Building "afni" failed

[frenchja@…]

After the previous ticket was closed, I ran a sudo port sync && sudo port clean && sudo port install afni.

sudo port install afni
Portfile changed since last build; discarding previous state.
--->  Computing dependencies for afni
--->  Fetching afni
--->  Verifying checksum(s) for afni
--->  Extracting afni
--->  Applying patches to afni
--->  Configuring afni
--->  Building afni
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_afni/work/AFNI_2009_12_31_1431" && /usr/bin/make -j2 all plugins " returned error 2
Command output: /usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_ratqr.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rebak.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rebakb.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_reduc.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_reduc2.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rg.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rgg.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rs.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rsb.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rsg.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rsgab.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rsgba.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rsm.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rsp.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rst.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_rt.c
/usr/bin/gcc-4.2 -m64 -O0 -no-cpp-precomp -DFUNCNAME=svd_slow_ -c eis_svd.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_svd.c
mv -f eis_svd.o eis_svd_slow.o
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tinvit.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tql1.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tql2.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tqlrat.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_trbak1.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_trbak3.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tred1.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tred2.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tred3.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tridib.c
/usr/bin/gcc-4.2 -O3 -ftree-vectorize -ffast-math -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -no-cpp-precomp -DDONT_USE_MCW_MALLOC  -c eis_tsturm.c

Error: Status 1 encountered during processing.
Before reporting a bug, first run the command again with the -d flag to get complete output.

[jmroot (Joshua Root)]

Please remember to cc the maintainer.

[nerdling (Jeremy Lavergne)]

Replying to frenchja@…:

Before reporting a bug, first run the command again with the -d flag to get complete output.

What you posted doesn't contain the error, I need you to rerun the build with the debug flag on. The code below will:

• clean the old build
• start a new debug build
• copy the messages to a file in your home directory
• compresses the file for easy uploading

sudo port clean afni
sudo port -d build afni 2>&1 | tee ~/afni.log
tar cjf ~/afni.log.bz2 ~/afni.log

[frenchja@…]

afni Debug Output

[nerdling (Jeremy Lavergne)]

The output you attached says the checksum was incorrect on the distribution files. Looks like both your checksum and the portfile's checksums are out of date.

They're doing silent changes to the source files :( and apparently many of them.

You can override the checksum presently by putting the appropriate lines from sudo port -d checksum afni into the portfile with sudo port edit afni.

[nerdling (Jeremy Lavergne)]

No update, and afni has sense been updated.

[nerdling (Jeremy Lavergne)]

since, even.