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Old 10-11-2012, 06:29 AM   #1
BIOinformatics
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Default Getting wise2 to compile on RHEL

I'm trying to get genewise to complie on RHEL 6 and I'm getting the standard glib-config not found. I've changed the make file to reflect the glib-2.0 but still getting the error. Please help.
$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config glib-2.0 --cflags`" libwisebase.a )
make[1]: Entering directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/base'
make[1]: `libwisebase.a' is up to date.
make[1]: Leaving directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/base'
(cd HMMer2 ; make CC="gcc" CFLAGS="-c -O2 `pkg-config glib-2.0 --cflags`" libhmmer.a )
make[1]: Entering directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/HMMer2'
make[1]: `libhmmer.a' is up to date.
make[1]: Leaving directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/HMMer2'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config glib-2.0 --cflags`" libdyna.a )
make[1]: Entering directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/dynlibsrc'
make[1]: `libdyna.a' is up to date.
make[1]: Leaving directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/dynlibsrc'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config glib-2.0 --cflags`" libdyna_glib.a )
make[1]: Entering directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/dynlibsrc'
make[1]: `libdyna_glib.a' is up to date.
make[1]: Leaving directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/dynlibsrc'
(cd external ; make CC="gcc" CFLAGS="-c -O2 `pkg-config glib-2.0 --cflags`" all )
make[1]: Entering directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/external'
(cd mott; make CC="gcc" CFLAGS="-c -O2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include " all)
make[2]: Entering directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/external/mott'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/external/mott'
make[1]: Leaving directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/external'
(cd models ; make CC="gcc" CFLAGS="-c -O2 `pkg-config glib-2.0 --cflags`" EXTRALIBS="" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all )
make[1]: Entering directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/models'
gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm
/bin/sh: glib-config: command not found
dnal.o: file not recognized: File format not recognized
collect2: ld returned 1 exit status
make[1]: *** [dnal] Error 1
make[1]: Leaving directory `/home/ian_usda/Downloads/wise2.2.3-rc7/src/models'
make: *** [realall] Error 2
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Old 10-12-2012, 10:52 PM   #2
Torst
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I think you are nearly there!

gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm

The linker line above is still calling `glib-config --libs`.

If you can edit the makefile, change it to `pkg-config --libs glib-2.0`, and it should work.
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Old 10-13-2012, 04:58 AM   #3
BIOinformatics
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I tried the above fix but I'm still getting the same error. It might be an issue with CFLAGS? I've attached the portion of the makefile where I attempted the fix.

# These are the CFLAGS to use. These days Wise2 is inherently
# pthreaded, and everything is compiled with threads. More
# info on running threads can be found in the documentation
CFLAGS = -c -O2 `pkg-config --libs glib-2.0 --cflags`
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Old 10-13-2012, 07:31 PM   #4
Torst
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What does typing this on the command line say?
% pkg-config --libs glib-2.0 --cflags

Mine says:
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0
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Old 10-14-2012, 05:05 AM   #5
BIOinformatics
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This is what mine says

-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0
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Old 03-29-2014, 12:47 AM   #6
amitbik
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Hi all,
I am trying to install genwise and i am getting following error

$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libwisebase.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/base'
make[1]: `libwisebase.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/base'
(cd HMMer2 ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libhmmer.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/HMMer2'
make[1]: `libhmmer.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/HMMer2'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libdyna.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
make[1]: `libdyna.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libdyna_glib.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
make[1]: `libdyna_glib.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
(cd external ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" all )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/external'
(cd mott; make CC="gcc" CFLAGS="-c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 " all)
make[2]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/external/mott'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/external/mott'
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/external'
(cd models ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" EXTRALIBS="" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/models'
gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm
/bin/sh: 1: glib-config: not found
dnal.o: file not recognized: File format not recognized
collect2: error: ld returned 1 exit status
make[1]: *** [dnal] Error 1
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/models'
make: *** [realall] Error 2

Can anybody help me to find out the error??

Thanks....
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Old 03-29-2014, 05:40 AM   #7
GenoMax
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Amit: What OS are you installing on? I assume you have tried the solutions above.

Sounds like you need to install libgtk.
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Old 04-08-2014, 09:30 PM   #8
amitbik
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Sorry for late reply..
Thanks for your reply GenoMax..
I am using ubuntu 14.04 and i have tried the above solutions but still i am getting error..

$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libwisebase.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/base'
make[1]: `libwisebase.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/base'
(cd HMMer2 ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libhmmer.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/HMMer2'
make[1]: `libhmmer.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/HMMer2'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libdyna.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
make[1]: `libdyna.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libdyna_glib.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
make[1]: `libdyna_glib.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
(cd external ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" all )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/external'
(cd mott; make CC="gcc" CFLAGS="-c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 " all)
make[2]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/external/mott'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/external/mott'
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/external'
(cd models ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" EXTRALIBS="" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/models'
gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `glib-config --libs` -ldyna_glib -ldyna -lwisebase -lm
/bin/sh: 1: glib-config: not found
dnal.o: file not recognized: File format not recognized
collect2: error: ld returned 1 exit status
make[1]: *** [dnal] Error 1
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/models'
make: *** [realall] Error 2

As you suggested to install libgtk i am woking on it, once i have finished i will post the result.
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Old 04-08-2014, 11:30 PM   #9
amitbik
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Quote:
Originally Posted by GenoMax View Post
Amit: What OS are you installing on? I assume you have tried the solutions above.

Sounds like you need to install libgtk.
I have installed libgtk3.0 then also i am getting error like this


$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libwisebase.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/base'
make[1]: `libwisebase.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/base'
(cd HMMer2 ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libhmmer.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/HMMer2'
make[1]: `libhmmer.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/HMMer2'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libdyna.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
make[1]: `libdyna.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libdyna_glib.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
make[1]: `libdyna_glib.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/dynlibsrc'
(cd external ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" all )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/external'
(cd mott; make CC="gcc" CFLAGS="-c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 " all)
make[2]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/external/mott'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/external/mott'
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/external'
(cd models ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" EXTRALIBS="" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/models'
gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0 --cflags` -ldyna_glib -ldyna -lwisebase -lm
dnal.o: file not recognized: File format not recognized
collect2: error: ld returned 1 exit status
make[1]: *** [dnal] Error 1
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/models'
make: *** [realall] Error 2

Can you tell me what is wrong in it why it is not installing??
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Old 04-09-2014, 01:15 AM   #10
GenoMax
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You have gone past the libgtk error. In compilations like this when you get an error it may be good to start with a clean slate (do a "make clean" and then "make all") once you install a new library etc.

Give that a try.
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Old 04-09-2014, 02:06 AM   #11
amitbik
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Quote:
Originally Posted by GenoMax View Post
You have gone past the libgtk error. In compilations like this when you get an error it may be good to start with a clean slate (do a "make clean" and then "make all") once you install a new library etc.

Give that a try.
As you said i did. I am getting error like this

$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libwisebase.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/base'
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 wiseconfig.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 wisestring.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 wiseerror.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 wisememman.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 wisefile.c
wisefile.dy: In function ‘Wise2_myfclose’:
wisefile.dy:70:3: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘struct FILE *’ [-Wformat=]
fprintf(stderr,"Closing %d\n",ofp);
^
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 wiserandom.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 wisetime.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 wiseoverlay.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 commandline.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 linesubs.c
ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o commandline.o linesubs.o
ar: creating libwisebase.a
if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/base'
(cd HMMer2 ; make CC="gcc" CFLAGS="-c -O2 `pkg-config --libs glib-2.0 --cflags`" libhmmer.a )
make[1]: Entering directory `/home/orf/AMIT/wise2.2.3-rc7/src/HMMer2'
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c alphabet.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c core_algorithms.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c debug.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c emit.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c emulation.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c histogram.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c hmmio.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c mathsupport.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c masks.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c misc.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c modelmakers.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c plan7.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c plan9.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c prior.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c tophits.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c trace.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c aligneval.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c alignio.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c cluster.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c dayhoff.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c file.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c getopt.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c gnuregex.c
gnuregex.c: In function ‘re_match_2’:
gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
if ((int) old_regend[r] >= (int) regstart[r])
^
gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
if ((int) old_regend[r] >= (int) regstart[r])
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (lowest_active_reg); \
^
gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (highest_active_reg); \
^
gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (lowest_active_reg); \
^
gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (highest_active_reg); \
^
gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (lowest_active_reg); \
^
gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (p + mcnt, d, -2);
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (highest_active_reg); \
^
gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (p + mcnt, d, -2);
^
gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
high_reg = (unsigned) POP_FAILURE_ITEM (); \
^
gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’
POP_FAILURE_POINT (sdummy, pdummy,
^
gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
low_reg = (unsigned) POP_FAILURE_ITEM (); \
^
gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’
POP_FAILURE_POINT (sdummy, pdummy,
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (lowest_active_reg); \
^
gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (0, 0, -2);
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (highest_active_reg); \
^
gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (0, 0, -2);
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (lowest_active_reg); \
^
gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (0, 0, -2);
^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
PUSH_FAILURE_ITEM (highest_active_reg); \
^
gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
PUSH_FAILURE_POINT (0, 0, -2);
^
gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
high_reg = (unsigned) POP_FAILURE_ITEM (); \
^
gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’
POP_FAILURE_POINT (d, p,
^
gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
low_reg = (unsigned) POP_FAILURE_ITEM (); \
^
gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’
POP_FAILURE_POINT (d, p,
^
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c interleaved.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c iupac.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c msf.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c revcomp.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c selex.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c sqerror.c
gcc -c -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -lglib-2.0 -c sqio.c
sqio.c:232:1: error: conflicting types for ‘getline’
getline(struct ReadSeqVars *V)
^
In file included from sqio.c:27:0:
/usr/include/stdio.h:678:20: note: previous declaration of ‘getline’ was here
extern _IO_ssize_t getline (char **__restrict __lineptr,
^
make[1]: *** [sqio.o] Error 1
make[1]: Leaving directory `/home/orf/AMIT/wise2.2.3-rc7/src/HMMer2'
make: *** [realall] Error 2
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Old 04-09-2014, 06:25 AM   #12
GenoMax
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Posts: 7,143
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Nothing obvious seems to pop-up as the next step to try.

Is there a specific reason you are interested in running "wise2" (protein HMM's to DNA)? As suggested on the wise2 page you may want to try the newer package "exonerate" that is supposed to be both faster and has compiled binaries available that you can use right away.
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Old 04-09-2014, 10:33 PM   #13
amitbik
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Actually i am installing cegma for that i need to install geneid,genewise,hmmer and ncbi blast. I have installed all except genewise..
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Old 04-10-2014, 03:16 AM   #14
GenoMax
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I came across these instructions for cegma on ubuntu. They refer to an older version of ubuntu but the fix for "seqio" error mentioned should work for you. http://korflab.ucdavis.edu/datasets/...ructions_1.txt
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Old 04-10-2014, 04:26 AM   #15
amitbik
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Quote:
Originally Posted by GenoMax View Post
I came across these instructions for cegma on ubuntu. They refer to an older version of ubuntu but the fix for "seqio" error mentioned should work for you. http://korflab.ucdavis.edu/datasets/...ructions_1.txt
I already did it as they instructed but it is not working. The error is coming like this

$ make all
(cd base ; make CC="gcc" CFLAGS="-c -O3 `glib-config --cflags --libs glib-2.0`" libwisebase.a )
/bin/sh: 1: glib-config: not found
make[1]: Entering directory `/home/orf/AMIT/wise2.4.1/src/base'
make[1]: `libwisebase.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.4.1/src/base'
(cd HMMer2 ; make CC="gcc" CFLAGS="-c -O3 `glib-config --cflags --libs glib-2.0`" libhmmer.a )
/bin/sh: 1: glib-config: not found
make[1]: Entering directory `/home/orf/AMIT/wise2.4.1/src/HMMer2'
make[1]: `libhmmer.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.4.1/src/HMMer2'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O3 `glib-config --cflags --libs glib-2.0`" libdyna.a )
/bin/sh: 1: glib-config: not found
make[1]: Entering directory `/home/orf/AMIT/wise2.4.1/src/dynlibsrc'
make[1]: `libdyna.a' is up to date.
make[1]: Leaving directory `/home/orf/AMIT/wise2.4.1/src/dynlibsrc'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O3 `glib-config --cflags --libs glib-2.0`" libdyna_glib.a )
/bin/sh: 1: glib-config: not found
make[1]: Entering directory `/home/orf/AMIT/wise2.4.1/src/dynlibsrc'
gcc -c -O3 -I../base/ subseqhash.c
In file included from subseqhash.c:4:0:
subseqhash.h:9:18: fatal error: glib.h: No such file or directory
#include "glib.h"
^
compilation terminated.
make[1]: *** [subseqhash.o] Error 1
make[1]: Leaving directory `/home/orf/AMIT/wise2.4.1/src/dynlibsrc'
make: *** [realall] Error 2

I have already installed glib and libgtk but it is still showing error.

$ sudo apt-get install libgtk2.0
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'libgtk2.0-doc' for regex 'libgtk2.0'
Note, selecting 'libgtk2.0-cil' for regex 'libgtk2.0'
Note, selecting 'libgtk2.0-bin' for regex 'libgtk2.0'
Note, selecting 'libgtk2.0-common' for regex 'libgtk2.0'
Note, selecting 'libgtk2.0-0' for regex 'libgtk2.0'
Note, selecting 'libgtk2.0-cil-dev' for regex 'libgtk2.0'
Note, selecting 'libgtk2.0-0-dbg' for regex 'libgtk2.0'
Note, selecting 'libgtk2.0-dev' for regex 'libgtk2.0'
libgtk2.0-0 is already the newest version.
libgtk2.0-0-dbg is already the newest version.
libgtk2.0-bin is already the newest version.
libgtk2.0-cil is already the newest version.
libgtk2.0-cil-dev is already the newest version.
libgtk2.0-common is already the newest version.
libgtk2.0-dev is already the newest version.
libgtk2.0-doc is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ sudo apt-get install libglib2.0-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libglib2.0-dev is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

I really confused now why it is still showing error after doing all the things..
I think it is because of i am using ubuntu 14.04 and they gave instruction for ubuntu 10.04.
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