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* gnu/packages/arcan.scm (arcan)[arguments]: Use
'search-input-directory' for "include/libdrm" and "include/apr-1".
* gnu/packages/bioinformatics.scm (sailfish): Likewise for jellyfish.
* gnu/packages/boost.scm (boost-for-irods): Likewise for libcxx headers.
* gnu/packages/cedille.scm (cedille): Likewise for IAL headers.
* gnu/packages/compression.scm (snappy-with-clang6): Likewise for libcxx
headers.
* gnu/packages/cups.scm (hplip): Likewise for libusb headers.
* gnu/packages/emulators.scm (pcsxr): Likewise for libcdio headers.
* gnu/packages/game-development.scm (python2-renpy): Likewise for
fribidi headers.
* gnu/packages/games.scm (pokerth): Likewise for libircclient.
* gnu/packages/guile-xyz.scm (guile-persist): Likewise for Guile.
* gnu/packages/hurd.scm (hurd): Likewise for libtirpc.
* gnu/packages/irods.scm (irods, irods-client-icommands): Likewise for
libcxx, catch2, and nlohmann-json-cpp.
* gnu/packages/julia.scm (julia): Use 'search-input-file' for libuv's
errno.h.
* gnu/packages/kde-pim.scm (kdepim-runtime): Use
'search-input-directory' for "include/KF5".
(kmessagelib): Likewise.
* gnu/packages/kde.scm (kdeconnect): Likewise.
* gnu/packages/llvm.scm (clang-runtime-3.5): Likewise for libtirpc.
* gnu/packages/mpi.scm (openmpi): Likewise for "include/infiniband".
* gnu/packages/pumpio.scm (pumpa): Use 'search-input-file' for "tidy.h"
and "aspell.h".
* gnu/packages/radio.scm (dream): Use 'search-input-file' and
'search-input-directory' for pulseaudio, sndfile, etc.
* gnu/packages/selinux.scm (policycoreutils): Likewise for PAM and
libaudit.
* gnu/packages/serialization.scm (avro-cpp-1.9-for-irods): Likewise for
libcxx.
* gnu/packages/sync.scm (nextcloud-client): Likewise for "include/KF5".
* gnu/packages/video.scm (mkvtoolnix): Likewise for "include/gtest".
(libopenshot): Likewise for "include/UnitTest++".
* gnu/packages/virtualization.scm (criu): Likewise for libnl3 and for
protobuf file.
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* gnu/packages/gnome.scm (gnome-desktop)[arguments]: Use
'search-input-directory' when searching for glibc's "lib/locale".
* gnu/packages/gnome.scm (geocode-glib): Likewise.
* gnu/packages/package-management.scm (flatpak): Likewise.
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* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-directory' when searching for Eigen headers.
* gnu/packages/bioinformatics.scm (nanopolish): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
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* gnu/packages/audio.scm (libsbsms)[arguments]: Use 'search-input-file'
when searching for Automake file.
* gnu/packages/maths.scm (hdf-java): Likewise.
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* gnu/packages/graphics.scm (blender): Use 'search-input-directory' when
searching for "include/OpenEXR".
(blender-2.79): Likewise.
* gnu/packages/image-processing.scm (opencv): Likewise.
* gnu/packages/image-viewers.scm (luminance-hdr): Likewise.
* gnu/packages/photo.scm (darktable): Likewise.
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* gnu/packages/education.scm (gcompris)[arguments]: Use
'search-input-directory' when searching for SDL headers.
* gnu/packages/education.scm (t4k-common): Likewise.
(tuxmath): Likewise.
* gnu/packages/game-development.scm (tesseract-engine): Likewise.
* gnu/packages/games.scm (foobillard++): Likewise.
(ltris): Likewise.
(prboom-plus): Likewise.
(abbaye): Likewise.
(red-eclipse): Likewise.
(kiki): Likewise.
(tome4): Likewise.
(btanks): Likewise.
(4dtris): Likewise.
(edgar): Likewise.
* gnu/packages/python-xyz.scm (python-kivy): Likewise.
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* gnu/packages/backup.scm (duplicity)[arguments]: Use
'search-input-directory' for "share/zoneinfo".
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Likewise.
(pigx-bsseq): Likewise.
* gnu/packages/calcurse.scm (calcurse): Likewise.
* gnu/packages/calendar.scm (date): Likewise.
* gnu/packages/compression.scm (lhasa): Likewise.
* gnu/packages/cran.scm (r-rstan): Likewise.
* gnu/packages/django.scm (python-django): Likewise.
* gnu/packages/dlang.scm (ldc-bootstrap): Likewise.
* gnu/packages/finance.scm (ledger): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/kde-frameworks.scm (kcalendarcore): Likewise.
(kdelibs4support): Likewise.
* gnu/packages/kodi.scm (kodi): Likewise.
* gnu/packages/mail.scm (mu): Likewise.
* gnu/packages/perl.scm (perl-libtime-parsedate): Likewise.
* gnu/packages/python-xyz.scm (python-robotframework): Likewise.
(python-dparse): Likewise.
* gnu/packages/rrdtool.scm (rrdtool): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/vim.scm (vim): Likewise.
* gnu/packages/virtualization.scm (ganeti): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
* gnu/packages/xfce.scm (xfce4-panel): Likewise.
* gnu/packages/mate.scm (libmateweather): Use 'search-input-file' for
"share/zoneinfo/zone.tab".
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* gnu/packages/geo.scm (qgis)[arguments]: Simplify invocation of 'Xvfb'
in 'check' phase, assuming 'Xvfb' is in $PATH.
* gnu/packages/graphics.scm (opensubdiv)[arguments]: Likewise.
* gnu/packages/java-graphics.scm (java-piccolo2d-extras)[arguments]:
Likewise.
* gnu/packages/kde-frameworks.scm (kcontacts)[arguments]: Likewise.
(kdeclarative)[arguments]: Likewise.
* gnu/packages/kde-multimedia.scm (elisa)[arguments]: Likewise.
* gnu/packages/kde-plasma.scm (kscreenlocker)[arguments]: Likewise.
* gnu/packages/radio.scm (gnuradio)[arguments]: Likewise.
* gnu/packages/education.scm (gcompris-qt)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (weston)[arguments]: Likewise.
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* gnu/packages/base.scm (tzdata)[arguments]: Turn flags and phases into
a gexp.
[inputs]: Turn into a plain list.
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* gnu/packages/commencement.scm (tcc-boot): Remove stale comments.
(gcc-core-mesboot0)[native-inputs]: Remove "boot-patch".
[arguments]: Turn flags and phases into gexps. Use 'local-file' in the
'apply-boot-patch' phase to refer to the patch.
(glibc-mesboot0)[native-inputs]: Remove "boot-patch" and "system-patch".
[arguments]: Turn flags and phases into gexps. Use 'local-file' in the
'apply-boot-patch' phase to refer to the patches.
(gcc-mesboot0)[native-inputs]: Remove "boot-patch".
[arguments]: Turn phases into a gexp.
(gcc-core-mesboot1)[native-inputs]: Remove "boot-patch".
[arguments]: Turn flags and phases into gexps. Use 'local-file' in the
'apply-boot-patch' phase to refer to the patch.
(gcc-mesboot1)[arguments]: Turn flags and phases into gexps.
(glibc-headers-mesboot)[arguments]: Likewise.
(glibc-mesboot)[arguments]: Likewise.
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* gnu/packages/python.scm (python-2.7)[arguments]: Remove "--with-lto" and
"--enable-optimizations" from #:configure-flags.
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* gnu/packages/python.scm (python-2.7)[arguments]: Ensure the post-install
phases run in order. Move rebuild-bytecode last and run it on every output.
* gnu/packages/python.scm (python-3.9)[arguments]: Run the rebuild-bytecode
phase on every output.
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* gnu/packages/python.scm (python-3.9)[arguments]: Delete existing pycs before
calling "compileall".
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* gnu/packages/python.scm (python-3.9)[arguments]: In the rebuild-bytecode
phase, actully run Python instead of defining an anonymous procedure. While
at it, create all optimization levels with the same command instead of running
once for each level.
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* gnu/packages/python.scm (python-3.9)[arguments]: Reset timestamps before
zipping wheels. While at it, remove redundant regex argument.
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* gnu/packages/graphviz.scm (graphviz): Update to 2.48.0.
[source](uri): Adjust for upstream change.
[source](file-name): Remove.
[inputs]: Change from GUILE-2.0 to GUILE-3.0.
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* gnu/packages/graphviz.scm (graphviz)[arguments]: Install Guile bindings for
the version of Guile provided as input.
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* gnu/packages/graphviz.scm (graphviz)[arguments]: Use a gexp for the
modify-phases block. Remove trailing #t's while at it.
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* gnu/packages/perl-check.scm (perl-test-needs): Update to 0.002009.
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* gnu/packages/linux.scm (libcap): Update to 2.51.
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* gnu/packages/gnupg.scm (libksba): Update to 1.6.0.
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* gnu/packages/gnupg.scm (libgcrypt): Update to 1.8.8.
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* gnu/packages/patches/libxml2-parent-pointers.patch,
gnu/packages/patches/libxml2-terminating-newline.patch,
gnu/packages/patches/libxml2-xpath-recursion-limit.patch: New files.
* gnu/packages/patches/python-libxml2-python39-compat.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/xml.scm (libxml2): Update to 2.9.12.
(python-lxml)[source](modules, snippet): New fields.
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* gnu/packages/image.scm (libtiff): Update to 4.3.0.
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* gnu/packages/sqlite.scm (sqlite): Update to 3.36.0.
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* gnu/packages/pdf.scm (poppler): Update to 21.07.0.
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* gnu/packages/linux.scm (util-linux): Update to 2.37.
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* gnu/packages/gtk.scm (pango): Update to 1.48.7.
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* gnu/packages/gtk.scm (harfbuzz): Update to 2.8.2.
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* gnu/packages/ghostscript.scm (libspectre): Update to 0.2.9.
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* gnu/packages/fontutils.scm (fontconfig): Update to 2.13.94.
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* gnu/packages/patches/binutils-loongson-workaround.patch: Adjust for upstream
changes.
* gnu/packages/patches/binutils-libiberty-endianness-bug.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/base.scm (binutils): Update to 2.37.
[source](patches): Remove obsolete patch.
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* gnu/packages/attr.scm (attr): Update to 2.5.1.
[arguments]: Remove trailing #t.
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* gnu/packages/acl.scm (acl): Update to 2.3.1.
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* gnu/packages/ncurses.scm (ncurses)[version]: Set to 6.2.20210619.
[source](uri): Adjust accordingly.
[arguments]: Remove trailing #t's. Rewrite apply-rollup-patch phase to work
in the absence of the patch. Run the phase.
[native-inputs]: Add "rollup-patch".
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* gnu/packages/libevent.scm (libuv): Update to 1.41.1.
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* gnu/packages/web.scm (nghttp2): Update to 1.44.0.
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* gnu/packages/perl.scm (perl)[inputs]: Add COREUTILS-MINIMAL.
[arguments]: Unconditionally patch /bin/pwd in Cwd.pm. While at it, remove
trailing #t's.
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...and avoid an upcoming circular dependency on Perl.
* gnu/packages/base.scm (coreutils-minimal)[native-inputs]: Empty field.
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* gnu/packages/perl.scm (perl)[native-inputs]: Update "perl-cross" to 1.3.6.
[arguments]: Remove obsolete patch.
* gnu/packages/patches/perl-cross.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
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* gnu/packages/perl.scm (perl): Update to 5.34.0.
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* gnu/packages/crypto.scm (rhash): Update to 1.4.2.
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* gnu/packages/crypto.scm (rhash)[arguments]: Turn into gexp, and use #$OUTPUT
instead of the %OUTPUT variable.
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* gnu/packages/base.scm (tzdata-for-tests): Update to 2021a.
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* gnu/packages/commencement.scm (python-boot0)[arguments]: Do not use
SUBSTITUTE-KEYWORD-ARGUMENTS to make it easier to change Python without a full
bootstrap.
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* gnu/packages/base.scm (glibc)[source](patches): Remove
glibc-hidden-visibility-ldconfig.patch.
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* gnu/packages/python.scm (python-2.7)[source, arguments]: Remove trailing
#t's.
(wrap-python3)[arguments]: Likewise.
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* gnu/packages/python.scm (python-3.9): Update to 3.9.6.
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* gnu/packages/gnome.scm (glib-networking)[native-inputs]: Remove INTLTOOL.
Add GETTEXT-MINIMAL.
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* gnu/packages/gnome.scm (gsettings-desktop-schemas)[native-inputs]: Remove
INTLTOOL. Add GETTEXT-MINIMAL.
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