unable to install dev-libs/glib-2.42.2 - missing Docbook DTD

Message

Schol-R-LEA · Post by **Schol-R-LEA** » Thu Apr 09, 2015 2:15 pm

I am currently unable to emerge most programs, as a critical system library, dev-libs/glib, is unable to install and is blocking everything else. The error message I am getting in specific is

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checking for XML catalog (/etc/xml/catalog)... not found
checking for xmlcatalog... no
checking for DocBook XML DTD V4.1.2 in XML catalog... not found
configure: error: DocBook DTD is required for --enable-man

I have checked /etc/xml, and found the catalog and docbook files present. Following the recommendations of this post, I have tried deleting the contents of /etc/xml (or rather, I renamed the directory and replaced it with a new, empty one with the correct permissions) and attempted to re-emerge libxml2, docbook-xml-dtd, and docbook-xsl-stylesheets, but found that the first two of these had a dependency on glib themselves, while the stylesheet install is also failing with the following error:

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>>> Emerging (1 of 1) app-text/docbook-xsl-stylesheets-1.78.0-r1::gentoo
 * docbook-xsl-1.78.0.tar.bz2 SHA256 SHA512 WHIRLPOOL size ;-) ...                                                               [ ok ]
>>> Unpacking source...
>>> Unpacking docbook-xsl-1.78.0.tar.bz2 to /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work
>>> Source unpacked in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work
>>> Preparing source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source compiled.
 * Skipping make test/check due to ebuild restriction.
>>> Test phase [disabled because of RESTRICT=test]: app-text/docbook-xsl-stylesheets-1.78.0-r1

>>> Install docbook-xsl-stylesheets-1.78.0-r1 into /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/image/ category app-text
>>> Completed installing docbook-xsl-stylesheets-1.78.0-r1 into /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/image/

ecompressdir: bzip2 -9 /usr/share/doc

>>> Installing (1 of 1) app-text/docbook-xsl-stylesheets-1.78.0-r1::gentoo
Creating XML Catalog root /etc/xml/catalog
/usr/sbin/build-docbook-catalog: line 165: xmlcatalog: command not found
build-docbook-catalog: failed creating /etc/xml/catalog, aborting
Creating XML Catalog root /etc/xml/catalog
/usr/sbin/build-docbook-catalog: line 165: xmlcatalog: command not found
build-docbook-catalog: failed creating /etc/xml/catalog, aborting
>>> Auto-cleaning packages...

I would rather avoid having to perform a full reinstall of the system (I have a separate partition for /home, fortunately, but it would mean rebuilding not only the root but /etc as well). Can anyone give any recommendations on how to resolve this?

cwr · Post by **cwr** » Thu Apr 09, 2015 3:29 pm

xmlcatalog is part of libxml2; perhaps emerging the specific docbook packages you need with --nodeps
might work, or emerging libxml2 with "USE=-doc" if you haven't already.

Will

Schol-R-LEA · Post by **Schol-R-LEA** » Fri Apr 10, 2015 1:44 am

OK, I tried both of those suggestions; however, with --nodeps, both docbook-xml-dtd and docbook-xsl-stylesheets individually, but libxml2 got the following error:

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Checking lzma
/var/tmp/portage/dev-libs/libxml2-2.9.2/work/libxml2-2.9.2/configure: line 13107: syntax error near unexpected token `LZMA,liblzma,'
/var/tmp/portage/dev-libs/libxml2-2.9.2/work/libxml2-2.9.2/configure: line 13107: `    PKG_CHECK_MODULES(LZMA,liblzma,'

When I ran it as either

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USE=-doc emerge libxml2

or

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USE=-glib emerge libxml2

It simply began trying to emerge glib again.

Finally, when I tried to emerge the other libraries required by libxml2 (sys-libs/readline, virtual/pkgconfig, and dev-util/pkgconfig) with --nodeps set, each came back with essentially the same error:

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configure: creating ./config.status
config.status: creating Makefile
gawk: symbol lookup error: /lib64/libreadline.so.6: undefined symbol: UP
config.status: error: could not create Makefile

cwr · Post by **cwr** » Fri Apr 10, 2015 1:27 pm

I have a nasty feeling that this problem isn't due to emerge alone; libxml2 configuration really shouldn't throw syntax errors. It's checking for a (missing) liblzma module, but there are several of those and I don't know which one supplies the library configure wants. You'd have to check the actual build configuration under /var/tmp/portage to see that, and perhaps explicitly emerge the necessary package.

The fact that some error messages include lib64 paths make me suspect that you are entangled by some sort of multilib problem; it might be worth re-emerging without the multilib flag (if it's set) and seeing if things run more smoothly.

Good luck - Will

Schol-R-LEA · Post by **Schol-R-LEA** » Sat Apr 11, 2015 1:03 pm

cwr wrote: You'd have to check the actual build configuration under /var/tmp/portage to see that, and perhaps explicitly emerge the necessary package.

I'm not entirely what I would check there, aside from the .ebuild file:

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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-libs/libxml2/libxml2-2.9.2.ebuild,v 1.12 2015/03/07 02:50:26 tetromino Exp $

EAPI="5"
PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3,3_4} )
PYTHON_REQ_USE="xml"

inherit libtool flag-o-matic eutils python-r1 autotools prefix multilib-minimal

DESCRIPTION="Version 2 of the library to manipulate XML files"
HOMEPAGE="http://www.xmlsoft.org/"

LICENSE="MIT"
SLOT="2"
KEYWORDS="alpha amd64 arm arm64 hppa ia64 m68k ~mips ppc ppc64 s390 sh sparc x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris ~x86-winnt"
IUSE="debug examples icu ipv6 lzma python readline static-libs test"

XSTS_HOME="http://www.w3.org/XML/2004/xml-schema-test-suite"
XSTS_NAME_1="xmlschema2002-01-16"
XSTS_NAME_2="xmlschema2004-01-14"
XSTS_TARBALL_1="xsts-2002-01-16.tar.gz"
XSTS_TARBALL_2="xsts-2004-01-14.tar.gz"
XMLCONF_TARBALL="xmlts20080827.tar.gz"

SRC_URI="ftp://xmlsoft.org/${PN}/${PN}-${PV/_rc/-rc}.tar.gz
	test? (
		${XSTS_HOME}/${XSTS_NAME_1}/${XSTS_TARBALL_1}
		${XSTS_HOME}/${XSTS_NAME_2}/${XSTS_TARBALL_2}
		http://www.w3.org/XML/Test/${XMLCONF_TARBALL} )"

COMMON_DEPEND="
	>=sys-libs/zlib-1.2.8-r1:=[${MULTILIB_USEDEP}]
	icu? ( >=dev-libs/icu-51.2-r1:=[${MULTILIB_USEDEP}] )
	lzma? ( >=app-arch/xz-utils-5.0.5-r1:=[${MULTILIB_USEDEP}] )
	python? ( ${PYTHON_DEPS} )
	readline? ( sys-libs/readline:= )
"
RDEPEND="${COMMON_DEPEND}
	abi_x86_32? ( !<=app-emulation/emul-linux-x86-baselibs-20131008-r6
		!app-emulation/emul-linux-x86-baselibs[-abi_x86_32(-)] )
"
DEPEND="${COMMON_DEPEND}
	dev-util/gtk-doc-am
	virtual/pkgconfig
	hppa? ( >=sys-devel/binutils-2.15.92.0.2 )
"

S="${WORKDIR}/${PN}-${PV%_rc*}"

MULTILIB_CHOST_TOOLS=(
	/usr/bin/xml2-config
)

src_unpack() {
	# ${A} isn't used to avoid unpacking of test tarballs into $WORKDIR,
	# as they are needed as tarballs in ${S}/xstc instead and not unpacked
	unpack ${P/_rc/-rc}.tar.gz
	cd "${S}"

	if use test; then
		cp "${DISTDIR}/${XSTS_TARBALL_1}" \
			"${DISTDIR}/${XSTS_TARBALL_2}" \
			"${S}"/xstc/ \
			|| die "Failed to install test tarballs"
		unpack ${XMLCONF_TARBALL}
	fi
}

src_prepare() {
	DOCS=( AUTHORS ChangeLog NEWS README* TODO* )

	# Patches needed for prefix support
	epatch "${FILESDIR}"/${PN}-2.7.1-catalog_path.patch
	epatch "${FILESDIR}"/${PN}-2.8.0_rc1-winnt.patch

	eprefixify catalog.c xmlcatalog.c runtest.c xmllint.c

#	epunt_cxx # if we don't eautoreconf

	# Important patches from master
	epatch \
		"${FILESDIR}/${PN}-2.9.2-revert-missing-initialization.patch"

	# Please do not remove, as else we get references to PORTAGE_TMPDIR
	# in /usr/lib/python?.?/site-packages/libxml2mod.la among things.
	# We now need to run eautoreconf at the end to prevent maintainer mode.
#	elibtoolize

	# Use pkgconfig to find icu to properly support multilib, upstream bug #738751
	epatch "${FILESDIR}/${PN}-2.9.2-icu-pkgconfig.patch"

	eautoreconf
}

multilib_src_configure() {
	# filter seemingly problematic CFLAGS (#26320)
	filter-flags -fprefetch-loop-arrays -funroll-loops

	# USE zlib support breaks gnome2
	# (libgnomeprint for instance fails to compile with
	# fresh install, and existing) - <azarah@gentoo.org> (22 Dec 2002).

	# The meaning of the 'debug' USE flag does not apply to the --with-debug
	# switch (enabling the libxml2 debug module). See bug #100898.

	# --with-mem-debug causes unusual segmentation faults (bug #105120).

	libxml2_configure() {
		ECONF_SOURCE="${S}" econf \
			--with-html-subdir=${PF}/html \
			--docdir="${EPREFIX}/usr/share/doc/${PF}" \
			$(use_with debug run-debug) \
			$(use_with icu) \
			$(use_with lzma) \
			$(use_enable ipv6) \
			$(use_enable static-libs static) \
			$(multilib_native_use_with readline) \
			$(multilib_native_use_with readline history) \
			"$@"
	}

	libxml2_py_configure() {
		mkdir -p "${BUILD_DIR}" || die # ensure python build dirs exist
		run_in_build_dir libxml2_configure "--with-python=${PYTHON}" # odd build system
	}

	libxml2_configure --without-python # build python bindings separately

	if multilib_is_native_abi && use python; then
		python_foreach_impl libxml2_py_configure
	fi
}

multilib_src_compile() {
	default
	if multilib_is_native_abi && use python; then
		local native_builddir=${BUILD_DIR}
		python_foreach_impl libxml2_py_emake top_builddir="${native_builddir}" all
	fi
}

multilib_src_test() {
	default
	multilib_is_native_abi && use python && python_foreach_impl libxml2_py_emake test
}

multilib_src_install() {
	emake DESTDIR="${D}" \
		EXAMPLES_DIR="${EPREFIX}"/usr/share/doc/${PF}/examples install

	if multilib_is_native_abi && use python; then
		python_foreach_impl libxml2_py_emake DESTDIR="${D}" install
		python_foreach_impl python_optimize
	fi
}

multilib_src_install_all() {
	# on windows, xmllint is installed by interix libxml2 in parent prefix.
	# this is the version to use. the native winnt version does not support
	# symlinks, which makes repoman fail if the portage tree is linked in
	# from another location (which is my default). -- mduft
	if [[ ${CHOST} == *-winnt* ]]; then
		rm -rf "${ED}"/usr/bin/xmllint
		rm -rf "${ED}"/usr/bin/xmlcatalog
	fi

	rm -rf "${ED}"/usr/share/doc/${P}
	einstalldocs

	if ! use python; then
		rm -rf "${ED}"/usr/share/doc/${PF}/python
		rm -rf "${ED}"/usr/share/doc/${PN}-python-${PV}
	fi

	if ! use examples; then
		rm -rf "${ED}/usr/share/doc/${PF}/examples"
		rm -rf "${ED}/usr/share/doc/${PF}/python/examples"
	fi

	prune_libtool_files --modules
}

pkg_postinst() {
	# We don't want to do the xmlcatalog during stage1, as xmlcatalog will not
	# be in / and stage1 builds to ROOT=/tmp/stage1root. This fixes bug #208887.
	if [[ "${ROOT}" != "/" ]]; then
		elog "Skipping XML catalog creation for stage building (bug #208887)."
	else
		# need an XML catalog, so no-one writes to a non-existent one
		CATALOG="${EROOT}etc/xml/catalog"

		# we dont want to clobber an existing catalog though,
		# only ensure that one is there
		# <obz@gentoo.org>
		if [[ ! -e ${CATALOG} ]]; then
			[[ -d "${EROOT}etc/xml" ]] || mkdir -p "${EROOT}etc/xml"
			"${EPREFIX}"/usr/bin/xmlcatalog --create > "${CATALOG}"
			einfo "Created XML catalog in ${CATALOG}"
		fi
	fi
}

libxml2_py_emake() {
	pushd "${BUILD_DIR}/python" > /dev/null || die
	emake "$@"
	popd > /dev/null
}

The three references to lzma in that are too non-specific to really be of help.

cwr wrote:The fact that some error messages include lib64 paths make me suspect that you are entangled by some sort of multilib problem; it might be worth re-emerging without the multilib flag (if it's set) and seeing if things run more smoothly.

No, multilib is not set, at least not globally - quite a few individual programs and libraries have 'abi_x86_32' set, but the default is the x86-64 ABI. Here is the make.conf for the system in question:

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CFLAGS="-march=native -O2 -pipe"
CXXFLAGS="${CFLAGS}"

# WARNING: Changing your CHOST is not something that should be done lightly.
# Please consult http://www.gentoo.org/doc/en/change-chost.xml before changing.
CHOST="x86_64-pc-linux-gnu"

ABI_X86="64"
ACCEPT_KEYWORDS=~amd64

# These are the USE flags that were used in addition to what is provided by the
# profile used for building.
USE="mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3  \
     amd64 acl cli berkdb X gnome gtk alsa cdr dvd systemd \
     readline iconv ipv6 justify libav minizip a52 acpi \
     ao bash-completion branding cdda cddb cdparanoia ctype \
     css cxx sasl dbus dri emacs exif fftw fontconfig gcj \
     gimp guile gzip jit jack java jpeg lame latex ldap \
     lock matroska mime modules mozilla mysql mysqli ncurses \
     nls msplugin opengl pcre pie png policykit posix \
     pulseaudio python samba scanner session startup-notification \
     snmp sockets source spell svg threads usb v4l upower \
     truetype wifi webkit xine networking smp urandom bzip2 \
     zlib pam hardened crypt dmcrypt \
     -kde -minimal"

CPU_FLAGS_X86="mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3"

GENTOO_MIRRORS="rsync://rsync.gtlib.gatech.edu/gentoo http://gentoo.cites.uiuc.edu/pub/gentoo/"

VIDEO_CARDS="nvidia"

USE_PYTHON="2.7 3.3"

PYTHON_TARGETS="python2_7 python3_3"

# Set PORTDIR for backward compatibility with various tools:
#   gentoo-bashcomp - bug #478444
#   euse - bug #474574
#   euses and ufed - bug #478318
PORTDIR="/usr/portage"

SANE_BACKENDS="hp"
PORTDIR_OVERLAY="/usr/local/portage"

CONFIG_SND_HDA_PREALLOC_SIZE=4096

DRACUT_MODULES="syslog biosdevname crypt \
                crypt-gpg ssh-client cifs"
source /var/lib/layman/make.conf