Error in Compiling BFAST

CS Student · 11-27-2011, 09:26 AM

Hi,

I am trying to compile the source code of BFAST and I am getting the below error message when trying to "make". Appreciate any advice on the error message.

* I use "./configure" before "make".

Thanks
=====================
make all-recursive
make[1]: Entering directory `/hadoop/bfast-files’
Making all in bfast
make[2]: Entering directory `/hadoop/bfast-files’
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 -lbz2 -lz
AlignedEnd.o: file not recognized: File format not recognized
collect2: ld returned 1 exit status
make[2]: *** [bfast] Error 1
make[2]: Leaving directory `/hadoop/bfast-files’
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/hadoop/bfast-files’
make: *** [all] Error 2

nilshomer · 11-27-2011, 09:30 PM

Could you try"./configure && make clean && make" and post all output?

CS Student · 11-27-2011, 11:22 PM

It works fine now using "make clean" before "make".

Thanks a lot Nils!

peas1127 · 04-17-2012, 03:54 PM

I am having similar problem but solution didn't work for me here is what i did

sh autogen.sh
./configure
then make

i get this error:

make all-recursive
make[1]: Entering directory `/directory/BFAST/bfast-0.7.0a'
Making all in bfast
make[2]: Entering directory `/directory/BFAST/bfast-0.7.0a/bfast'
depbase=`echo BLib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BLib.o -MD -MP -MF "$depbase.Tpo" -c -o BLib.o BLib.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
BLib.c: In function 'OpenTmpFile':
BLib.c:480: error: 'ZLIB_VERNUM' undeclared (first use in this function)
BLib.c:480: error: (Each undeclared identifier is reported only once
BLib.c:480: error: for each function it appears in.)
BLib.c: In function 'OpenTmpGZFile':
BLib.c:553: error: 'ZLIB_VERNUM' undeclared (first use in this function)
make[2]: *** [BLib.o] Error 1
make[2]: Leaving directory `/directory/BFAST/bfast-0.7.0a/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/directory/BFAST/bfast-0.7.0a'
make: *** [all] Error 2

i tried make clean but it still gave me this:

make all-recursive
make[1]: Entering directory `/directory/BFAST/bfast-0.7.0a'
Making all in bfast
make[2]: Entering directory `/directory/BFAST/bfast-0.7.0a/bfast'
depbase=`echo AlignedEnd.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedEnd.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedEnd.o AlignedEnd.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo AlignedEntry.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedEntry.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedEntry.o AlignedEntry.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo AlignedRead.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedRead.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedRead.o AlignedRead.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo AlignedReadConvert.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedReadConvert.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedReadConvert.o AlignedReadConvert.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo BError.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BError.o -MD -MP -MF "$depbase.Tpo" -c -o BError.o BError.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo BLib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BLib.o -MD -MP -MF "$depbase.Tpo" -c -o BLib.o BLib.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
BLib.c: In function 'OpenTmpFile':
BLib.c:480: error: 'ZLIB_VERNUM' undeclared (first use in this function)
BLib.c:480: error: (Each undeclared identifier is reported only once
BLib.c:480: error: for each function it appears in.)
BLib.c: In function 'OpenTmpGZFile':
BLib.c:553: error: 'ZLIB_VERNUM' undeclared (first use in this function)
make[2]: *** [BLib.o] Error 1
make[2]: Leaving directory `/directory/BFAST/bfast-0.7.0a/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/directory/BFAST/bfast-0.7.0a'
make: *** [all] Error 2

can someone please help me.?

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11-27-2011, 09:26 AM	#1
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	Error in Compiling BFAST Hi, I am trying to compile the source code of BFAST and I am getting the below error message when trying to "make". Appreciate any advice on the error message. * I use "./configure" before "make". Thanks ===================== make all-recursive make[1]: Entering directory `/hadoop/bfast-files’ Making all in bfast make[2]: Entering directory `/hadoop/bfast-files’ 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 -lbz2 -lz AlignedEnd.o: file not recognized: File format not recognized collect2: ld returned 1 exit status make[2]: * [bfast] Error 1 make[2]: Leaving directory `/hadoop/bfast-files’ make[1]: * [all-recursive] Error 1 make[1]: Leaving directory `/hadoop/bfast-files’ make: *** [all] Error 2

11-27-2011, 09:30 PM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Could you try"./configure && make clean && make" and post all output?

11-27-2011, 11:22 PM	#3
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	It works fine now using "make clean" before "make". Thanks a lot Nils!

04-17-2012, 03:54 PM	#4
peas1127 Junior Member Location: Houston, TX Join Date: Mar 2012 Posts: 4	I am having similar problem but solution didn't work for me here is what i did sh autogen.sh ./configure then make i get this error: make all-recursive make[1]: Entering directory `/directory/BFAST/bfast-0.7.0a' Making all in bfast make[2]: Entering directory `/directory/BFAST/bfast-0.7.0a/bfast' depbase=`echo BLib.o \| sed 's\|[^/]$\|.deps/&\|;s\|\.o$\|\|'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BLib.o -MD -MP -MF "$depbase.Tpo" -c -o BLib.o BLib.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi BLib.c: In function 'OpenTmpFile': BLib.c:480: error: 'ZLIB_VERNUM' undeclared (first use in this function) BLib.c:480: error: (Each undeclared identifier is reported only once BLib.c:480: error: for each function it appears in.) BLib.c: In function 'OpenTmpGZFile': BLib.c:553: error: 'ZLIB_VERNUM' undeclared (first use in this function) make[2]: [BLib.o] Error 1 make[2]: Leaving directory `/directory/BFAST/bfast-0.7.0a/bfast' make[1]: * [all-recursive] Error 1 make[1]: Leaving directory `/directory/BFAST/bfast-0.7.0a' make: *** [all] Error 2 i tried make clean but it still gave me this: make all-recursive make[1]: Entering directory `/directory/BFAST/bfast-0.7.0a' Making all in bfast make[2]: Entering directory `/directory/BFAST/bfast-0.7.0a/bfast' depbase=`echo AlignedEnd.o \| sed 's\|[^/]$\|.deps/&\|;s\|\.o$\|\|'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedEnd.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedEnd.o AlignedEnd.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo AlignedEntry.o \| sed 's\|[^/]$\|.deps/&\|;s\|\.o$\|\|'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedEntry.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedEntry.o AlignedEntry.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo AlignedRead.o \| sed 's\|[^/]$\|.deps/&\|;s\|\.o$\|\|'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedRead.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedRead.o AlignedRead.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo AlignedReadConvert.o \| sed 's\|[^/]$\|.deps/&\|;s\|\.o$\|\|'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedReadConvert.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedReadConvert.o AlignedReadConvert.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo BError.o \| sed 's\|[^/]$\|.deps/&\|;s\|\.o$\|\|'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BError.o -MD -MP -MF "$depbase.Tpo" -c -o BError.o BError.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi depbase=`echo BLib.o \| sed 's\|[^/]$\|.deps/&\|;s\|\.o$\|\|'`; \ if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BLib.o -MD -MP -MF "$depbase.Tpo" -c -o BLib.o BLib.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi BLib.c: In function 'OpenTmpFile': BLib.c:480: error: 'ZLIB_VERNUM' undeclared (first use in this function) BLib.c:480: error: (Each undeclared identifier is reported only once BLib.c:480: error: for each function it appears in.) BLib.c: In function 'OpenTmpGZFile': BLib.c:553: error: 'ZLIB_VERNUM' undeclared (first use in this function) make[2]: * [BLib.o] Error 1 make[2]: Leaving directory `/directory/BFAST/bfast-0.7.0a/bfast' make[1]: * [all-recursive] Error 1 make[1]: Leaving directory `/directory/BFAST/bfast-0.7.0a' make: *** [all] Error 2 can someone please help me.?