Bug 484766 – sci-biology/ncbi-tools++-0.2010.06.15-r1 should depend on net-libs/gnutls[lzo] ? - /work/ncbi_cxx--Jun_15_2010/src/connect/ncbi_gnutls.c:101:5: error: 'GNUTLS_COMP_LZO' undeclared here (not in a function)

• Status: RESOLVED OBSOLETE
• Product: Gentoo Linux

[Description Martin Mokrejš 2013-09-13 13:37:41 UTC]

Created attachment 358578 [details]
build.log

Seems that the old ncbitools++ ebuilds are not converted to the nice robustness of the one for 9.0 series (in sci overlay). I just ran into this issue which seems to me that gnutls has to be compiled with lzo support. But, there is no IUSE=lzo in gnutls ebuilds. Further, configure summary printed by gnutls ebuild does not list lzo being tested, so maybe my interpretation is wrong.

make[5]: Entering directory `/mnt/external/var/tmp/portage/sci-biology/ncbi-tools++-0.2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC473-ReleaseMTDLL64/build/connect'
/usr/bin/x86_64-pc-linux-gnu-gcc  -c -Wall -Wno-format-y2k  -pthread -O2 -pipe -maes -mpclmul -mpopcnt -march=native -fPIC    -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -D_MT -D_REENTRANT -D_THREAD_SAFE -I/mnt/external/var/tmp/portage/sci-biology/ncbi-tools++-0.2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC473-ReleaseMTDLL64/inc -I/mnt/external/var/tmp/portage/sci-biology/ncbi-tools++-0.2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/include  /mnt/external/var/tmp/portage/sci-biology/ncbi-tools++-0.2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/connect/ncbi_gnutls.c -o ncbi_gnutls.o 
/mnt/external/var/tmp/portage/sci-biology/ncbi-tools++-0.2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/connect/ncbi_gnutls.c:101:5: error: 'GNUTLS_COMP_LZO' undeclared here (not in a function)

[Comment 1 Hongjiu Zhang 2013-12-12 17:25:59 UTC]

Same problem here. Maybe --without-gnutls?

https://github.com/Homebrew/homebrew-science/issues/161

[Comment 2 Hongjiu Zhang 2013-12-17 16:29:54 UTC]

Created attachment 365538 [details, diff]
Patch to disable LZO compression

According to the page I gave, it seems to be some legacy code and can be safely removed. This patch just disable LZO compression support, and try to minimise the change.

[Comment 3 Martin Mokrejš 2013-12-17 21:07:56 UTC]

I just asked abou this Aaron Ucko from NCBI dev team and he replied:

I can confirm that the correct fix is to remove the reference to GNUTLS_COMP_LZO outright.

[Comment 4 Martin Mokrejš 2014-06-26 14:39:18 UTC]

Some update on this specific to 12.0.0 which I just committed to sci overlay:

sci-biology/ncbi-tools++-12.0.0:
dropped altogether openssl-related USE flags and configure arguments (per upstream info nothing in the public code uses openssl and the configure test is there for their internal reasonings);
dropped gnutls[lzo] requirement which was only need for unpatched 9.0.0 version;
however, --with-lzo is still advantageous for
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.html


Did same to 9.0.0* ebuilds in the overlay.

[Comment 5 Robin Johnson 2014-08-03 20:35:18 UTC]

ncbi-tools++ was removed from the tree it seems, so these bugs aren't relevant anymore.

[Comment 6 Darrell Medina 2024-03-25 03:40:45 UTC]

ncbi-tools++ has been removed from the tree, it seems this is no longer relevant. https://doodlebaseball.io/