Compilation error

[BernardoBello]

Hi, I have this error when typing make:

Thank you, Bernardo

usuario@bernardo:~/Desktop/TMAP-master$ make make all-recursive make[1]: Entering directory /home/usuario/Desktop/TMAP-master' Making all in . make[2]: Entering directory/home/usuario/Desktop/TMAP-master' depbase=echo src/util/tmap_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/util/tmap_alloc.o -MD -MP -MF $depbase.Tpo -c -o src/util/tmap_alloc.o src/util/tmap_alloc.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=echo src/util/tmap_definitions.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/util/tmap_definitions.o -MD -MP -MF $depbase.Tpo -c -o src/util/tmap_definitions.o src/util/tmap_definitions.c &&\ mv -f $depbase.Tpo $depbase.Po In file included from src/util/../seq/tmap_seq.h:8:0, from src/util/tmap_definitions.c:14: src/util/../seq/tmap_sam.h:6:29: fatal error: ../samtools/bam.h: No such file or directory compilation terminated. make[2]: * [src/util/tmap_definitions.o] Error 1 make[2]: Leaving directory `/home/usuario/Desktop/TMAP-master' make[1]: * [all-recursive] Error 1 make[1]: Leaving directory`/home/usuario/Desktop/TMAP-master' make: *\ [all] Error 2 usuario@bernardo:~/Desktop/TMAP-master$

[shahm3]

Did you run "git submodule init" before running make?

From: BernardoBello notifications@github.com<mailto:notifications@github.com> Reply-To: iontorrent/TMAP reply@reply.github.com<mailto:reply@reply.github.com> Date: Friday, April 19, 2013 8:49 AM To: iontorrent/TMAP TMAP@noreply.github.com<mailto:TMAP@noreply.github.com> Subject: [TMAP] Compilation error (#7)

Hi, I have this error when typing make:

Thank you, Bernardo

usuario@bernardo:~/Desktop/TMAP-master$ make make all-recursive make[1]: Entering directory /home/usuario/Desktop/TMAP-master' Making all in . make[2]: Entering directory/home/usuario/Desktop/TMAP-master' depbase=echo src/util/tmapalloc.o | sed 's|[^/]$|.deps/&|;s|.o$||';\ gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/util/tmap_alloc.o -MD -MP -MF $depbase.Tpo -c -o src/util/tmap_alloc.o src/util/tmap_alloc.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=echo src/util/tmapdefinitions.o | sed 's|[^/]$|.deps/&|;s|.o$||';\ gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/util/tmap_definitions.o -MD -MP -MF $depbase.Tpo -c -o src/util/tmap_definitions.o src/util/tmap_definitions.c &&\ mv -f $depbase.Tpo $depbase.Po In file included from src/util/../seq/tmap_seq.h:8:0, from src/util/tmap_definitions.c:14: src/util/../seq/tmap_sam.h:6:29: fatal error: ../samtools/bam.h: No such file or directory compilation terminated. make[2]: * [src/util/tmap_definitions.o] Error 1 make[2]: Leaving directory /home/usuario/Desktop/TMAP-master' make[1]: * [all-recursive] Error 1 make[1]: Leaving directory/home/usuario/Desktop/TMAP-master' make: *\ [all] Error 2 usuario@bernardo:~/Desktop/TMAP-master$

— Reply to this email directly or view it on GitHubhttps://github.com/iontorrent/TMAP/issues/7.

[BernardoBello]

No, since "git clone" is not working for me (left if in shell but nothing happened).

I downloaded "TMAP-tmap.3.4.0.tar.gz", extracted, cd TMAP-tmap.3.4.0, and executed:

sh autogen.sh && ./configure && make

There I had the issue.

Bernardo

[BernardoBello]

Hi,

Trying:

git clone https://github.com/iontorrent/TMAP.git

instead of:

git clone git://github.com/iontorrent/TMAP.git

seems TMAP was installed OK.

Thank you,

Bernardo