AFNI build failure #3

TheChymera · 2017-11-01T14:45:30Z

While the nipype issue has since been addressed on our RAP machines, it is now becoming apparent that I cannot emerge sci-biology/afni on them.

AFNI can successfully be emerged on all our other machines, and the one difference that seems to overlap perfectly with AFNI not building is that glibc is built with -multilib. This seems consistent with the error I am getting:

 * Package:    sci-biology/afni-9999
 * Repository: neurogentoo
 * Maintainer: [email protected] sci-biology
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux prefix userland_GNU
 * FEATURES:   preserve-libs
>>> Unpacking source...
 * Fetching �[1mhttps://github.com/AFNI/AFNI�[22m ...
git fetch https://github.com/AFNI/AFNI +HEAD:refs/git-r3/HEAD
git symbolic-ref refs/git-r3/sci-biology/afni/0/__main__ refs/git-r3/HEAD
 * Checking out �[1mhttps://github.com/AFNI/AFNI�[22m to �[1m/home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work/afni-9999�[22m ...
git checkout --quiet refs/git-r3/HEAD
GIT update -->
   repository:               https://github.com/AFNI/AFNI
   at the commit:            0dbe9690081c85714c5293b78ea7fced35af23fd
>>> Source unpacked in /home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work
>>> Preparing source in /home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work/afni-9999/src ...
/home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/temp/environment: line 2575: CC: command not found
>>> Source prepared.
>>> Configuring source in /home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work/afni-9999/src ...
>>> Source configured.
>>> Compiling source in /home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work/afni-9999/src ...
make -j40 -j1 all plugins suma_exec 
/bin/cp -f niml/niml.h .
echo "#undef  AFNI_VERSION_LABEL" > AFNI_version.h ;                 \
echo '#define AFNI_VERSION_LABEL    "'`cat AFNI_version_base.txt`'"' \
             >> AFNI_version.h ;                                             \
echo "#undef  AFNI_VERSION_PLATFORM" >> AFNI_version.h ;             \
echo '#define AFNI_VERSION_PLATFORM "'linux_fedora_19_64'"'              \
             >> AFNI_version.h ;
( cd niml/ ; make all 'CC=x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY' ; /bin/mv -f *.o .. ; )
make[1]: Entering directory '/home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work/afni-9999/src/niml'
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_b64.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_element.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_elemio.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_registry.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_util.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_byteorder.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_header.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_malloc.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_rowtype.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_uuid.c
�[01m�[Kniml_uuid.c:�[m�[K In function ‘�[01m�[Kget_UNIQ_string�[m�[K’:
�[01m�[Kniml_uuid.c:93:10:�[m�[K �[01;35m�[Kwarning: �[m�[Kignoring return value of ‘�[01m�[Kfread�[m�[K’, declared with attribute warn_unused_result [�[01;35m�[K-Wunused-result�[m�[K]
          �[01;35m�[Kfread( &urr , 1,NURR, ufp )�[m�[K; fclose(ufp);
          �[01;35m�[K^~~~~~~~~~~~~~~~~~~~~~~~~~~�[m�[K
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_do.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_htable.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_md5.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_url.c
�[01m�[Kniml_url.c:�[m�[K In function ‘�[01m�[Kread_URL_http�[m�[K’:
�[01m�[Kniml_url.c:248:7:�[m�[K �[01;35m�[Kwarning: �[m�[Kignoring return value of ‘�[01m�[Kfread�[m�[K’, declared with attribute warn_unused_result [�[01;35m�[K-Wunused-result�[m�[K]
       �[01;35m�[Kfread( buf , 1 , nuse , cfile )�[m�[K ;             /* read file in */
       �[01;35m�[K^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~�[m�[K
�[01m�[Kniml_url.c:�[m�[K In function ‘�[01m�[Kread_URL_ftp�[m�[K’:
�[01m�[Kniml_url.c:355:4:�[m�[K �[01;35m�[Kwarning: �[m�[Kignoring return value of ‘�[01m�[Ksystem�[m�[K’, declared with attribute warn_unused_result [�[01;35m�[K-Wunused-result�[m�[K]
    �[01;35m�[Ksystem( sname )�[m�[K ; unlink( sname ) ;
    �[01;35m�[K^~~~~~~~~~~~~~~�[m�[K
�[01m�[Kniml_url.c:379:4:�[m�[K �[01;35m�[Kwarning: �[m�[Kignoring return value of ‘�[01m�[Kfread�[m�[K’, declared with attribute warn_unused_result [�[01;35m�[K-Wunused-result�[m�[K]
    �[01;35m�[Kfread( buf , 1 , nuse , sp )�[m�[K ;  /* AT LAST! */
    �[01;35m�[K^~~~~~~~~~~~~~~~~~~~~~~~~~~~�[m�[K
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_stream.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_struct.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_dataset.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_vector.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_stat.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_dtable.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c niml_sucker.c
make[1]: Leaving directory '/home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work/afni-9999/src/niml'
/bin/rm -f mri_cfft.o
x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE  -DDONT_USE_XTDESTROY -c mri_cfft.c -I. -I/usr/include -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -DHAVE_ZLIB -DHAVE_GIFTI
In file included from �[01m�[K/usr/include/features.h:367:0�[m�[K,
                 from �[01m�[K/usr/include/math.h:26�[m�[K,
                 from �[01m�[Kmri_cfft.c:7�[m�[K:
�[01m�[K/home/hioanas/gentoo/usr/include/sys/cdefs.h:481:49:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GNUC_PREREQ (4,8) || __glibc_clang_prereq �[01;31m�[K(�[m�[K3,5)
                                                 �[01;31m�[K^�[m�[K
In file included from �[01m�[K/usr/include/math.h:48:0�[m�[K,
                 from �[01m�[Kmri_cfft.c:7�[m�[K:
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathdef.h:19:3:�[m�[K �[01;31m�[Kerror: �[m�[K#error "Never use <bits/mathdef.h> directly; include <complex.h> instead"
 # �[01;31m�[Kerror�[m�[K "Never use <bits/mathdef.h> directly; include <complex.h> instead"
   �[01;31m�[K^~~~~�[m�[K
In file included from �[01m�[K/usr/include/math.h:83:0�[m�[K,
                 from �[01m�[Kmri_cfft.c:7�[m�[K:
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:118:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_FUNCS_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:299:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:318:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:387:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
In file included from �[01m�[K/usr/include/math.h:104:0�[m�[K,
                 from �[01m�[Kmri_cfft.c:7�[m�[K:
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:118:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_FUNCS_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:299:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:318:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:387:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
In file included from �[01m�[K/usr/include/math.h:151:0�[m�[K,
                 from �[01m�[Kmri_cfft.c:7�[m�[K:
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:118:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_FUNCS_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:299:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:318:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
�[01m�[K/home/hioanas/gentoo/usr/include/bits/mathcalls.h:387:17:�[m�[K �[01;31m�[Kerror: �[m�[Kmissing binary operator before token "("
 #if __GLIBC_USE �[01;31m�[K(�[m�[KIEC_60559_BFP_EXT)
                 �[01;31m�[K^�[m�[K
make: *** [Makefile.INCLUDE:1565: mri_cfft.o] Error 1
 * ERROR: sci-biology/afni-9999::neurogentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/afni-9999::neurogentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/afni-9999::neurogentoo'`.
 * The complete build log is located at '/home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/temp/build.log'.
 * The ebuild environment file is located at '/home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/temp/environment'.
 * Working directory: '/home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work/afni-9999/src'
 * S: '/home/hioanas/gentoo/var/tmp/portage/sci-biology/afni-9999/work/afni-9999/src'

Is there any (easy) way to make a RAP install multilib? I don't see the point of keeping it no-multilib.

EDIT turns out this is entirely unrelated to multilib, but rather a prefix issue.

The text was updated successfully, but these errors were encountered:

Doeme · 2017-11-01T17:24:32Z

Hm, I can't really see why multilib on glibc should make any difference, especially if the errors appear in the header-files and not the shared library. Actually I don't see why we should build a multilib-profile in the first place, since we won't run either wine or pre-compiled 32bit-binaries.

By the way, the problem is there:

x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -fPIC -DREAD_WRITE_64 -DLINUX2 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_XTDESTROY -c mri_cfft.c -I. -I/usr/include -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -DHAVE_ZLIB -DHAVE_GIFTI

Emphasis mine. This is hardcoded in many Makefiles.

Doeme · 2017-11-01T18:31:20Z

As a quick fix sed'ing away all -I/usr/include might work, since every sane compiler should add this implicitly anyways

TheChymera · 2017-11-04T01:07:15Z

Fix submitted upstream.

Doeme · 2017-11-04T08:55:56Z

It's actually only a partial fix.
Only really works combined with the ugly patching here

Doeme added the upstream-bug label Nov 1, 2017

TheChymera changed the title ~~No-Multilib on Prefix/RAP~~ AFNI build failure Nov 4, 2017

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AFNI build failure #3

AFNI build failure #3

TheChymera commented Nov 1, 2017 •

edited

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Doeme commented Nov 1, 2017

Doeme commented Nov 1, 2017

TheChymera commented Nov 4, 2017

Doeme commented Nov 4, 2017

AFNI build failure #3

AFNI build failure #3

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TheChymera commented Nov 1, 2017 • edited Loading

Doeme commented Nov 1, 2017

Doeme commented Nov 1, 2017

TheChymera commented Nov 4, 2017

Doeme commented Nov 4, 2017

TheChymera commented Nov 1, 2017 •

edited

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