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Old 07-29-2010, 12:37 AM   #1
schmima
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Default EMBOSS and BFAST interference?

Hi together

Tried to install BFAST and ran into a small Problem. (BTW - autogen.sh did not work)

./configure worked fine

While executing 'make' I got a couple of errors of the type
...undefined reference to 'egzXXX'

Here two examples:
BLib.o: In function `gzread64':
.../bfast-0.6.4d/bfast/BLib.c:1676: undefined reference to `egzread'
BLib.o: In function `gzwrite64':
.../bfast-0.6.4d/bfast/BLib.c:1656: undefined reference to `egzwrite'

Searching for it I found in the zlibemboss.h file:
...
#define gzopen egzopen
#define gzread egzread
#define gzwrite egzwrite
...
(full version on: http://b-src.cbrc.jp/source/EMBOSS-6...b/zlibemboss.h)

Seems to me that EMBOSS messed up some definitions (?).

Anyone had a similar problem/knows an easy explanation or even solution?
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Old 07-29-2010, 07:48 AM   #2
nilshomer
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Quote:
Originally Posted by schmima View Post
Hi together

Tried to install BFAST and ran into a small Problem. (BTW - autogen.sh did not work)

./configure worked fine

While executing 'make' I got a couple of errors of the type
...undefined reference to 'egzXXX'

Here two examples:
BLib.o: In function `gzread64':
.../bfast-0.6.4d/bfast/BLib.c:1676: undefined reference to `egzread'
BLib.o: In function `gzwrite64':
.../bfast-0.6.4d/bfast/BLib.c:1656: undefined reference to `egzwrite'

Searching for it I found in the zlibemboss.h file:
...
#define gzopen egzopen
#define gzread egzread
#define gzwrite egzwrite
...
(full version on: http://b-src.cbrc.jp/source/EMBOSS-6...b/zlibemboss.h)

Seems to me that EMBOSS messed up some definitions (?).

Anyone had a similar problem/knows an easy explanation or even solution?
Post the output of autogen.sh and configure.
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Old 07-29-2010, 10:50 PM   #3
schmima
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Good morning... ^^
Here's the output:

root@Marc-ZOD:/home/marc/Bioinformatics/bfast-0.6.4d# sh autogen.sh
running:
aclocal
eval: 1: aclocal: not found
error: while running 'aclocal'

root@Marc-ZOD:/home/marc/Bioinformatics/bfast-0.6.4d# ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
./configure: line 3462: git: command not found
checking for BZ2_bzRead in -lbz2... yes
checking for an ANSI C-conforming const... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -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 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 pow in -lm... yes
checking for gzread in -lz... yes
checking for floor... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking for strdup... yes
checking for strpbrk... yes
checking for strstr... yes
checking for strtok_r... yes
checking for int8_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for short int... yes
checking size of short int... 2
checking for int... yes
checking size of int... 4
checking for long int... yes
checking size of long int... 8
checking for ANSI C header files... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) 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 float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bfast/Makefile
config.status: creating butil/Makefile
config.status: creating scripts/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands

Here also the make output:
root@Marc-ZOD:/home/marc/Bioinformatics/bfast-0.6.4d# make
make all-recursive
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d'
Making all in bfast
make[2]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/bfast'
gcc -Wall -g -O2 -pthread -m64 -D_FILE_OFFSET_BITS=64 -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lz -lm -lbz2
BLib.o: In function `gzread64':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:1676: undefined reference to `egzread'
BLib.o: In function `gzwrite64':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:1656: undefined reference to `egzwrite'
BLib.o: In function `CloseTmpGZFile':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:574: undefined reference to `egzclose'
BLib.o: In function `ReopenTmpGZFile':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:594: undefined reference to `egzopen'
BLib.o: In function `OpenTmpGZFile':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:549: undefined reference to `egzdopen'
BLib.o: In function `CheckRGIndexes':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:388: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:347: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:432: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BLib.c:393: undefined reference to `egzopen'
RGBinary.o: In function `RGBinaryWriteBinary':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGBinary.c:436: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGBinary.c:451: undefined reference to `egzclose'
RGBinary.o: In function `RGBinaryPrintInfo':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGBinary.c:965: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGBinary.c:973: undefined reference to `egzclose'
RGBinary.o: In function `RGBinaryReadBinary':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGBinary.c:344: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGBinary.c:370: undefined reference to `egzclose'
RGIndex.o: In function `RGIndexOpenForWriting':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndex.c:2695: undefined reference to `egzdopen'
RGIndex.o: In function `RGIndexGetHeader':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndex.c:1834: undefined reference to `egzopen'
RGIndex.o: In function `RGIndexPrintInfo':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndex.c:1762: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndex.c:1797: undefined reference to `egzclose'
RGIndex.o: In function `RGIndexRead':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndex.c:1683: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndex.c:1740: undefined reference to `egzclose'
RGIndex.o: In function `RGIndexGetHeader':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndex.c:1840: undefined reference to `egzclose'
RGIndex.o: In function `RGIndexPrint':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndex.c:1667: undefined reference to `egzclose'
RGIndexAccuracy.o: In function `RGIndexAccuracySetReadFromRGIndexes':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndexAccuracy.c:571: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndexAccuracy.c:586: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndexAccuracy.c:592: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RGIndexAccuracy.c:607: undefined reference to `egzclose'
RunMatch.o: In function `FindMatchesInIndexSet':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunMatch.c:695: undefined reference to `egzclose'
RunMatch.o: In function `RunMatch':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunMatch.c:161: undefined reference to `egzdopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunMatch.c:237: undefined reference to `egzclose'
RunLocalAlign.o: In function `RunAligner':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunLocalAlign.c:70: undefined reference to `egzdopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunLocalAlign.c:87: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunLocalAlign.c:119: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunLocalAlign.c:122: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunLocalAlign.c:82: undefined reference to `egzdopen'
RunPostProcess.o: In function `GetPEDBins':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:812: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:899: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:807: undefined reference to `egzdopen'
RunPostProcess.o: In function `ReadInputFilterAndOutput':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:100: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:117: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:299: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:302: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:95: undefined reference to `egzdopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:293: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/RunPostProcess.c:107: undefined reference to `egzdopen'
BfastBAFConvert.o: In function `BfastBAFConvert':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BfastBAFConvert.c:201: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BfastBAFConvert.c:194: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BfastBAFConvert.c:148: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BfastBAFConvert.c:137: undefined reference to `egzopen'
BfastBMFConvert.o: In function `BfastBMFConvert':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BfastBMFConvert.c:120: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BfastBMFConvert.c:109: undefined reference to `egzopen'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BfastBMFConvert.c:167: undefined reference to `egzclose'
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/BfastBMFConvert.c:160: undefined reference to `egzclose'
aflib.o: In function `AFILE_afwrite':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/aflib.c:244: undefined reference to `egzwrite'
aflib.o: In function `AFILE_afread':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/aflib.c:220: undefined reference to `egzread'
aflib.o: In function `AFILE_afclose':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/aflib.c:159: undefined reference to `egzclose'
aflib.o: In function `AFILE_afdopen':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/aflib.c:129: undefined reference to `egzdopen'
aflib.o: In function `AFILE_afopen':
/home/marc/Bioinformatics/bfast-0.6.4d/bfast/aflib.c:67: undefined reference to `egzopen'
collect2: ld returned 1 exit status
make[2]: *** [bfast] Fehler 1
make[2]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/bfast'
make[1]: *** [all-recursive] Fehler 1
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d'
make: *** [all] Fehler 2


Thanks in advance
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Old 07-30-2010, 07:42 AM   #4
nilshomer
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Here's the answer (via google): https://stat.ethz.ch/pipermail/bioco...ay/033328.html
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Old 07-30-2010, 08:03 AM   #5
schmima
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thanks a lot for the quick answer.
make worked now.
make check gave some errors:

root@Marc-ZOD:/home/marc/Bioinformatics/bfast-0.6.4d# make check
Making check in bfast
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/bfast'
make[1]: Für das Ziel »check« ist nichts zu tun.
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/bfast'
Making check in butil
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/butil'
make[1]: Für das Ziel »check« ist nichts zu tun.
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/butil'
Making check in scripts
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/scripts'
make[1]: Für das Ziel »check« ist nichts zu tun.
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/scripts'
Making check in tests
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/tests'
make check-TESTS
make[2]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/tests'
.: 3: test.definitions.sh: not found
FAIL: test.initialize.sh
.: 3: test.definitions.sh: not found
FAIL: test.fasta2brg.sh
.: 2: test.definitions.sh: not found
FAIL: test.index.sh
.: 3: test.definitions.sh: not found
FAIL: test.match.sh
.: 3: test.definitions.sh: not found
FAIL: test.localalign.sh
.: 3: test.definitions.sh: not found
FAIL: test.postprocess.sh
.: 3: test.definitions.sh: not found
FAIL: test.diff.sh
.: 3: test.definitions.sh: not found
FAIL: test.cleanup.sh
=================================================
8 of 8 tests failed
Please report to bfast-help@lists.sourceforge.net
=================================================
make[2]: *** [check-TESTS] Fehler 1
make[2]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/tests'
make[1]: *** [check-am] Fehler 2
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/tests'
make: *** [check-recursive] Fehler 1

make install worked.

Hm - I did not try yet the program. I'm leaving this weekend for some weeks for vacation. I will try the program as soon as I'm back and I will let you know if it works or not.

Thanks again
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Old 07-30-2010, 06:48 PM   #6
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Quote:
Originally Posted by schmima View Post
thanks a lot for the quick answer.
make worked now.
make check gave some errors:

root@Marc-ZOD:/home/marc/Bioinformatics/bfast-0.6.4d# make check
Making check in bfast
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/bfast'
make[1]: Für das Ziel »check« ist nichts zu tun.
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/bfast'
Making check in butil
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/butil'
make[1]: Für das Ziel »check« ist nichts zu tun.
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/butil'
Making check in scripts
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/scripts'
make[1]: Für das Ziel »check« ist nichts zu tun.
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/scripts'
Making check in tests
make[1]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/tests'
make check-TESTS
make[2]: Betrete Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/tests'
.: 3: test.definitions.sh: not found
FAIL: test.initialize.sh
.: 3: test.definitions.sh: not found
FAIL: test.fasta2brg.sh
.: 2: test.definitions.sh: not found
FAIL: test.index.sh
.: 3: test.definitions.sh: not found
FAIL: test.match.sh
.: 3: test.definitions.sh: not found
FAIL: test.localalign.sh
.: 3: test.definitions.sh: not found
FAIL: test.postprocess.sh
.: 3: test.definitions.sh: not found
FAIL: test.diff.sh
.: 3: test.definitions.sh: not found
FAIL: test.cleanup.sh
=================================================
8 of 8 tests failed
Please report to bfast-help@lists.sourceforge.net
=================================================
make[2]: *** [check-TESTS] Fehler 1
make[2]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/tests'
make[1]: *** [check-am] Fehler 2
make[1]: Verlasse Verzeichnis '/home/marc/Bioinformatics/bfast-0.6.4d/tests'
make: *** [check-recursive] Fehler 1

make install worked.

Hm - I did not try yet the program. I'm leaving this weekend for some weeks for vacation. I will try the program as soon as I'm back and I will let you know if it works or not.

Thanks again
It should work. The above has to do with how bash is not properly including files. If someone knows why the "." include statement doesn't work, please post here.
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Old 07-31-2010, 05:53 AM   #7
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This also happened to samtools/bwa. This is really a bug of emboss and someone should report it.
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Old 12-04-2010, 12:32 AM   #8
patto
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Just in case anyone is monitoring this thread, I have a very similar error compiling bfast-0.6.4e, ie

BLib.o: In function `gzread64':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:1676: undefined reference to `gzread'
BLib.o: In function `gzwrite64':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:1656: undefined reference to `gzwrite'
BLib.o: In function `CloseTmpGZFile':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:574: undefined reference to `gzclose'

I tried to find a rogue zlib.h, but found about 10 of them. I moved all but the one in /usr/include to no avail.

Here's the full make output:

patto@linuxubuntu1:~/src/bfast-0.6.4e$ make
make all-recursive
make[1]: Entering directory `/home/patto/src/bfast-0.6.4e'
Making all in bfast
make[2]: Entering directory `/home/patto/src/bfast-0.6.4e/bfast'
gcc -Wall -g -O2 -pthread -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lm
BLib.o: In function `gzread64':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:1676: undefined reference to `gzread'
BLib.o: In function `gzwrite64':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:1656: undefined reference to `gzwrite'
BLib.o: In function `CloseTmpGZFile':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:574: undefined reference to `gzclose'
BLib.o: In function `ReopenTmpGZFile':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:594: undefined reference to `gzopen'
BLib.o: In function `OpenTmpGZFile':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:549: undefined reference to `gzdopen'
BLib.o: In function `CheckRGIndexes':
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:388: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:347: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:432: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/BLib.c:393: undefined reference to `gzopen'
RGBinary.o: In function `RGBinaryWriteBinary':
/home/patto/src/bfast-0.6.4e/bfast/RGBinary.c:436: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RGBinary.c:451: undefined reference to `gzclose'
RGBinary.o: In function `RGBinaryPrintInfo':
/home/patto/src/bfast-0.6.4e/bfast/RGBinary.c:965: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RGBinary.c:973: undefined reference to `gzclose'
RGBinary.o: In function `RGBinaryReadBinary':
/home/patto/src/bfast-0.6.4e/bfast/RGBinary.c:344: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RGBinary.c:370: undefined reference to `gzclose'
RGIndex.o: In function `RGIndexOpenForWriting':
/home/patto/src/bfast-0.6.4e/bfast/RGIndex.c:2695: undefined reference to `gzdopen'
RGIndex.o: In function `RGIndexGetHeader':
/home/patto/src/bfast-0.6.4e/bfast/RGIndex.c:1834: undefined reference to `gzopen'
RGIndex.o: In function `RGIndexPrintInfo':
/home/patto/src/bfast-0.6.4e/bfast/RGIndex.c:1762: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RGIndex.c:1797: undefined reference to `gzclose'
RGIndex.o: In function `RGIndexRead':
/home/patto/src/bfast-0.6.4e/bfast/RGIndex.c:1683: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RGIndex.c:1740: undefined reference to `gzclose'
RGIndex.o: In function `RGIndexGetHeader':
/home/patto/src/bfast-0.6.4e/bfast/RGIndex.c:1840: undefined reference to `gzclose'
RGIndex.o: In function `RGIndexPrint':
/home/patto/src/bfast-0.6.4e/bfast/RGIndex.c:1667: undefined reference to `gzclose'
RGIndexAccuracy.o: In function `RGIndexAccuracySetReadFromRGIndexes':
/home/patto/src/bfast-0.6.4e/bfast/RGIndexAccuracy.c:571: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RGIndexAccuracy.c:586: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/RGIndexAccuracy.c:592: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RGIndexAccuracy.c:607: undefined reference to `gzclose'
RunMatch.o: In function `FindMatchesInIndexSet':
/home/patto/src/bfast-0.6.4e/bfast/RunMatch.c:695: undefined reference to `gzclose'
RunMatch.o: In function `RunMatch':
/home/patto/src/bfast-0.6.4e/bfast/RunMatch.c:161: undefined reference to `gzdopen'
/home/patto/src/bfast-0.6.4e/bfast/RunMatch.c:237: undefined reference to `gzclose'
RunLocalAlign.o: In function `RunAligner':
/home/patto/src/bfast-0.6.4e/bfast/RunLocalAlign.c:70: undefined reference to `gzdopen'
/home/patto/src/bfast-0.6.4e/bfast/RunLocalAlign.c:87: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RunLocalAlign.c:119: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/RunLocalAlign.c:122: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/RunLocalAlign.c:82: undefined reference to `gzdopen'
RunPostProcess.o: In function `ReadInputFilterAndOutput':
/home/patto/src/bfast-0.6.4e/bfast/RunPostProcess.c:139: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/RunPostProcess.c:353: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/RunPostProcess.c:134: undefined reference to `gzdopen'
/home/patto/src/bfast-0.6.4e/bfast/RunPostProcess.c:347: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/RunPostProcess.c:146: undefined reference to `gzdopen'
BfastBAFConvert.o: In function `BfastBAFConvert':
/home/patto/src/bfast-0.6.4e/bfast/BfastBAFConvert.c:202: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/BfastBAFConvert.c:195: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/BfastBAFConvert.c:148: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/BfastBAFConvert.c:137: undefined reference to `gzopen'
BfastBMFConvert.o: In function `BfastBMFConvert':
/home/patto/src/bfast-0.6.4e/bfast/BfastBMFConvert.c:120: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/BfastBMFConvert.c:109: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/BfastBMFConvert.c:167: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/BfastBMFConvert.c:160: undefined reference to `gzclose'
aflib.o: In function `AFILE_afread':
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:220: undefined reference to `gzread'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:185: undefined reference to `BZ2_bzRead'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:192: undefined reference to `BZ2_bzReadGetUnused'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:199: undefined reference to `BZ2_bzReadClose'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:207: undefined reference to `BZ2_bzReadOpen'
aflib.o: In function `AFILE_afclose':
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:159: undefined reference to `gzclose'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:150: undefined reference to `BZ2_bzWriteClose'
aflib.o: In function `AFILE_afdopen':
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:125: undefined reference to `BZ2_bzWriteOpen'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:129: undefined reference to `gzdopen'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:115: undefined reference to `BZ2_bzReadOpen'
aflib.o: In function `AFILE_afopen':
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:67: undefined reference to `gzopen'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:52: undefined reference to `BZ2_bzReadOpen'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:62: undefined reference to `BZ2_bzWriteOpen'
aflib.o: In function `AFILE_afwrite':
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:244: undefined reference to `gzwrite'
/home/patto/src/bfast-0.6.4e/bfast/aflib.c:241: undefined reference to `BZ2_bzwrite'
collect2: ld returned 1 exit status
make[2]: *** [bfast] Error 1
make[2]: Leaving directory `/home/patto/src/bfast-0.6.4e/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/patto/src/bfast-0.6.4e'
make: *** [all] Error 2
patto is offline   Reply With Quote
Old 04-25-2011, 05:50 PM   #9
fenciso
Junior Member
 
Location: bogota, colombia

Join Date: Apr 2011
Posts: 5
Default

Hi, could someone help me find the solution to this error???

felix-VirtualBox bfast+bwa-0.6.5a # make check
Making check in bfast
make[1]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/bfast'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/bfast'
Making check in butil
make[1]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/butil'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/butil'
Making check in scripts
make[1]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/scripts'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/scripts'
Making check in tests
make[1]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/tests'
make check-TESTS
make[2]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/tests'
.: 3: test.definitions.sh: not found
FAIL: test.initialize.sh
.: 3: test.definitions.sh: not found
FAIL: test.fasta2brg.sh
.: 2: test.definitions.sh: not found
FAIL: test.index.sh
.: 3: test.definitions.sh: not found
FAIL: test.match.sh
.: 3: test.definitions.sh: not found
FAIL: test.localalign.sh
.: 3: test.definitions.sh: not found
FAIL: test.postprocess.sh
.: 3: test.definitions.sh: not found
FAIL: test.diff.sh
.: 3: test.definitions.sh: not found
FAIL: test.cleanup.sh
=================================================
8 of 8 tests failed
Please report to bfast-help@lists.sourceforge.net
=================================================
make[2]: *** [check-TESTS] Error 1
make[2]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/tests'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/tests'
make: *** [check-recursive] Error 1

Thanks
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Old 04-25-2011, 06:00 PM   #10
nilshomer
Nils Homer
 
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by fenciso View Post
Hi, could someone help me find the solution to this error???

felix-VirtualBox bfast+bwa-0.6.5a # make check
Making check in bfast
make[1]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/bfast'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/bfast'
Making check in butil
make[1]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/butil'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/butil'
Making check in scripts
make[1]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/scripts'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/scripts'
Making check in tests
make[1]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/tests'
make check-TESTS
make[2]: Entering directory `/home/felix/Documents/bfast+bwa-0.6.5a/tests'
.: 3: test.definitions.sh: not found
FAIL: test.initialize.sh
.: 3: test.definitions.sh: not found
FAIL: test.fasta2brg.sh
.: 2: test.definitions.sh: not found
FAIL: test.index.sh
.: 3: test.definitions.sh: not found
FAIL: test.match.sh
.: 3: test.definitions.sh: not found
FAIL: test.localalign.sh
.: 3: test.definitions.sh: not found
FAIL: test.postprocess.sh
.: 3: test.definitions.sh: not found
FAIL: test.diff.sh
.: 3: test.definitions.sh: not found
FAIL: test.cleanup.sh
=================================================
8 of 8 tests failed
Please report to bfast-help@lists.sourceforge.net
=================================================
make[2]: *** [check-TESTS] Error 1
make[2]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/tests'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/felix/Documents/bfast+bwa-0.6.5a/tests'
make: *** [check-recursive] Error 1

Thanks
Sure, send your question to bfast-help@lists.sourceforge.net. Also, in the future could you please start a new thread instead of hijacking an old one?
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