STRDUP=1 -DHAVE_STRSPN=1 -DHAVE_STRSTR=1 -DHAVE_UNAME=1 -I. -I. -DBUILD_DATE=\"Sun\ Apr\ 12\ 11:16:56\ CEST\ 2009\" -DUNAME=\"Linux\ MartijnDesktop\ 2.6.27-11-generic\ #1\ SMP\ Wed\ Apr\ 1\ 20:53:41\ UTC\ 2009\ x86_64\ GNU/Linux\" -DGCC_VER=\"gcc\ Ubuntu\ 4.3.2-1ubuntu12\ 4.3.2\" -g -O2 -Wall -c seqio.c
seqio.c: In function ‘seqfgcgify’:
seqio.c:2744: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:2748: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:2750: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘seqfungcgify’:
seqio.c:2968: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:3025: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘putline’:
seqio.c:13542: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:13590: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘simple_putseq’:
seqio.c:13723: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘genbank_putseq’:
seqio.c:13937: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:13952: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:13997: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘pir_putseq’:
seqio.c:14151: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:14194: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘embl_putseq’:
seqio.c:14321: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:14337: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:14393: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘sprot_putseq’:
seqio.c:14536: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:14599: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘nbrf_putseq’:
seqio.c:14686: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:14732: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘nbrfold_putseq’:
seqio.c:14797: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:14802: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘fasta_putseq’:
seqio.c:14839: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:14875: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘fastaold_putseq’:
seqio.c:14919: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘stanford_putseq’:
seqio.c:14981: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15007: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘stanfordold_putseq’:
seqio.c:15052: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15062: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘gcg_putseq’:
seqio.c:15118: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘asn_putseq’:
seqio.c:15801: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15807: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15811: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15825: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15832: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15839: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15846: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:15953: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘genbank_annotate’:
seqio.c:16074: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16114: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16128: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16140: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘pir_annotate’:
seqio.c:16179: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16219: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16233: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16245: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘embl_annotate’:
seqio.c:16294: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16348: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16362: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16377: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘sprot_annotate’:
seqio.c:16425: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16464: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16478: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16490: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘fasta_annotate’:
seqio.c:16519: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16558: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16573: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16585: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘nbrf_annotate’:
seqio.c:16630: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16637: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16677: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16691: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16704: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘stanford_annotate’:
seqio.c:16772: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16786: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16798: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c: In function ‘asn_annotate’:
seqio.c:16907: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16965: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16991: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16992: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:16997: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
seqio.c:17018: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
gcc -DPACKAGE=\"tacg\" -DVERSION=\"4.1.0\" -DHAVE_ST_BLKSIZE=1 -DHAVE_LIBM=1 -DHAVE_LIBPCRE=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_UNISTD_H=1 -DHAVE_GETPAGESIZE=1 -DHAVE_MMAP=1 -DHAVE_STRFTIME=1 -DHAVE_VPRINTF=1 -DHAVE_ALLOCA_H=1 -DHAVE_ALLOCA=1 -DHAVE_PUTENV=1 -DHAVE_STRSEP=1 -DHAVE_STRDUP=1 -DHAVE_STRSPN=1 -DHAVE_STRSTR=1 -DHAVE_UNAME=1 -I. -I. -DBUILD_DATE=\"Sun\ Apr\ 12\ 11:16:56\ CEST\ 2009\" -DUNAME=\"Linux\ MartijnDesktop\ 2.6.27-11-generic\ #1\ SMP\ Wed\ Apr\ 1\ 20:53:41\ UTC\ 2009\ x86_64\ GNU/Linux\" -DGCC_VER=\"gcc\ Ubuntu\ 4.3.2-1ubuntu12\ 4.3.2\" -g -O2 -Wall-c Cutting.c
In file included from Cutting.c:17:
tacg.h:176: error: array type has incomplete element type
tacg.h:178: error: array type has incomplete element type
make: *** [Cutting.o] Error 1
martijn@MartijnDesktop:~/tacg-4.1.0-src$
As you can see, the ./CONFIGURE seems to work properly, no giant errors. The make command however, seems to give trouble. It yells about ignoring output from fwrite, and finally it says it has problems with an incomplete element type of an array... suuuure. Then it stops the make file, and if you were to try make install after that it gives basically the same error as when terminating the make.
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