Summary: | 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) | ||
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Product: | Gentoo Linux | Reporter: | Martin Mokrejš <mmokrejs> |
Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
Status: | RESOLVED OBSOLETE | ||
Severity: | normal | CC: | kkimdavenport |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: |
build.log
Patch to disable LZO compression |
Same problem here. Maybe --without-gnutls? https://github.com/Homebrew/homebrew-science/issues/161 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.
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. 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. ncbi-tools++ was removed from the tree it seems, so these bugs aren't relevant anymore. ncbi-tools++ has been removed from the tree, it seems this is no longer relevant. https://doodlebaseball.io/ |
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)