Update: Searching the web found an Unbutu Maq patch that may address the issue.
SBB
Hello bioinformatics gurus,
I am trying to run Maq under vmware fusion using an Unbuntu 64 bit virtual machine on my MacPro. I have the Maq linux 64 bit distribution. When I try to ./configure, make, make install, I get an error 2 message in make. Initially it suggested that maybe I needed to get the latest versions of Autoconf and GNU m4 - which I did. This did not solve the problem. Currently the problem seems to be associated with an inability to find zlib.h. I used the package manager to add the latest version of the zlib dev package, and specifically added zlib.h to my path. However ./configure still does not seem to be able to identify zlib.h, and make fails with the same error message. The ./configure and make output are below. Thanks in advance for any assistance.
S. Beres
Molecular biologist by training--Bioinformaticist by necessity
sbberes@ubuntu:~/Desktop/Bioinformatics/MAQ/maq-0.7.1$ ./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... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking if gcc accepts -m64... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... no
checking zlib.h presence... no
checking for zlib.h... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
sbberes@ubuntu:~/Desktop/Bioinformatics/MAQ/maq-0.7.1$ make
make all-am
make[1]: Entering directory `/home/sbberes/Desktop/Bioinformatics/MAQ/maq-0.7.1'
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c main.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c const.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c seq.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c bfa.c
bfa.c:1:18: error: zlib.h: No such file or directory
bfa.c: In function ‘nst_load_bfa1’:
bfa.c:31: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:32: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:33: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:35: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:37: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c: In function ‘nst_bfa_len’:
bfa.c:46: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:48: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
make[1]: *** [bfa.o] Error 1
make[1]: Leaving directory `/home/sbberes/Desktop/Bioinformatics/MAQ/maq-0.7.1'
make: *** [all] Error 2
SBB
Hello bioinformatics gurus,
I am trying to run Maq under vmware fusion using an Unbuntu 64 bit virtual machine on my MacPro. I have the Maq linux 64 bit distribution. When I try to ./configure, make, make install, I get an error 2 message in make. Initially it suggested that maybe I needed to get the latest versions of Autoconf and GNU m4 - which I did. This did not solve the problem. Currently the problem seems to be associated with an inability to find zlib.h. I used the package manager to add the latest version of the zlib dev package, and specifically added zlib.h to my path. However ./configure still does not seem to be able to identify zlib.h, and make fails with the same error message. The ./configure and make output are below. Thanks in advance for any assistance.
S. Beres
Molecular biologist by training--Bioinformaticist by necessity
sbberes@ubuntu:~/Desktop/Bioinformatics/MAQ/maq-0.7.1$ ./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... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking if gcc accepts -m64... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... no
checking zlib.h presence... no
checking for zlib.h... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
sbberes@ubuntu:~/Desktop/Bioinformatics/MAQ/maq-0.7.1$ make
make all-am
make[1]: Entering directory `/home/sbberes/Desktop/Bioinformatics/MAQ/maq-0.7.1'
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c main.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c const.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c seq.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c bfa.c
bfa.c:1:18: error: zlib.h: No such file or directory
bfa.c: In function ‘nst_load_bfa1’:
bfa.c:31: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:32: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:33: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:35: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:37: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c: In function ‘nst_bfa_len’:
bfa.c:46: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bfa.c:48: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
make[1]: *** [bfa.o] Error 1
make[1]: Leaving directory `/home/sbberes/Desktop/Bioinformatics/MAQ/maq-0.7.1'
make: *** [all] Error 2
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