sci-biology:ncbi-tools-2.2.26-r2:20200220-182627.log

sci-biology:ncbi-tools-2.2.26-r2:20200220-182627.log (text/plain), 2.67 KB, created by Toralf Förster on 2020-02-20 18:37:38 UTC

 * Package:    sci-biology/ncbi-tools-2.2.26-r2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        X abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

 * Please note that the NCBI toolkit (and especially the X
 * applications) are known to have compilation and run-time
 * problems when compiled with agressive compilation flags. The
 * "-O3" flag is filtered by the ebuild on the x86 architecture if
 * X support is enabled.

>>> Unpacking source...
>>> Unpacking ncbi-tools-2.2.26.tar.gz to /var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work
>>> Preparing source in /var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work/ncbi ...
 * Applying ncbi-tools-extra_vib.patch ...
 [ ok ]
 * Applying ncbi-tools-2.2.26-bfr-overflow.patch ...
 [ ok ]
 * Applying ncbi-tools-2.2.26-format-security.patch ...
 [ ok ]
 * Applying ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch ...
 [ ok ]
sed: -e expression #9, char 82: unknown option to `s'
 * ERROR: sci-biology/ncbi-tools-2.2.26-r2::gentoo failed (prepare phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line 125:  Called src_prepare
 *   environment, line 2323:  Called die
 * The specific snippet of code:
 *       sed -e "s:-O[s0-9]\?::g" -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' -e 's:-x[A-Z]*::g' -e 's:-pipe::g' -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" -i * || die;
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/ncbi-tools-2.2.26-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/ncbi-tools-2.2.26-r2::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:ncbi-tools-2.2.26-r2:20200220-182627.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work/ncbi/platform'
 * S: '/var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work/ncbi'