From c7ba4643a963999cb63e6d7835fdabf71d3e95a1 Mon Sep 17 00:00:00 2001 From: Connor Clark Date: Tue, 3 Jan 2017 18:54:13 -0800 Subject: [PATCH 01/94] nix-prefetch-git: remove call to non-existent print_metadata command; improve hash mismatch error message. --- pkgs/build-support/fetchgit/nix-prefetch-git | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pkgs/build-support/fetchgit/nix-prefetch-git b/pkgs/build-support/fetchgit/nix-prefetch-git index f71d9ac55bc..3d656eba5ff 100755 --- a/pkgs/build-support/fetchgit/nix-prefetch-git +++ b/pkgs/build-support/fetchgit/nix-prefetch-git @@ -406,8 +406,7 @@ else finalPath=$(nix-store --add-fixed --recursive "$hashType" "$tmpFile") if test -n "$expHash" -a "$expHash" != "$hash"; then - print_metadata - echo "hash mismatch for URL \`$url'" >&2 + echo "hash mismatch for URL \`$url'. Got \`$hash'; expected \`$expHash'." >&2 exit 1 fi fi From e9ab1a614f31e4eb61dc864fcfb404eabc28084b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maximilian=20G=C3=BCntner?= Date: Wed, 4 Jan 2017 10:42:13 +0100 Subject: [PATCH 02/94] cpp-ipfs-api: 2016-11-09 -> 2017-01-04 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Maximilian Güntner --- pkgs/development/libraries/cpp-ipfs-api/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/development/libraries/cpp-ipfs-api/default.nix b/pkgs/development/libraries/cpp-ipfs-api/default.nix index 2c9d36154a2..c13b32a67b0 100644 --- a/pkgs/development/libraries/cpp-ipfs-api/default.nix +++ b/pkgs/development/libraries/cpp-ipfs-api/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "cpp-ipfs-api-${version}"; - version = "2016-11-09"; + version = "2017-01-04"; src = fetchFromGitHub { owner = "vasild"; repo = "cpp-ipfs-api"; - rev = "46e473e49ede4fd829235f1d4930754d5356a747"; - sha256 = "10c5hmg9857zb0fp262ca4a42gq9iqdyqz7f975cp3qs70x12q08"; + rev = "96a890f4518665a56581a2a52311eaa65928eac8"; + sha256 = "1z6gbd7npg4pd9wmdyzcp9h12sg84d7a43c69pp4lzqkyqg8pz1g"; }; buildInputs = [ cmake curl ]; From 6edb3793d3c71ffce23ffaf2b6929bb5aba2f715 Mon Sep 17 00:00:00 2001 From: Dhananjay Balan Date: Wed, 4 Jan 2017 17:43:05 +0100 Subject: [PATCH 03/94] ldns 1.6.17 -> 1.7.0 Release notes: http://git.nlnetlabs.nl/ldns/tree/Changelog?id=release-1.7.0 Openssl-1.1.0 is used to enable offline DANE verification (Needed for the DANE-TA usage type) ``` configure: error: OpenSSL does not support offline DANE verification (Needed for the DANE-TA usage type). Please upgrade OpenSSL to version >= 1.1.0 or rerun with --disable-dane-verify or --disable-dane-ta-usage builder /nix/store/m6n021fbk5h4iywzi3n26j95ksps9mwc-ldns-1.7.0. failed with exit code 1 error: build /nix/store/m6n021fbk5h4iywzi3n26j95ksps9mwc-ldns-1.7.0. failed drvof drvfor ``` --- pkgs/development/libraries/ldns/default.nix | 19 ++++++++++--------- .../libraries/ldns/perl-5.22-compat.patch | 12 ------------ pkgs/top-level/all-packages.nix | 4 +++- 3 files changed, 13 insertions(+), 22 deletions(-) delete mode 100644 pkgs/development/libraries/ldns/perl-5.22-compat.patch diff --git a/pkgs/development/libraries/ldns/default.nix b/pkgs/development/libraries/ldns/default.nix index 883625e551a..c35cc588314 100644 --- a/pkgs/development/libraries/ldns/default.nix +++ b/pkgs/development/libraries/ldns/default.nix @@ -1,25 +1,26 @@ {stdenv, fetchurl, openssl, perl}: stdenv.mkDerivation rec { - name = "ldns-1.6.17"; + pname = "ldns"; + version = "1.7.0"; + + name = "${pname}-${version}"; src = fetchurl { - url = "http://www.nlnetlabs.nl/downloads/ldns/${name}.tar.gz"; - sha256 = "1kf8pkwhcssvgzhh6ha1pjjiziwvwmfaali7kaafh6118mcy124b"; + url = "https://www.nlnetlabs.nl/downloads/ldns/${name}.tar.gz"; + sha1 = "ceeeccf8a27e61a854762737f6ee02f44662c1b8"; }; - outputs = [ "out" "dev" ]; - - patches = [ ./perl-5.22-compat.patch ]; - - postPatch = '' + patchPhase = '' patchShebangs doc/doxyparse.pl ''; + outputs = [ "out" "dev" ]; + nativeBuildInputs = [ perl ]; buildInputs = [ openssl ]; - configureFlags = [ "--with-ssl=${openssl.dev}" "--with-drill" ]; + configureFlags = [ "--with-ssl=${openssl.dev}" "--with-drill"]; postInstall = '' moveToOutput "bin/ldns-config" "$dev" diff --git a/pkgs/development/libraries/ldns/perl-5.22-compat.patch b/pkgs/development/libraries/ldns/perl-5.22-compat.patch deleted file mode 100644 index ddf711cef5d..00000000000 --- a/pkgs/development/libraries/ldns/perl-5.22-compat.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur old/doc/doxyparse.pl new/doc/doxyparse.pl ---- old/doc/doxyparse.pl 2014-01-11 06:04:41.000000000 +0900 -+++ new/doc/doxyparse.pl 2015-08-08 22:29:34.216889652 +0900 -@@ -273,7 +273,7 @@ - - print MAN $MAN_MIDDLE; - -- if (defined(@$also)) { -+ if (@$also) { - print MAN "\n.SH SEE ALSO\n\\fI"; - print MAN join "\\fR, \\fI", @$also; - print MAN "\\fR.\nAnd "; diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 7c247b5dddf..987da00bfce 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -2579,7 +2579,9 @@ in ldapvi = callPackage ../tools/misc/ldapvi { }; - ldns = callPackage ../development/libraries/ldns { }; + ldns = callPackage ../development/libraries/ldns { + openssl = openssl_1_1_0; + }; leafpad = callPackage ../applications/editors/leafpad { }; From 3f9cb55dce4b1e006c13f5423b368b9282d65db9 Mon Sep 17 00:00:00 2001 From: Will Dietz Date: Thu, 5 Jan 2017 16:26:35 -0600 Subject: [PATCH 04/94] skype: paxmark to fix execution on PaX-enabled kernels --- .../networking/instant-messengers/skype/default.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/applications/networking/instant-messengers/skype/default.nix b/pkgs/applications/networking/instant-messengers/skype/default.nix index 5bb2121b1fd..a84b9cbf31c 100644 --- a/pkgs/applications/networking/instant-messengers/skype/default.nix +++ b/pkgs/applications/networking/instant-messengers/skype/default.nix @@ -38,6 +38,9 @@ stdenv.mkDerivation rec { mkdir -p $out/{libexec/skype/,bin} cp -r * $out/libexec/skype/ + # Fix execution on PaX-enabled kernels + paxmark m $out/libexec/skype/skype + patchelf --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \ --set-rpath "${lib.makeLibraryPath buildInputs}" $out/libexec/skype/skype From 5fad2a943bb4f4f35474fb8bbabd3c40374061d4 Mon Sep 17 00:00:00 2001 From: Alex Ivanov Date: Fri, 6 Jan 2017 06:18:26 +0300 Subject: [PATCH 05/94] kde-gtk-config: follow symlinks for cursors --- .../kde-gtk-config/0001-follow-symlinks.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/pkgs/desktops/kde-5/plasma/kde-gtk-config/0001-follow-symlinks.patch b/pkgs/desktops/kde-5/plasma/kde-gtk-config/0001-follow-symlinks.patch index 759eda4cc13..d610d19eedd 100644 --- a/pkgs/desktops/kde-5/plasma/kde-gtk-config/0001-follow-symlinks.patch +++ b/pkgs/desktops/kde-5/plasma/kde-gtk-config/0001-follow-symlinks.patch @@ -37,3 +37,16 @@ index 07c7ad7..b04d978 100644 -- 2.6.2 +diff --git a/src/cursorthemesmodel.cpp b/src/cursorthemesmodel.cpp +index 926a666..85b10f8 100644 +--- a/src/cursorthemesmodel.cpp ++++ b/src/cursorthemesmodel.cpp +@@ -47,7 +47,7 @@ QList CursorThemesModel::installedThemesPaths() + + foreach(const QString& dir, dirs) { + QDir userIconsDir(dir); +- QDirIterator it(userIconsDir.path(), QDir::NoDotAndDotDot|QDir::AllDirs|QDir::NoSymLinks); ++ QDirIterator it(userIconsDir.path(), QDir::NoDotAndDotDot|QDir::AllDirs); + while(it.hasNext()) { + QString currentPath = it.next(); + QDir dir(currentPath); From ba9803079c93799f66b0f0ac6800f883e2fb479e Mon Sep 17 00:00:00 2001 From: Maurizio Di Pietro Date: Fri, 6 Jan 2017 11:00:43 +0100 Subject: [PATCH 06/94] chase: avoided using fq attribute names --- pkgs/tools/system/chase/default.nix | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/tools/system/chase/default.nix b/pkgs/tools/system/chase/default.nix index 15d2b16faee..ebad6933936 100644 --- a/pkgs/tools/system/chase/default.nix +++ b/pkgs/tools/system/chase/default.nix @@ -14,14 +14,14 @@ stdenv.mkDerivation rec { makeFlags = [ "-e" ]; makeFlagsArray="LIBS=-lgc"; - meta = { + meta = with stdenv.lib ; { description = "Follow a symlink and print out its target file"; longDescription = '' A commandline program that chases symbolic filesystems links to the original file ''; homepage = "https://qa.debian.org/developer.php?login=rotty%40debian.org"; - license = stdenv.lib.licenses.gpl2Plus; - maintainers = [ stdenv.lib.maintainers.polyrod ]; - platforms = stdenv.lib.platforms.all; + license = licenses.gpl2Plus; + maintainers = [ maintainers.polyrod ]; + platforms = platforms.all; }; } From 25e34e0baec184668f9322b7050023f66146fcfc Mon Sep 17 00:00:00 2001 From: Maurizio Di Pietro Date: Fri, 6 Jan 2017 11:02:05 +0100 Subject: [PATCH 07/94] sakura: fixed GLib-GIO-ERROR #21698 #21700 --- pkgs/applications/misc/sakura/default.nix | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/sakura/default.nix b/pkgs/applications/misc/sakura/default.nix index 75866cbb971..66e40befe7c 100644 --- a/pkgs/applications/misc/sakura/default.nix +++ b/pkgs/applications/misc/sakura/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, pkgconfig, gtk3, perl, vte, pcre, glib }: +{ stdenv, fetchurl, cmake, pkgconfig, gtk3, perl, vte, pcre, glib , makeWrapper }: stdenv.mkDerivation rec { name = "sakura-${version}"; @@ -11,7 +11,10 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake perl pkgconfig ]; - buildInputs = [ gtk3 vte pcre glib ]; + buildInputs = [ makeWrapper gtk3 vte pcre glib ]; + + # Wrapper sets path to gsettings-schemata so sakura knows where to find colorchooser, fontchooser ... + postInstall = "wrapProgram $out/bin/sakura --suffix XDG_DATA_DIRS : ${gtk3}/share/gsettings-schemas/${gtk3.name}/"; meta = with stdenv.lib; { description = "A terminal emulator based on GTK and VTE"; From 6f9124e11860095d90515e7fb8f702f1779b3fe8 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 17:11:23 +0100 Subject: [PATCH 08/94] r-modules: fix Cairo package --- pkgs/development/r-modules/default.nix | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 093bc2f7884..529c6db091d 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -247,7 +247,7 @@ let bnpmr = [ pkgs.gsl_1 ]; BNSP = [ pkgs.gsl_1 ]; cairoDevice = [ pkgs.gtk2 ]; - Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ]; + Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ]; Cardinal = [ pkgs.which ]; chebpol = [ pkgs.fftw ]; ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ]; @@ -1791,6 +1791,10 @@ let ''; }); + Cairo = old.Cairo.overrideDerivation (attrs: { + NIX_LDFLAGS = "-lfontconfig"; + }); + curl = old.curl.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); From 88fcfafafe33625edefc5b195ce5fd744ba72d95 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 17:30:04 +0100 Subject: [PATCH 09/94] r-modules: fix BayesXsrc package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 529c6db091d..6f1807b4138 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -240,7 +240,7 @@ let audio = [ pkgs.portaudio ]; BayesSAE = [ pkgs.gsl_1 ]; BayesVarSel = [ pkgs.gsl_1 ]; - BayesXsrc = [ pkgs.readline pkgs.ncurses ]; + BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ]; bigGP = [ pkgs.openmpi ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; From f7175388663e600b792c1c22a5b0ba887a7c45aa Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 17:34:21 +0100 Subject: [PATCH 10/94] r-modules: fix git2r package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 6f1807b4138..64e889d7612 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -260,7 +260,7 @@ let fftwtools = [ pkgs.fftw ]; Formula = [ pkgs.gmp ]; geoCount = [ pkgs.gsl_1 ]; - git2r = [ pkgs.zlib pkgs.openssl ]; + git2r = [ pkgs.zlib.dev pkgs.openssl.dev ]; GLAD = [ pkgs.gsl_1 ]; glpkAPI = [ pkgs.gmp pkgs.glpk ]; gmp = [ pkgs.gmp ]; From 6c6aab3e5b545d4d58c80b29c839f23e0f86fa73 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 17:41:42 +0100 Subject: [PATCH 11/94] r-modules: fix cairoDevice package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 64e889d7612..29859f37509 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -246,7 +246,7 @@ let Biostrings = [ pkgs.zlib ]; bnpmr = [ pkgs.gsl_1 ]; BNSP = [ pkgs.gsl_1 ]; - cairoDevice = [ pkgs.gtk2 ]; + cairoDevice = [ pkgs.gtk2.dev ]; Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ]; Cardinal = [ pkgs.which ]; chebpol = [ pkgs.fftw ]; From b88b8ea05b530170a355798ec44940490cb0352f Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 17:58:58 +0100 Subject: [PATCH 12/94] r-modules: fix devEMF package --- pkgs/development/r-modules/default.nix | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 29859f37509..16c6d22eeeb 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -253,7 +253,7 @@ let ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ]; cit = [ pkgs.gsl_1 ]; curl = [ pkgs.curl.dev ]; - devEMF = [ pkgs.xorg.libXft ]; + devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ]; diversitree = [ pkgs.gsl_1 pkgs.fftw ]; EMCluster = [ pkgs.liblapack ]; fftw = [ pkgs.fftw ]; @@ -1863,6 +1863,7 @@ let devEMF = old.devEMF.overrideDerivation (attrs: { NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft"; + NIX_LDFLAGS = "-lX11"; }); slfm = old.slfm.overrideDerivation (attrs: { From 427c4d954a0c1c4447fd6ee3973de6eafe71699d Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 18:15:14 +0100 Subject: [PATCH 13/94] r-modules: fix fftw package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 16c6d22eeeb..d4747910523 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -256,7 +256,7 @@ let devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ]; diversitree = [ pkgs.gsl_1 pkgs.fftw ]; EMCluster = [ pkgs.liblapack ]; - fftw = [ pkgs.fftw ]; + fftw = [ pkgs.fftw.dev ]; fftwtools = [ pkgs.fftw ]; Formula = [ pkgs.gmp ]; geoCount = [ pkgs.gsl_1 ]; From 72eb6a8644ec073bf0a2fc9556388922a9e78c19 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 18:16:44 +0100 Subject: [PATCH 14/94] r-modules: fix fftwtools package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index d4747910523..96d0d8af457 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -257,7 +257,7 @@ let diversitree = [ pkgs.gsl_1 pkgs.fftw ]; EMCluster = [ pkgs.liblapack ]; fftw = [ pkgs.fftw.dev ]; - fftwtools = [ pkgs.fftw ]; + fftwtools = [ pkgs.fftw.dev ]; Formula = [ pkgs.gmp ]; geoCount = [ pkgs.gsl_1 ]; git2r = [ pkgs.zlib.dev pkgs.openssl.dev ]; From e3a2c97c7b8cdb783cd655cc6d093ff539d47b2b Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 18:20:41 +0100 Subject: [PATCH 15/94] r-modules: fix gmp package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 96d0d8af457..37c6b4e8134 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -263,7 +263,7 @@ let git2r = [ pkgs.zlib.dev pkgs.openssl.dev ]; GLAD = [ pkgs.gsl_1 ]; glpkAPI = [ pkgs.gmp pkgs.glpk ]; - gmp = [ pkgs.gmp ]; + gmp = [ pkgs.gmp.dev ]; graphscan = [ pkgs.gsl_1 ]; gsl = [ pkgs.gsl_1 ]; h5 = [ pkgs.hdf5-cpp pkgs.which ]; From debb12ce1a5e06fb2348746ac34c1dbc8567a496 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:17:19 +0100 Subject: [PATCH 16/94] r-module: fix jpeg package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 37c6b4e8134..509dba07f98 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -272,7 +272,7 @@ let iBMQ = [ pkgs.gsl_1 ]; igraph = [ pkgs.gmp ]; JavaGD = [ pkgs.jdk ]; - jpeg = [ pkgs.libjpeg ]; + jpeg = [ pkgs.libjpeg.dev ]; KFKSDS = [ pkgs.gsl_1 ]; kza = [ pkgs.fftw ]; libamtrack = [ pkgs.gsl_1 ]; From 4e7de52c26580f9bad962d2507bc1239df4abffd Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:18:27 +0100 Subject: [PATCH 17/94] r-module: fix kza package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 509dba07f98..a81fc649a46 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -274,7 +274,7 @@ let JavaGD = [ pkgs.jdk ]; jpeg = [ pkgs.libjpeg.dev ]; KFKSDS = [ pkgs.gsl_1 ]; - kza = [ pkgs.fftw ]; + kza = [ pkgs.fftw.dev ]; libamtrack = [ pkgs.gsl_1 ]; mixcat = [ pkgs.gsl_1 ]; mvabund = [ pkgs.gsl_1 ]; From 1e9071948f646be2d459fbb2403619a8c6ddffbb Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:19:27 +0100 Subject: [PATCH 18/94] r-modules: fix mwaved package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index a81fc649a46..3e3bb65d1bb 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -278,7 +278,7 @@ let libamtrack = [ pkgs.gsl_1 ]; mixcat = [ pkgs.gsl_1 ]; mvabund = [ pkgs.gsl_1 ]; - mwaved = [ pkgs.fftw ]; + mwaved = [ pkgs.fftw.dev ]; ncdf4 = [ pkgs.netcdf ]; nloptr = [ pkgs.nlopt ]; openssl = [ pkgs.openssl.dev ]; From c5ef08cc655bab0f06c0f81402e64b87269593e0 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:23:42 +0100 Subject: [PATCH 19/94] r-modules: fix PKI package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 3e3bb65d1bb..07070a6e775 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -287,7 +287,7 @@ let pbdMPI = [ pkgs.openmpi ]; pbdNCDF4 = [ pkgs.netcdf ]; pbdPROF = [ pkgs.openmpi ]; - PKI = [ pkgs.openssl ]; + PKI = [ pkgs.openssl.dev ]; png = [ pkgs.libpng.dev ]; PopGenome = [ pkgs.zlib ]; proj4 = [ pkgs.proj ]; From 062c9037d144ae4b7c49f6d4212a994485d4aa6a Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:25:06 +0100 Subject: [PATCH 20/94] r-modules: fix PopGenome package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 07070a6e775..193b8b7baac 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -289,7 +289,7 @@ let pbdPROF = [ pkgs.openmpi ]; PKI = [ pkgs.openssl.dev ]; png = [ pkgs.libpng.dev ]; - PopGenome = [ pkgs.zlib ]; + PopGenome = [ pkgs.zlib.dev ]; proj4 = [ pkgs.proj ]; qtbase = [ pkgs.qt4 ]; qtpaint = [ pkgs.qt4 ]; From 277efe9896d805ac1fa98d69cc0c4a480533b83b Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:27:45 +0100 Subject: [PATCH 21/94] r-modules: fix sysfonts package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 193b8b7baac..c861f29223f 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -352,7 +352,7 @@ let stsm = [ pkgs.gsl_1 ]; stringi = [ pkgs.icu.dev ]; survSNP = [ pkgs.gsl_1 ]; - sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; + sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; TAQMNGR = [ pkgs.zlib ]; tiff = [ pkgs.libtiff ]; TKF = [ pkgs.gsl_1 ]; From 558f67e85f93268f172d3b30439a66fe221f87ac Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:30:56 +0100 Subject: [PATCH 22/94] r-modules: fix R2SWF package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index c861f29223f..f5b4009dd85 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -294,7 +294,7 @@ let qtbase = [ pkgs.qt4 ]; qtpaint = [ pkgs.qt4 ]; R2GUESS = [ pkgs.gsl_1 ]; - R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; + R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; RAppArmor = [ pkgs.libapparmor ]; rapportools = [ pkgs.which ]; rapport = [ pkgs.which ]; From 8b229baf334cb0df5a691523206ea6df914bcabf Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:33:45 +0100 Subject: [PATCH 23/94] r-modules: fix rbamtools package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index f5b4009dd85..45645e87c27 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -298,7 +298,7 @@ let RAppArmor = [ pkgs.libapparmor ]; rapportools = [ pkgs.which ]; rapport = [ pkgs.which ]; - rbamtools = [ pkgs.zlib ]; + rbamtools = [ pkgs.zlib.dev ]; rcdd = [ pkgs.gmp ]; RcppCNPy = [ pkgs.zlib ]; RcppGSL = [ pkgs.gsl_1 ]; From dd159d06b6c793fb6f06c3b4bb5267f314b8e614 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:34:30 +0100 Subject: [PATCH 24/94] r-modules: fix rcdd package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 45645e87c27..c7ac571ce4c 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -299,7 +299,7 @@ let rapportools = [ pkgs.which ]; rapport = [ pkgs.which ]; rbamtools = [ pkgs.zlib.dev ]; - rcdd = [ pkgs.gmp ]; + rcdd = [ pkgs.gmp.dev ]; RcppCNPy = [ pkgs.zlib ]; RcppGSL = [ pkgs.gsl_1 ]; RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ]; From ba86a3964566cbefdd1badcad84c5054f84604ea Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:35:20 +0100 Subject: [PATCH 25/94] r-modules: fix RcppCNPy package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index c7ac571ce4c..1908c08d52c 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -300,7 +300,7 @@ let rapport = [ pkgs.which ]; rbamtools = [ pkgs.zlib.dev ]; rcdd = [ pkgs.gmp.dev ]; - RcppCNPy = [ pkgs.zlib ]; + RcppCNPy = [ pkgs.zlib.dev ]; RcppGSL = [ pkgs.gsl_1 ]; RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ]; RcppZiggurat = [ pkgs.gsl_1 ]; From 3342f8bd59728902c915434d215492587100cd2e Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:38:00 +0100 Subject: [PATCH 26/94] r-modules: fix RcppOctave package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 1908c08d52c..b79d945d2a9 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -302,7 +302,7 @@ let rcdd = [ pkgs.gmp.dev ]; RcppCNPy = [ pkgs.zlib.dev ]; RcppGSL = [ pkgs.gsl_1 ]; - RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ]; + RcppOctave = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.octave ]; RcppZiggurat = [ pkgs.gsl_1 ]; rgdal = [ pkgs.proj pkgs.gdal ]; rgeos = [ pkgs.geos ]; From 9f2b5e0425c1cde3594ffc274ea07c343554a749 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:51:28 +0100 Subject: [PATCH 27/94] r-modules: fix RGtk2 package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index b79d945d2a9..65d1dcd6bc2 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -309,7 +309,7 @@ let rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ]; rgl = [ pkgs.mesa pkgs.xlibsWrapper ]; Rglpk = [ pkgs.glpk ]; - RGtk2 = [ pkgs.gtk2 ]; + RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ]; Rhtslib = [ pkgs.zlib ]; From e1bc505da9a5c2b292929937c5fea59c8b9ab064 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:54:01 +0100 Subject: [PATCH 28/94] r-modules: fix rggobi package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 65d1dcd6bc2..a5fe9b5cd90 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -306,7 +306,7 @@ let RcppZiggurat = [ pkgs.gsl_1 ]; rgdal = [ pkgs.proj pkgs.gdal ]; rgeos = [ pkgs.geos ]; - rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ]; + rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ]; rgl = [ pkgs.mesa pkgs.xlibsWrapper ]; Rglpk = [ pkgs.glpk ]; RGtk2 = [ pkgs.gtk2.dev ]; From bb60f939aeb108ab4bdfbfa5fddfc403168e22e4 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:56:22 +0100 Subject: [PATCH 29/94] r-modules: fix Rhpc package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index a5fe9b5cd90..8ea725401eb 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -311,7 +311,7 @@ let Rglpk = [ pkgs.glpk ]; RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; - Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ]; + Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; Rhtslib = [ pkgs.zlib ]; RJaCGH = [ pkgs.zlib ]; rjags = [ pkgs.jags ]; From 9922867fa889ec8b5ebd8b8ac39bc6effcdaeb30 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:57:30 +0100 Subject: [PATCH 30/94] r-modules: fix Rhtslib package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 8ea725401eb..9e4952dc54a 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -312,7 +312,7 @@ let RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; - Rhtslib = [ pkgs.zlib ]; + Rhtslib = [ pkgs.zlib.dev ]; RJaCGH = [ pkgs.zlib ]; rjags = [ pkgs.jags ]; rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ]; From 13a582688f3358381820d17bdceef5670ee97585 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 19:59:17 +0100 Subject: [PATCH 31/94] r-modules: fix RJaCGH package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 9e4952dc54a..d1ce64aad04 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -313,7 +313,7 @@ let rhdf5 = [ pkgs.zlib ]; Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; Rhtslib = [ pkgs.zlib.dev ]; - RJaCGH = [ pkgs.zlib ]; + RJaCGH = [ pkgs.zlib.dev ]; rjags = [ pkgs.jags ]; rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ]; Rlibeemd = [ pkgs.gsl_1 ]; From 674a2077dd10600e2f56c0824a0d0a0f5456e0ec Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:00:33 +0100 Subject: [PATCH 32/94] r-modules: fix rJava package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index d1ce64aad04..5d8ed3769a6 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -315,7 +315,7 @@ let Rhtslib = [ pkgs.zlib.dev ]; RJaCGH = [ pkgs.zlib.dev ]; rjags = [ pkgs.jags ]; - rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ]; + rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; Rlibeemd = [ pkgs.gsl_1 ]; rmatio = [ pkgs.zlib ]; Rmpfr = [ pkgs.gmp pkgs.mpfr ]; From a58db75ccb51734a3e345c48017438a25b015645 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:01:17 +0100 Subject: [PATCH 33/94] r-modules: fix rmatio package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 5d8ed3769a6..3765c88119e 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -317,7 +317,7 @@ let rjags = [ pkgs.jags ]; rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; Rlibeemd = [ pkgs.gsl_1 ]; - rmatio = [ pkgs.zlib ]; + rmatio = [ pkgs.zlib.dev ]; Rmpfr = [ pkgs.gmp pkgs.mpfr ]; Rmpi = [ pkgs.openmpi ]; RMySQL = [ pkgs.zlib pkgs.mysql.lib ]; From 780fb79e32671e18c9fcdbe6b6a06b87e69a9a62 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:02:17 +0100 Subject: [PATCH 34/94] r-modules: fix Rmpfr package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 3765c88119e..a669d08381b 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -318,7 +318,7 @@ let rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; Rlibeemd = [ pkgs.gsl_1 ]; rmatio = [ pkgs.zlib.dev ]; - Rmpfr = [ pkgs.gmp pkgs.mpfr ]; + Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ]; Rmpi = [ pkgs.openmpi ]; RMySQL = [ pkgs.zlib pkgs.mysql.lib ]; RNetCDF = [ pkgs.netcdf pkgs.udunits ]; From 53235dbe1487264c9785e6357b6f40ab5a2fa5b8 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:06:44 +0100 Subject: [PATCH 35/94] r-modules: fix rphast package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index a669d08381b..2014192ce94 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -325,7 +325,7 @@ let RODBCext = [ pkgs.libiodbc ]; RODBC = [ pkgs.libiodbc ]; rpg = [ pkgs.postgresql ]; - rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ]; + rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ]; Rpoppler = [ pkgs.poppler ]; RPostgreSQL = [ pkgs.postgresql ]; RProtoBuf = [ pkgs.protobuf ]; From bd2aaada6eac1f68a2790737c5b85d037040ae00 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:09:43 +0100 Subject: [PATCH 36/94] r-modules: fix RSclient package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 2014192ce94..293cdbaa7d2 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -330,7 +330,7 @@ let RPostgreSQL = [ pkgs.postgresql ]; RProtoBuf = [ pkgs.protobuf ]; rPython = [ pkgs.python ]; - RSclient = [ pkgs.openssl ]; + RSclient = [ pkgs.openssl.dev ]; Rserve = [ pkgs.openssl ]; Rssa = [ pkgs.fftw ]; rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ]; From fd175e4084d961c7466be90d2723da646a6397f4 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:13:30 +0100 Subject: [PATCH 37/94] r-modules: fix Rssa package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 293cdbaa7d2..4ab142891c4 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -332,7 +332,7 @@ let rPython = [ pkgs.python ]; RSclient = [ pkgs.openssl.dev ]; Rserve = [ pkgs.openssl ]; - Rssa = [ pkgs.fftw ]; + Rssa = [ pkgs.fftw.dev ]; rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ]; rtiff = [ pkgs.libtiff ]; runjags = [ pkgs.jags ]; From d7ac90dd0c7a5169ff570fce1d672c43365b1571 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:16:49 +0100 Subject: [PATCH 38/94] r-modules: fix rtfbs package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 4ab142891c4..6802bd1d539 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -333,7 +333,7 @@ let RSclient = [ pkgs.openssl.dev ]; Rserve = [ pkgs.openssl ]; Rssa = [ pkgs.fftw.dev ]; - rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ]; + rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ]; rtiff = [ pkgs.libtiff ]; runjags = [ pkgs.jags ]; RVowpalWabbit = [ pkgs.zlib pkgs.boost ]; From ae2723a1442e698ec74d9eca09ced7e0ce9c5a77 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:17:42 +0100 Subject: [PATCH 39/94] r-modules: fix rtiff package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 6802bd1d539..ed1e276dbbb 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -334,7 +334,7 @@ let Rserve = [ pkgs.openssl ]; Rssa = [ pkgs.fftw.dev ]; rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ]; - rtiff = [ pkgs.libtiff ]; + rtiff = [ pkgs.libtiff.dev ]; runjags = [ pkgs.jags ]; RVowpalWabbit = [ pkgs.zlib pkgs.boost ]; rzmq = [ pkgs.zeromq3 ]; From 1ef67b9e781efd72aebeb8db1507a10e4e6adbae Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:22:07 +0100 Subject: [PATCH 40/94] r-modules: fix RVowpalWabbit package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index ed1e276dbbb..f731e1498e8 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -336,7 +336,7 @@ let rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ]; rtiff = [ pkgs.libtiff.dev ]; runjags = [ pkgs.jags ]; - RVowpalWabbit = [ pkgs.zlib pkgs.boost ]; + RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ]; rzmq = [ pkgs.zeromq3 ]; SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ]; sdcTable = [ pkgs.gmp pkgs.glpk ]; From e1a5eeef06e1b83066ca0645fb2e29e3dbca1f17 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:26:40 +0100 Subject: [PATCH 41/94] r-modules: fix seqinr package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index f731e1498e8..a2570c8384f 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -341,7 +341,7 @@ let SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ]; sdcTable = [ pkgs.gmp pkgs.glpk ]; seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ]; - seqinr = [ pkgs.zlib ]; + seqinr = [ pkgs.zlib.dev ]; seqminer = [ pkgs.zlib pkgs.bzip2 ]; showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ]; simplexreg = [ pkgs.gsl_1 ]; From 8a6b58d51d767e043206b3d821e14b4c543ec1d4 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:28:22 +0100 Subject: [PATCH 42/94] r-modules: fix seqminer package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index a2570c8384f..6a36f9ca7b4 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -342,7 +342,7 @@ let sdcTable = [ pkgs.gmp pkgs.glpk ]; seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ]; seqinr = [ pkgs.zlib.dev ]; - seqminer = [ pkgs.zlib pkgs.bzip2 ]; + seqminer = [ pkgs.zlib.dev pkgs.bzip2 ]; showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ]; simplexreg = [ pkgs.gsl_1 ]; SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h From fcbed4b6549e30a5ac696acd9d068db58ce07451 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:29:12 +0100 Subject: [PATCH 43/94] r-modules: fix showtext package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 6a36f9ca7b4..5069d67ad72 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -343,7 +343,7 @@ let seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ]; seqinr = [ pkgs.zlib.dev ]; seqminer = [ pkgs.zlib.dev pkgs.bzip2 ]; - showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ]; + showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ]; simplexreg = [ pkgs.gsl_1 ]; SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h spate = [ pkgs.fftw ]; From 2303e631165727b94467bd5c1ec16cf8c5c2d3cc Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:30:01 +0100 Subject: [PATCH 44/94] r-modules: fix spate package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 5069d67ad72..be7b7a8143e 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -346,7 +346,7 @@ let showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ]; simplexreg = [ pkgs.gsl_1 ]; SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h - spate = [ pkgs.fftw ]; + spate = [ pkgs.fftw.dev ]; sprint = [ pkgs.openmpi ]; ssanv = [ pkgs.proj ]; stsm = [ pkgs.gsl_1 ]; From 9420fa23c65dd5276e7214cff01949e1818504d5 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:31:16 +0100 Subject: [PATCH 45/94] r-modules: fix TAQMNGR package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index be7b7a8143e..0fcf06b25f5 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -353,7 +353,7 @@ let stringi = [ pkgs.icu.dev ]; survSNP = [ pkgs.gsl_1 ]; sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; - TAQMNGR = [ pkgs.zlib ]; + TAQMNGR = [ pkgs.zlib.dev ]; tiff = [ pkgs.libtiff ]; TKF = [ pkgs.gsl_1 ]; tkrplot = [ pkgs.xorg.libX11 ]; From 0b3e62bb125d6f57dc50b9c0c085e22075a2e1a3 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:32:48 +0100 Subject: [PATCH 46/94] r-modules: fix tiff package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 0fcf06b25f5..14006311607 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -354,7 +354,7 @@ let survSNP = [ pkgs.gsl_1 ]; sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; TAQMNGR = [ pkgs.zlib.dev ]; - tiff = [ pkgs.libtiff ]; + tiff = [ pkgs.libtiff.dev ]; TKF = [ pkgs.gsl_1 ]; tkrplot = [ pkgs.xorg.libX11 ]; topicmodels = [ pkgs.gsl_1 ]; From f9d84f8b65be0aecd17802f13fc7de2845ef26d9 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:37:33 +0100 Subject: [PATCH 47/94] r-modules: fix tkrplot package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 14006311607..3b47fd9f3de 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -356,7 +356,7 @@ let TAQMNGR = [ pkgs.zlib.dev ]; tiff = [ pkgs.libtiff.dev ]; TKF = [ pkgs.gsl_1 ]; - tkrplot = [ pkgs.xorg.libX11 ]; + tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ]; topicmodels = [ pkgs.gsl_1 ]; udunits2 = [ pkgs.udunits pkgs.expat ]; V8 = [ pkgs.v8 ]; From 512be9e14ac2f2b37ff7b6ea181cd3854b21acbb Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:39:10 +0100 Subject: [PATCH 48/94] r-modules: fix WhopGenome package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 3b47fd9f3de..4d12d3ea8b1 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -362,7 +362,7 @@ let V8 = [ pkgs.v8 ]; VBLPCM = [ pkgs.gsl_1 ]; VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ]; - WhopGenome = [ pkgs.zlib ]; + WhopGenome = [ pkgs.zlib.dev ]; XBRL = [ pkgs.zlib pkgs.libxml2 ]; xml2 = [ pkgs.libxml2 ]; XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; From 5b813c2ab0f8469ed76323d6551e67479173e407 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:39:44 +0100 Subject: [PATCH 49/94] r-modules: fix XBRL package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 4d12d3ea8b1..61b9dd8ba44 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -363,7 +363,7 @@ let VBLPCM = [ pkgs.gsl_1 ]; VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ]; WhopGenome = [ pkgs.zlib.dev ]; - XBRL = [ pkgs.zlib pkgs.libxml2 ]; + XBRL = [ pkgs.zlib pkgs.libxml2.dev ]; xml2 = [ pkgs.libxml2 ]; XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; affyPLM = [ pkgs.zlib ]; From 1d7fd8f3c4c27e3cece2fb606639a29955b25162 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:40:43 +0100 Subject: [PATCH 50/94] r-modules: fix xml2 package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 61b9dd8ba44..f382a125501 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -364,7 +364,7 @@ let VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ]; WhopGenome = [ pkgs.zlib.dev ]; XBRL = [ pkgs.zlib pkgs.libxml2.dev ]; - xml2 = [ pkgs.libxml2 ]; + xml2 = [ pkgs.libxml2.dev ]; XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; affyPLM = [ pkgs.zlib ]; bamsignals = [ pkgs.zlib ]; From c5e4754ca7c7db5b43d7eeb0ccc9cb024120e742 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:42:00 +0100 Subject: [PATCH 51/94] r-modules: fix affyPLM package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index f382a125501..77453c4e533 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -366,7 +366,7 @@ let XBRL = [ pkgs.zlib pkgs.libxml2.dev ]; xml2 = [ pkgs.libxml2.dev ]; XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; - affyPLM = [ pkgs.zlib ]; + affyPLM = [ pkgs.zlib.dev ]; bamsignals = [ pkgs.zlib ]; BitSeq = [ pkgs.zlib ]; DiffBind = [ pkgs.zlib ]; From 272b447ea75677ec44843aafabd9c799ebd14ee8 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:43:55 +0100 Subject: [PATCH 52/94] r-modules: fix bamsignals package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 77453c4e533..a983db5245e 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -367,7 +367,7 @@ let xml2 = [ pkgs.libxml2.dev ]; XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; affyPLM = [ pkgs.zlib.dev ]; - bamsignals = [ pkgs.zlib ]; + bamsignals = [ pkgs.zlib.dev ]; BitSeq = [ pkgs.zlib ]; DiffBind = [ pkgs.zlib ]; ShortRead = [ pkgs.zlib.dev ]; From 4c0c3c74938e2fb4440059e37f6ab3edae2b1634 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:45:14 +0100 Subject: [PATCH 53/94] r-modules: fix BitSeq package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index a983db5245e..9275736a377 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -368,7 +368,7 @@ let XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; affyPLM = [ pkgs.zlib.dev ]; bamsignals = [ pkgs.zlib.dev ]; - BitSeq = [ pkgs.zlib ]; + BitSeq = [ pkgs.zlib.dev ]; DiffBind = [ pkgs.zlib ]; ShortRead = [ pkgs.zlib.dev ]; oligo = [ pkgs.zlib ]; From afd1a4c93366ea2de74f6536874f375ff544e3ee Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:47:08 +0100 Subject: [PATCH 54/94] r-modules: fix affyio package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 9275736a377..061c930ff83 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -377,7 +377,7 @@ let XVector = [ pkgs.zlib.dev ]; Rsamtools = [ pkgs.zlib.dev ]; rtracklayer = [ pkgs.zlib ]; - affyio = [ pkgs.zlib ]; + affyio = [ pkgs.zlib.dev ]; VariantAnnotation = [ pkgs.zlib ]; snpStats = [ pkgs.zlib ]; }; From 286e86f3a5a9be1fb71e97924667f01e11372557 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:49:49 +0100 Subject: [PATCH 55/94] r-modules: fix oligo package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 061c930ff83..4fd1a1991b5 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -371,7 +371,7 @@ let BitSeq = [ pkgs.zlib.dev ]; DiffBind = [ pkgs.zlib ]; ShortRead = [ pkgs.zlib.dev ]; - oligo = [ pkgs.zlib ]; + oligo = [ pkgs.zlib.dev ]; gmapR = [ pkgs.zlib ]; Rsubread = [ pkgs.zlib ]; XVector = [ pkgs.zlib.dev ]; From 9ebab25442a1f0bab96d1a39882b8b780e9acf60 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:51:14 +0100 Subject: [PATCH 56/94] r-modules: fix gmapR package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 4fd1a1991b5..5ce0c0f1344 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -372,7 +372,7 @@ let DiffBind = [ pkgs.zlib ]; ShortRead = [ pkgs.zlib.dev ]; oligo = [ pkgs.zlib.dev ]; - gmapR = [ pkgs.zlib ]; + gmapR = [ pkgs.zlib.dev ]; Rsubread = [ pkgs.zlib ]; XVector = [ pkgs.zlib.dev ]; Rsamtools = [ pkgs.zlib.dev ]; From baf65d50006138e755f3c53cf1315bed0426533d Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:52:16 +0100 Subject: [PATCH 57/94] r-modules: fix Rsubread package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 5ce0c0f1344..b1f29791a50 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -373,7 +373,7 @@ let ShortRead = [ pkgs.zlib.dev ]; oligo = [ pkgs.zlib.dev ]; gmapR = [ pkgs.zlib.dev ]; - Rsubread = [ pkgs.zlib ]; + Rsubread = [ pkgs.zlib.dev ]; XVector = [ pkgs.zlib.dev ]; Rsamtools = [ pkgs.zlib.dev ]; rtracklayer = [ pkgs.zlib ]; From 6540b6507dc4d790197240f34141bca82f9dba03 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:53:12 +0100 Subject: [PATCH 58/94] r-modules: fix rtracklayer package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index b1f29791a50..ca59771bd36 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -376,7 +376,7 @@ let Rsubread = [ pkgs.zlib.dev ]; XVector = [ pkgs.zlib.dev ]; Rsamtools = [ pkgs.zlib.dev ]; - rtracklayer = [ pkgs.zlib ]; + rtracklayer = [ pkgs.zlib.dev ]; affyio = [ pkgs.zlib.dev ]; VariantAnnotation = [ pkgs.zlib ]; snpStats = [ pkgs.zlib ]; From b5a0925663fa90a7e8eaa7847e6cce5fc7e87d6f Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:53:49 +0100 Subject: [PATCH 59/94] r-modules: fix VariantAnnotation package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index ca59771bd36..c2c5e24b37f 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -378,7 +378,7 @@ let Rsamtools = [ pkgs.zlib.dev ]; rtracklayer = [ pkgs.zlib.dev ]; affyio = [ pkgs.zlib.dev ]; - VariantAnnotation = [ pkgs.zlib ]; + VariantAnnotation = [ pkgs.zlib.dev ]; snpStats = [ pkgs.zlib ]; }; From 8954412fccc04772ac9663fc9c53686f0524a785 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Fri, 6 Jan 2017 20:54:40 +0100 Subject: [PATCH 60/94] r-modules: fix snpStats package --- pkgs/development/r-modules/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index c2c5e24b37f..49273e34c7e 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -379,7 +379,7 @@ let rtracklayer = [ pkgs.zlib.dev ]; affyio = [ pkgs.zlib.dev ]; VariantAnnotation = [ pkgs.zlib.dev ]; - snpStats = [ pkgs.zlib ]; + snpStats = [ pkgs.zlib.dev ]; }; packagesWithBuildInputs = { From 1e253d54f5aafd5200ad8c814242d88d3384c4ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vladim=C3=ADr=20=C4=8Cun=C3=A1t?= Date: Fri, 6 Jan 2017 21:11:16 +0100 Subject: [PATCH 61/94] libpng12: security 1.2.56 -> 1.2.57 CVE-2016-10087 --- pkgs/development/libraries/libpng/12.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/libpng/12.nix b/pkgs/development/libraries/libpng/12.nix index 8e17c44fa63..b3f7f96e936 100644 --- a/pkgs/development/libraries/libpng/12.nix +++ b/pkgs/development/libraries/libpng/12.nix @@ -3,11 +3,11 @@ assert !(stdenv ? cross) -> zlib != null; stdenv.mkDerivation rec { - name = "libpng-1.2.56"; + name = "libpng-1.2.57"; src = fetchurl { url = "mirror://sourceforge/libpng/${name}.tar.xz"; - sha256 = "1ghd03p353x0vi4dk83n1nlldg11w7vqdk3f99rkgfb82ic59ki4"; + sha256 = "1n2lrzjkm5jhfg2bs10q398lkwbbx742fi27zgdgx0x23zhj0ihg"; }; outputs = [ "out" "dev" "man" ]; From 8fda707027968c15704f75b00a0086644a03ed18 Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Fri, 6 Jan 2017 16:14:30 -0500 Subject: [PATCH 62/94] kernel: 4.4.39 -> 4.4.40 --- pkgs/os-specific/linux/kernel/linux-4.4.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/linux-4.4.nix b/pkgs/os-specific/linux/kernel/linux-4.4.nix index 6eb6e4663e9..649cf013591 100644 --- a/pkgs/os-specific/linux/kernel/linux-4.4.nix +++ b/pkgs/os-specific/linux/kernel/linux-4.4.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl, perl, buildLinux, ... } @ args: import ./generic.nix (args // rec { - version = "4.4.39"; + version = "4.4.40"; extraMeta.branch = "4.4"; src = fetchurl { url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz"; - sha256 = "188ij72z05sbzrn438r9awpf2pvpv8p2iykfcxs2kxibn23c2jw6"; + sha256 = "1qd431bk3q9xcvnlw4fvcsw4l8k44s14nwdkq4y3kmrywzb5xg64"; }; kernelPatches = args.kernelPatches; From ecf87b11f2b9c44fe54f3188fdc665d3d9ad670c Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Fri, 6 Jan 2017 16:15:02 -0500 Subject: [PATCH 63/94] kernel: 4.8.15 -> 4.8.16 --- pkgs/os-specific/linux/kernel/linux-4.8.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/linux-4.8.nix b/pkgs/os-specific/linux/kernel/linux-4.8.nix index 7a6ce4533e9..8a71a771c4f 100644 --- a/pkgs/os-specific/linux/kernel/linux-4.8.nix +++ b/pkgs/os-specific/linux/kernel/linux-4.8.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl, perl, buildLinux, ... } @ args: import ./generic.nix (args // rec { - version = "4.8.15"; + version = "4.8.16"; extraMeta.branch = "4.8"; src = fetchurl { url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz"; - sha256 = "1vlgacsdcww333n9vm2pmdfkcpkjhavrh1aalrr7p6vj2c4jc18n"; + sha256 = "1aml6vhsfpvm8rsadraff7qj0ivgd9aw75k2q65drz4iby1pqb9h"; }; kernelPatches = args.kernelPatches; From c1d20ea50cf119c61ef446fde8491dd57f5dac07 Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Fri, 6 Jan 2017 16:15:18 -0500 Subject: [PATCH 64/94] kernel: 4.9.0 -> 4.9.1 --- pkgs/os-specific/linux/kernel/linux-4.9.nix | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/linux-4.9.nix b/pkgs/os-specific/linux/kernel/linux-4.9.nix index f154e143e03..25e9eac0365 100644 --- a/pkgs/os-specific/linux/kernel/linux-4.9.nix +++ b/pkgs/os-specific/linux/kernel/linux-4.9.nix @@ -1,13 +1,12 @@ { stdenv, fetchurl, perl, buildLinux, ... } @ args: import ./generic.nix (args // rec { - version = "4.9"; - modDirVersion = "4.9.0"; + version = "4.9.1"; extraMeta.branch = "4.9"; src = fetchurl { url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz"; - sha256 = "029098dcffab74875e086ae970e3828456838da6e0ba22ce3f64ef764f3d7f1a"; + sha256 = "06jlfdmfgmhj80q1q9pglkjygjc1s1b5fslhf5bzkicsw4r2369j"; }; kernelPatches = args.kernelPatches; From e6708cea37b86b59cc5b35e434b4711bdbbe5064 Mon Sep 17 00:00:00 2001 From: Franz Pletz Date: Thu, 5 Jan 2017 19:58:26 +0100 Subject: [PATCH 65/94] bind: fix collision of binaries in outputs Using outputsToInstall the intended behaviour of including host and dnsutils when bind is installed can be implemented instead of using symlinks to fix installing all outputs individually with nix-env. Fixes #19761. --- nixos/modules/services/networking/bind.nix | 2 +- pkgs/servers/dns/bind/default.nix | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/nixos/modules/services/networking/bind.nix b/nixos/modules/services/networking/bind.nix index 72110e62576..0272b6ceff2 100644 --- a/nixos/modules/services/networking/bind.nix +++ b/nixos/modules/services/networking/bind.nix @@ -155,7 +155,7 @@ in chown ${bindUser} /var/run/named ''; - script = "${pkgs.bind.bin}/sbin/named -u ${bindUser} ${optionalString cfg.ipv4Only "-4"} -c ${cfg.configFile} -f"; + script = "${pkgs.bind.out}/sbin/named -u ${bindUser} ${optionalString cfg.ipv4Only "-4"} -c ${cfg.configFile} -f"; unitConfig.Documentation = "man:named(8)"; }; }; diff --git a/pkgs/servers/dns/bind/default.nix b/pkgs/servers/dns/bind/default.nix index e3f2364463b..d3daad1e0cb 100644 --- a/pkgs/servers/dns/bind/default.nix +++ b/pkgs/servers/dns/bind/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { sha256 = "11lxkb7d79c75scrs28q4xmr0ii2li69zj1c650al3qxir8yf754"; }; - outputs = [ "bin" "lib" "dev" "out" "man" "dnsutils" "host" ]; + outputs = [ "out" "lib" "dev" "man" "dnsutils" "host" ]; patches = [ ./dont-keep-configure-flags.patch ./remove-mkdir-var.patch ] ++ stdenv.lib.optional stdenv.isDarwin ./darwin-openssl-linking-fix.patch; @@ -40,13 +40,10 @@ stdenv.mkDerivation rec { moveToOutput bin/isc-config.sh $dev moveToOutput bin/host $host - ln -sf $host/bin/host $bin/bin moveToOutput bin/dig $dnsutils moveToOutput bin/nslookup $dnsutils moveToOutput bin/nsupdate $dnsutils - ln -sf $dnsutils/bin/{dig,nslookup,nsupdate} $bin/bin - ln -sf $host/bin/host $dnsutils/bin for f in "$lib/lib/"*.la "$dev/bin/"{isc-config.sh,bind*-config}; do sed -i "$f" -e 's|-L${openssl.dev}|-L${openssl.out}|g' @@ -60,5 +57,7 @@ stdenv.mkDerivation rec { maintainers = with stdenv.lib.maintainers; [viric peti]; platforms = with stdenv.lib.platforms; unix; + + outputsToInstall = [ "out" "dnsutils" "host" ]; }; } From c5c7911ac22298a95a4128127b3e1427deb98fdc Mon Sep 17 00:00:00 2001 From: Shea Levy Date: Fri, 6 Jan 2017 21:09:49 -0500 Subject: [PATCH 66/94] libuv: disable getaddrinfo tests. Seem to require network access, at least on darwin --- pkgs/development/libraries/libuv/default.nix | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pkgs/development/libraries/libuv/default.nix b/pkgs/development/libraries/libuv/default.nix index fd422a514ef..2b062f58b24 100644 --- a/pkgs/development/libraries/libuv/default.nix +++ b/pkgs/development/libraries/libuv/default.nix @@ -16,6 +16,7 @@ stdenv.mkDerivation rec { toDisable = [ "getnameinfo_basic" # probably network-dependent "spawn_setuid_fails" "spawn_setgid_fails" "fs_chown" # user namespaces + "getaddrinfo_fail" "getaddrinfo_fail_sync" ]; tdRegexp = lib.concatStringsSep "\\|" toDisable; in lib.optionalString doCheck '' @@ -33,8 +34,6 @@ stdenv.mkDerivation rec { doCheck = true; - crossAttrs.doCheck = false; - meta = with lib; { description = "A multi-platform support library with a focus on asynchronous I/O"; homepage = https://github.com/libuv/libuv; From 845dd121f8922dd8171ded470ef302c3602de9ea Mon Sep 17 00:00:00 2001 From: Shea Levy Date: Fri, 6 Jan 2017 22:10:29 -0500 Subject: [PATCH 67/94] ghc-head: Put ./boot into commonPreConfigure --- pkgs/development/compilers/ghc/head.nix | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/pkgs/development/compilers/ghc/head.nix b/pkgs/development/compilers/ghc/head.nix index 081f554e06b..971365eda48 100644 --- a/pkgs/development/compilers/ghc/head.nix +++ b/pkgs/development/compilers/ghc/head.nix @@ -8,8 +8,12 @@ let commonBuildInputs = [ ghc perl autoconf automake happy alex python3 ]; version = "8.1.20170106"; + rev = "b4f2afe70ddbd0576b4eba3f82ba1ddc52e9b3bd"; commonPreConfigure = '' + echo ${version} >VERSION + echo ${rev} >GIT_COMMIT_ID + ./boot sed -i -e 's|-isysroot /Developer/SDKs/MacOSX10.5.sdk||' configure '' + stdenv.lib.optionalString (!stdenv.isDarwin) '' export NIX_LDFLAGS="$NIX_LDFLAGS -rpath $out/lib/ghc-${version}" @@ -17,9 +21,8 @@ let export NIX_LDFLAGS+=" -no_dtrace_dof" ''; in stdenv.mkDerivation (rec { - inherit version; + inherit version rev; name = "ghc-${version}"; - rev = "b4f2afe70ddbd0576b4eba3f82ba1ddc52e9b3bd"; src = fetchgit { url = "git://git.haskell.org/ghc.git"; @@ -29,11 +32,7 @@ in stdenv.mkDerivation (rec { postPatch = "patchShebangs ."; - preConfigure = '' - echo ${version} >VERSION - echo ${rev} >GIT_COMMIT_ID - ./boot - '' + commonPreConfigure ; + preConfigure = commonPreConfigure; buildInputs = commonBuildInputs; From 7027bbfba3058773ee0e1418666851c36c4d6b18 Mon Sep 17 00:00:00 2001 From: Benjamin Saunders Date: Fri, 6 Jan 2017 20:41:29 -0800 Subject: [PATCH 68/94] matrix-synapse: 0.18.6-rc3 -> 0.18.7-rc2 --- pkgs/servers/matrix-synapse/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/matrix-synapse/default.nix b/pkgs/servers/matrix-synapse/default.nix index ddbf35be83c..fd74ffe54c3 100644 --- a/pkgs/servers/matrix-synapse/default.nix +++ b/pkgs/servers/matrix-synapse/default.nix @@ -24,13 +24,13 @@ let }; in pythonPackages.buildPythonApplication rec { name = "matrix-synapse-${version}"; - version = "0.18.6-rc3"; + version = "0.18.7-rc2"; src = fetchFromGitHub { owner = "matrix-org"; repo = "synapse"; rev = "v${version}"; - sha256 = "1a2yj22s84sd3nm9lx4rcdjbpbfclz6cp0ljpilw6n7spmj1nhcd"; + sha256 = "13rx77xfcci7q8xpxxgnh84h6md53akjcy9glwn20vm9vpka3vvj"; }; patches = [ ./matrix-synapse.patch ]; From d6ff445f10a60e9565a895c91f4d220e2a6bbc2e Mon Sep 17 00:00:00 2001 From: Joachim Fasting Date: Sat, 7 Jan 2017 08:01:27 +0100 Subject: [PATCH 69/94] grsecurity: 4.8.15-201612301949 -> 4.8.16-201701062021 --- pkgs/os-specific/linux/kernel/linux-grsecurity.nix | 4 ++-- pkgs/os-specific/linux/kernel/patches.nix | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/linux-grsecurity.nix b/pkgs/os-specific/linux/kernel/linux-grsecurity.nix index 7a6ce4533e9..8a71a771c4f 100644 --- a/pkgs/os-specific/linux/kernel/linux-grsecurity.nix +++ b/pkgs/os-specific/linux/kernel/linux-grsecurity.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl, perl, buildLinux, ... } @ args: import ./generic.nix (args // rec { - version = "4.8.15"; + version = "4.8.16"; extraMeta.branch = "4.8"; src = fetchurl { url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz"; - sha256 = "1vlgacsdcww333n9vm2pmdfkcpkjhavrh1aalrr7p6vj2c4jc18n"; + sha256 = "1aml6vhsfpvm8rsadraff7qj0ivgd9aw75k2q65drz4iby1pqb9h"; }; kernelPatches = args.kernelPatches; diff --git a/pkgs/os-specific/linux/kernel/patches.nix b/pkgs/os-specific/linux/kernel/patches.nix index e54189b078a..42a6e0d037b 100644 --- a/pkgs/os-specific/linux/kernel/patches.nix +++ b/pkgs/os-specific/linux/kernel/patches.nix @@ -95,9 +95,9 @@ rec { }; grsecurity_testing = grsecPatch - { kver = "4.8.15"; - grrev = "201612301949"; - sha256 = "1083r30ipvdi3kjixlsp3f1mmf7848f2p32ds956caarvr4vkm3b"; + { kver = "4.8.16"; + grrev = "201701062021"; + sha256 = "0ivl9dpbyf0f7ywgh8kbzdf0za10yrh6s8plqk9vnns3dhgcnvnq"; }; # This patch relaxes grsec constraints on the location of usermode helpers, From 0f24e5672805bbda94e3a0c1dadeb28d941d472e Mon Sep 17 00:00:00 2001 From: Joachim Fasting Date: Sat, 7 Jan 2017 08:02:40 +0100 Subject: [PATCH 70/94] dnscrypt-proxy: 1.9.0 -> 1.9.1 --- pkgs/tools/networking/dnscrypt-proxy/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/networking/dnscrypt-proxy/default.nix b/pkgs/tools/networking/dnscrypt-proxy/default.nix index 73dfd3ab9ba..baa295c0b00 100644 --- a/pkgs/tools/networking/dnscrypt-proxy/default.nix +++ b/pkgs/tools/networking/dnscrypt-proxy/default.nix @@ -4,11 +4,11 @@ with stdenv.lib; stdenv.mkDerivation rec { name = "dnscrypt-proxy-${version}"; - version = "1.9.0"; + version = "1.9.1"; src = fetchurl { url = "https://download.dnscrypt.org/dnscrypt-proxy/${name}.tar.bz2"; - sha256 = "0v5rsn9zdakzn6rcf2qhjqfd2y4h8q0hj4xr5hwhvaskg213rsyp"; + sha256 = "0aa1qw59b72wl922lfhg24xq2gkv95v1s0daiiqv9b4zpap3ynag"; }; configureFlags = optional stdenv.isLinux "--with-systemd"; From 428927ffa6e5c255ef97f62435b0777f8f9481df Mon Sep 17 00:00:00 2001 From: Graham Christensen Date: Sat, 7 Jan 2017 06:50:02 -0500 Subject: [PATCH 71/94] openjpeg2: patch for multiple CVEs - Floating Point Exception (aka FPE or divide by zero) in opj_pi_next_cprl function in openjp2/pi.c:523 in OpenJPEG 2.1.2. (CVE-2016-9112) - There is a NULL Pointer Access in function imagetopnm of convert.c:1943(jp2) of OpenJPEG 2.1.2. image->comps[compno].data is not assigned a value after initialization(NULL). Impact is Denial of Service. (CVE-2016-9114) - NULL Pointer Access in function imagetopnm of convert.c:2226(jp2) in OpenJPEG 2.1.2. Impact is Denial of Service. Someone must open a crafted j2k file. (CVE-2016-9116) - Heap Buffer Overflow (WRITE of size 4) in function pnmtoimage of convert.c:1719 in OpenJPEG 2.1.2. (CVE-2016-9118) --- pkgs/development/libraries/openjpeg/2.1.nix | 23 ++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/pkgs/development/libraries/openjpeg/2.1.nix b/pkgs/development/libraries/openjpeg/2.1.nix index 9e3c4473b31..ae8710e58a2 100644 --- a/pkgs/development/libraries/openjpeg/2.1.nix +++ b/pkgs/development/libraries/openjpeg/2.1.nix @@ -1,4 +1,4 @@ -{ callPackage, ... } @ args: +{ callPackage, fetchpatch, ... } @ args: callPackage ./generic.nix (args // rec { version = "2.1.2"; @@ -12,5 +12,26 @@ callPackage ./generic.nix (args // rec { # Put in our source code to make sure we don't lose it, since that # referenced commit is someone else's fork, and not actually up-stream. ./CVE-2016-9580-and-CVE-2016-9581.patch + + (fetchpatch { + url = "https://bugzilla.suse.com/attachment.cgi?id=707359&action=diff&context=patch&collapsed=&headers=1&format=raw"; + name = "CVE-2016-9112.patch"; + sha256 = "18hqx73wdzfybr5n5k6pzhbhdlmawiqbjci8n82zykxiyfgp18pd"; + }) + (fetchpatch { + url = "https://bugzilla.suse.com/attachment.cgi?id=707354&action=diff&context=patch&collapsed=&headers=1&format=raw"; + name = "CVE-2016-9114.patch"; + sha256 = "0qam3arw9kdbh4501xim2pyldl708dnpyjwvjmwc9gc7hcq4gfi3"; + }) + (fetchpatch { + url = "https://bugzilla.suse.com/attachment.cgi?id=707356&action=diff&context=patch&collapsed=&headers=1&format=raw"; + name = "CVE-2016-9116.patch"; + sha256 = "0yyb3pxqi5sr44a48bacngzp206j4z49lzkg6hbkz1nra9na61a3"; + }) + (fetchpatch { + url = "https://bugzilla.suse.com/attachment.cgi?id=707358&action=diff&context=patch&collapsed=&headers=1&format=raw"; + name = "CVE-2016-9118.patch"; + sha256 = "125n8bmh07y7697s0y82ypb39rxgj0bdn8rcywbvamscagwg2wy9"; + }) ]; }) From da9e9061f1e952ed57d191ddf0003a3dd37e8546 Mon Sep 17 00:00:00 2001 From: Gabriel Ebner Date: Sat, 7 Jan 2017 15:16:36 +0100 Subject: [PATCH 72/94] haskellPackages.hledger-diff: 0.2.0.6 -> 0.2.0.7 Currently hledger-diff is broken because of the hledger-lib version bump. --- pkgs/development/haskell-modules/hackage-packages.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/haskell-modules/hackage-packages.nix b/pkgs/development/haskell-modules/hackage-packages.nix index 2528b8a8bef..107095b3d7c 100644 --- a/pkgs/development/haskell-modules/hackage-packages.nix +++ b/pkgs/development/haskell-modules/hackage-packages.nix @@ -91117,8 +91117,8 @@ self: { ({ mkDerivation, base, hledger-lib, text, time }: mkDerivation { pname = "hledger-diff"; - version = "0.2.0.6"; - sha256 = "0ef38d60055fb632f3a686b5ce8aee0af5637e51b17d4c5a27764dd485c52b75"; + version = "0.2.0.7"; + sha256 = "1x7ngm0h9hsbf4p8vx1h4z1w9hlqkqfa39v2dvmlxrcx6rs8dzsl"; isLibrary = false; isExecutable = true; executableHaskellDepends = [ base hledger-lib text time ]; From 24aae1effe0d7d65fb7117fc99e82890fb49d466 Mon Sep 17 00:00:00 2001 From: Peter Hoeg Date: Sat, 7 Jan 2017 22:58:45 +0800 Subject: [PATCH 73/94] qrcode: 2014-01-01 -> 2016-08-04 --- pkgs/tools/graphics/qrcode/default.nix | 39 +++++++++----------------- 1 file changed, 14 insertions(+), 25 deletions(-) diff --git a/pkgs/tools/graphics/qrcode/default.nix b/pkgs/tools/graphics/qrcode/default.nix index 606e546af29..44444e6148a 100644 --- a/pkgs/tools/graphics/qrcode/default.nix +++ b/pkgs/tools/graphics/qrcode/default.nix @@ -1,24 +1,14 @@ -{ stdenv, fetchgit }: -let - s = - rec { - baseName = "qrcode"; - date = "2014-01-01"; - version = "git-${date}"; - name = "${baseName}-${version}"; - url = "https://github.com/qsantos/qrcode"; - rev = "2843cbada3b768f60ee1ae13c65160083558cc03"; - sha256 = "1qli0b62yngqj66v6vdqqgcysy3q3fr5vwpf7yf0d9a0dg862x8a"; - }; - buildInputs = [ - ]; -in -stdenv.mkDerivation { - inherit (s) name version; - inherit buildInputs; +{ stdenv, fetchFromGitHub }: - src = fetchgit { - inherit (s) rev url sha256; +stdenv.mkDerivation rec { + name = "qrcode-git-${version}"; + version = "20160804"; + + src = fetchFromGitHub { + owner = "qsantos"; + repo = "qrcode"; + rev = "ad0fdb4aafd0d56b903f110f697abaeb27deee73"; + sha256 = "0v81745nx5gny2g05946k8j553j18a29ikmlyh6c3syq6c15k8cf"; }; NIX_CFLAGS_COMPILE = "-Wno-error=unused-result"; @@ -29,11 +19,10 @@ stdenv.mkDerivation { cp DOCUMENTATION LICENCE "$out/share/doc/qrcode" ''; - meta = { - inherit (s) version; + meta = with stdenv.lib; { description = ''A small QR-code tool''; - license = stdenv.lib.licenses.gpl3Plus; - maintainers = [stdenv.lib.maintainers.raskin]; - platforms = stdenv.lib.platforms.linux; + license = licenses.gpl3Plus; + maintainers = with maintainers; [ raskin ]; + platforms = with platforms; linux; }; } From 133ba5f08a33b747706e55e11900f1ebeac104a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Domen=20Ko=C5=BEar?= Date: Sat, 7 Jan 2017 16:17:33 +0100 Subject: [PATCH 74/94] GHC: 8.0.2-rc2 -> 8.0.2 --- pkgs/development/compilers/ghc/8.0.2.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/development/compilers/ghc/8.0.2.nix b/pkgs/development/compilers/ghc/8.0.2.nix index b2ae92e02c6..5979eba3e10 100644 --- a/pkgs/development/compilers/ghc/8.0.2.nix +++ b/pkgs/development/compilers/ghc/8.0.2.nix @@ -13,12 +13,12 @@ let }); in stdenv.mkDerivation rec { - version = "8.0.1.20161213"; + version = "8.0.2"; name = "ghc-${version}"; src = fetchurl { - url = "https://downloads.haskell.org/~ghc/8.0.2-rc2/${name}-src.tar.xz"; - sha256 = "0l1arhbh3rbs011f0y4pgc35yn07x3hz6lfqlvqbwn96f8ff5529"; + url = "https://downloads.haskell.org/~ghc/8.0.2/${name}-src.tar.xz"; + sha256 = "1c8qc4fhkycynk4g1f9hvk53dj6a1vvqi6bklqznns6hw59m8qhi"; }; patches = [] ++ stdenv.lib.optional stdenv.isLinux ./ghc-no-madv-free.patch; From 71fc7f97482739ba742b9bc2101c20225cc5cb35 Mon Sep 17 00:00:00 2001 From: Shea Levy Date: Sat, 7 Jan 2017 10:28:48 -0500 Subject: [PATCH 75/94] ghc-head: Fixes for new base and Cabal --- .../configuration-ghc-head.nix | 7 ++++ .../haskell-modules/hackage-packages.nix | 4 +- .../patches/atomic-primops-Cabal-1.25.patch | 37 +++++++++++++++++++ 3 files changed, 46 insertions(+), 2 deletions(-) create mode 100644 pkgs/development/haskell-modules/patches/atomic-primops-Cabal-1.25.patch diff --git a/pkgs/development/haskell-modules/configuration-ghc-head.nix b/pkgs/development/haskell-modules/configuration-ghc-head.nix index a2b6058b166..f093c0e427e 100644 --- a/pkgs/development/haskell-modules/configuration-ghc-head.nix +++ b/pkgs/development/haskell-modules/configuration-ghc-head.nix @@ -86,4 +86,11 @@ self: super: { # Won't work with LLVM 3.5. llvm-general = markBrokenVersion "3.4.5.3" super.llvm-general; + # A bunch of jailbreaks due to 'base' bump + old-locale = doJailbreak super.old-locale; + primitive = doJailbreak super.primitive; + test-framework = doJailbreak super.test-framework; + atomic-primops = doJailbreak (appendPatch super.atomic-primops ./patches/atomic-primops-Cabal-1.25.patch); + hashable = doJailbreak super.hashable; + stm = doJailbreak super.stm; } diff --git a/pkgs/development/haskell-modules/hackage-packages.nix b/pkgs/development/haskell-modules/hackage-packages.nix index 107095b3d7c..1922fb3efc3 100644 --- a/pkgs/development/haskell-modules/hackage-packages.nix +++ b/pkgs/development/haskell-modules/hackage-packages.nix @@ -106695,8 +106695,8 @@ self: { ({ mkDerivation, base, Cabal }: mkDerivation { pname = "jailbreak-cabal"; - version = "1.3.1"; - sha256 = "610d8dbd04281eee3d5da05c9eef45bfd1a1ddca20dfe54f283e15ddf6d5c235"; + version = "1.3.2"; + sha256 = "1x2h54sx4ycik34q8f9g698xc2b7fai18918cd08qx7w7ny8nai1"; isLibrary = false; isExecutable = true; executableHaskellDepends = [ base Cabal ]; diff --git a/pkgs/development/haskell-modules/patches/atomic-primops-Cabal-1.25.patch b/pkgs/development/haskell-modules/patches/atomic-primops-Cabal-1.25.patch new file mode 100644 index 00000000000..712bd53092f --- /dev/null +++ b/pkgs/development/haskell-modules/patches/atomic-primops-Cabal-1.25.patch @@ -0,0 +1,37 @@ +diff --git a/Setup.hs b/Setup.hs +index ddf5a02..7ad1f26 100644 +--- a/Setup.hs ++++ b/Setup.hs +@@ -1,4 +1,4 @@ +- ++{-# LANGUAGE CPP #-} + import Control.Monad (when) + import Language.Haskell.TH + import Distribution.Simple (defaultMainWithHooks, simpleUserHooks, UserHooks(postConf), Args) +@@ -6,14 +6,25 @@ import Distribution.Simple.Utils (cabalVersion) + import Distribution.Simple.LocalBuildInfo + import Distribution.Simple.Setup (ConfigFlags) + import Distribution.Version (Version(..)) ++#if MIN_VERSION_Cabal(1,25,0) ++import Distribution.Version (mkVersion) ++#endif + import Distribution.PackageDescription (PackageDescription) + import Debug.Trace + ++#if MIN_VERSION_Cabal(1,25,0) ++versionBranch :: Version -> Version ++versionBranch = id ++#else ++mkVersion :: [Int] -> Version ++mkVersion vs = Version vs [] ++#endif ++ + -- I couldn't figure out a way to do this check from the cabal file, so we drop down + -- here to do it instead: + checkGoodVersion :: IO () + checkGoodVersion = +- if cabalVersion >= Version [1,17,0] [] ++ if cabalVersion >= mkVersion [1,17,0] + then putStrLn (" [Setup.hs] This version of Cabal is ok for profiling: "++show cabalVersion) + else error (" [Setup.hs] This package should not be used in profiling mode with cabal version "++ + show (versionBranch cabalVersion)++" < 1.17.0\n"++ From 6a55b529445a4ca23ce8f7aafcb397a4777eb22a Mon Sep 17 00:00:00 2001 From: Nikolay Amiantov Date: Sat, 7 Jan 2017 18:47:55 +0300 Subject: [PATCH 76/94] warzone2100: 2.1.5 -> 2.2.2 --- pkgs/games/warzone2100/default.nix | 31 +++++++++++++++--------------- pkgs/top-level/all-packages.nix | 2 +- 2 files changed, 17 insertions(+), 16 deletions(-) diff --git a/pkgs/games/warzone2100/default.nix b/pkgs/games/warzone2100/default.nix index 7c578f370d7..dd21d13a027 100644 --- a/pkgs/games/warzone2100/default.nix +++ b/pkgs/games/warzone2100/default.nix @@ -1,7 +1,5 @@ -{ stdenv, fetchurl, bison, flex, gettext, pkgconfig, libpng -, libtheora, openal, physfs, mesa, fribidi, fontconfig -, freetype, qt4, glew, libogg, libvorbis, zlib, libX11 -, libXrandr, zip, unzip, which, perl +{ stdenv, lib, fetchurl, perl, unzip, zip, which, pkgconfig +, qtbase, qtscript, SDL2, libtheora, openal, glew, physfs, fribidi , withVideos ? false }: @@ -14,28 +12,31 @@ let in stdenv.mkDerivation rec { - version = "3.1.5"; + version = "3.2.2"; name = "${pname}-${version}"; + src = fetchurl { url = "mirror://sourceforge/${pname}/releases/${version}/${name}.tar.xz"; - sha256 = "0hm49i2knvvg3wlnryv7h4m84s3qa7jfyym5yy6365sx8wzcrai1"; + sha256 = "064xfxwkqpvqyy7kz46cwi71mxmimxi4wgjly9g51wwxkvz8snmg"; }; - buildInputs = [ bison flex gettext pkgconfig libpng libtheora openal - physfs mesa fribidi fontconfig freetype qt4 - glew libogg libvorbis zlib libX11 libXrandr zip - unzip perl - ]; - patchPhase = '' + + buildInputs = [ qtbase qtscript SDL2 libtheora openal glew physfs fribidi ]; + nativeBuildInputs = [ perl zip unzip pkgconfig ]; + + postPatch = '' substituteInPlace lib/exceptionhandler/dumpinfo.cpp \ --replace "which %s" "${which}/bin/which %s" substituteInPlace lib/exceptionhandler/exceptionhandler.cpp \ --replace "which %s" "${which}/bin/which %s" ''; - configureFlags = "--with-backend=qt --with-distributor=NixOS"; - NIX_CFLAGS_COMPILE = "-fpermissive"; # GL header minor incompatibility + configureFlags = [ "--with-distributor=NixOS" ]; - postInstall = stdenv.lib.optionalString withVideos "cp ${sequences_src} $out/share/warzone2100/sequences.wz"; + hardeningDisable = [ "format" ]; + + enableParallelBuilding = true; + + postInstall = lib.optionalString withVideos "cp ${sequences_src} $out/share/warzone2100/sequences.wz"; meta = with stdenv.lib; { description = "A free RTS game, originally developed by Pumpkin Studios"; diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 070aad1d029..4d538e21d24 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -16338,7 +16338,7 @@ in libjpeg = libjpeg62; }; - warzone2100 = callPackage ../games/warzone2100 { }; + warzone2100 = qt5.callPackage ../games/warzone2100 { }; wesnoth = callPackage ../games/wesnoth { }; From 969651aacaf79c96527931918dc3c6f6f6ba94ff Mon Sep 17 00:00:00 2001 From: Frederik Rietdijk Date: Sat, 7 Jan 2017 17:28:20 +0100 Subject: [PATCH 77/94] pythonPackages.pyjwt: use cryptography instead of pycrypto --- pkgs/top-level/python-packages.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 60fff564add..f1dc2bf86dc 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -20601,7 +20601,7 @@ in { }; buildInputs = with self; [ pytestrunner pytestcov pytest coverage ]; - propagatedBuildInputs = with self; [ pycrypto ecdsa ]; + propagatedBuildInputs = with self; [ cryptography ecdsa ]; # We don't need this specific version postPatch = '' From bbdca635cf0b2e1f7f0b33eebc07686cfcebf975 Mon Sep 17 00:00:00 2001 From: Johannes Bornhold Date: Fri, 23 Dec 2016 22:10:06 +0100 Subject: [PATCH 78/94] cairo: Add CoreText for darwin This helps so that fonts are properly rendered in gtk when used with the backend "quartz". --- pkgs/development/libraries/cairo/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/development/libraries/cairo/default.nix b/pkgs/development/libraries/cairo/default.nix index 5d201c52312..7df72bc0560 100644 --- a/pkgs/development/libraries/cairo/default.nix +++ b/pkgs/development/libraries/cairo/default.nix @@ -47,6 +47,7 @@ stdenv.mkDerivation rec { libiconv ] ++ libintlOrEmpty ++ optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ CoreGraphics + CoreText ApplicationServices Carbon ]); From 354c91df2e40e2f61719e33b7186fe089d2219e7 Mon Sep 17 00:00:00 2001 From: Johannes Bornhold Date: Fri, 23 Dec 2016 22:14:03 +0100 Subject: [PATCH 79/94] pango: Add darwin frameworks for fond rendering --- pkgs/development/libraries/pango/default.nix | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/pkgs/development/libraries/pango/default.nix b/pkgs/development/libraries/pango/default.nix index f39fc2afe7d..22cf7be84d0 100644 --- a/pkgs/development/libraries/pango/default.nix +++ b/pkgs/development/libraries/pango/default.nix @@ -1,5 +1,5 @@ { stdenv, fetchurl, pkgconfig, libXft, cairo, harfbuzz -, libintlOrEmpty, gobjectIntrospection +, libintlOrEmpty, gobjectIntrospection, darwin }: with stdenv.lib; @@ -19,7 +19,12 @@ stdenv.mkDerivation rec { outputs = [ "bin" "dev" "out" "devdoc" ]; buildInputs = [ gobjectIntrospection ]; - nativeBuildInputs = [ pkgconfig ]; + nativeBuildInputs = [ pkgconfig ] + ++ optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ + Carbon + CoreGraphics + CoreText + ]); propagatedBuildInputs = [ cairo harfbuzz libXft ] ++ libintlOrEmpty; enableParallelBuilding = true; @@ -48,6 +53,6 @@ stdenv.mkDerivation rec { license = licenses.lgpl2Plus; maintainers = with maintainers; [ raskin urkud ]; - platforms = with platforms; linux ++ darwin; + platforms = platforms.linux ++ platforms.darwin; }; } From 9f31633a5006c511c97df77dcc025138b4c38e48 Mon Sep 17 00:00:00 2001 From: Johannes Bornhold Date: Fri, 23 Dec 2016 22:16:02 +0100 Subject: [PATCH 80/94] librsvg: Add framework ApplicationServices for darwin --- pkgs/development/libraries/librsvg/default.nix | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/librsvg/default.nix b/pkgs/development/libraries/librsvg/default.nix index 409307fb52b..ebd0f79cd47 100644 --- a/pkgs/development/libraries/librsvg/default.nix +++ b/pkgs/development/libraries/librsvg/default.nix @@ -1,5 +1,5 @@ { lib, stdenv, fetchurl, pkgconfig, glib, gdk_pixbuf, pango, cairo, libxml2, libgsf -, bzip2, libcroco, libintlOrEmpty +, bzip2, libcroco, libintlOrEmpty, darwin , withGTK ? false, gtk3 ? null , gobjectIntrospection ? null, enableIntrospection ? false }: @@ -22,7 +22,10 @@ stdenv.mkDerivation rec { propagatedBuildInputs = [ glib gdk_pixbuf cairo ] ++ lib.optional withGTK gtk3; - nativeBuildInputs = [ pkgconfig ]; + nativeBuildInputs = [ pkgconfig ] + ++ lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ + ApplicationServices + ]); configureFlags = [ "--enable-introspection=auto" ] ++ stdenv.lib.optional stdenv.isDarwin "--disable-Bsymbolic"; From 5a572f80185b2ad2a06ca42ed61bbe08cd14198b Mon Sep 17 00:00:00 2001 From: Johannes Bornhold Date: Fri, 23 Dec 2016 22:18:25 +0100 Subject: [PATCH 81/94] gtk2: Use quartz backend on darwin --- pkgs/development/libraries/gtk+/2.x.nix | 17 ++++++++++++----- pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/pkgs/development/libraries/gtk+/2.x.nix b/pkgs/development/libraries/gtk+/2.x.nix index ba12b4eea93..bcbbecd242d 100644 --- a/pkgs/development/libraries/gtk+/2.x.nix +++ b/pkgs/development/libraries/gtk+/2.x.nix @@ -2,11 +2,15 @@ , gdk_pixbuf, libintlOrEmpty, xlibsWrapper , xineramaSupport ? stdenv.isLinux , cupsSupport ? true, cups ? null +, gdktarget ? "x11" +, AppKit, Cocoa }: assert xineramaSupport -> xorg.libXinerama != null; assert cupsSupport -> cups != null; +with stdenv.lib; + stdenv.mkDerivation rec { name = "gtk+-2.24.31"; @@ -20,7 +24,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - NIX_CFLAGS_COMPILE = stdenv.lib.optionalString (libintlOrEmpty != []) "-lintl"; + NIX_CFLAGS_COMPILE = optionalString (libintlOrEmpty != []) "-lintl"; setupHook = ./setup-hook.sh; @@ -28,7 +32,7 @@ stdenv.mkDerivation rec { patches = [ ./2.0-immodules.cache.patch ]; - propagatedBuildInputs = with xorg; with stdenv.lib; + propagatedBuildInputs = with xorg; [ glib cairo pango gdk_pixbuf atk ] ++ optionals (stdenv.isLinux || stdenv.isDarwin) [ libXrandr libXrender libXcomposite libXi libXcursor @@ -36,11 +40,13 @@ stdenv.mkDerivation rec { ++ optionals stdenv.isDarwin [ xlibsWrapper libXdamage ] ++ libintlOrEmpty ++ optional xineramaSupport libXinerama - ++ optionals cupsSupport [ cups ]; + ++ optionals cupsSupport [ cups ] + ++ optionals (gdktarget == "quartz") [ AppKit Cocoa ]; configureFlags = [ + "--with-gdktarget=${gdktarget}" "--with-xinput=yes" - ] ++ stdenv.lib.optionals stdenv.isDarwin [ + ] ++ optionals stdenv.isDarwin [ "--disable-glibtest" "--disable-introspection" "--disable-visibility" @@ -57,9 +63,10 @@ stdenv.mkDerivation rec { rm $out/lib/gtk-2.0/2.10.0/immodules.cache $out/bin/gtk-query-immodules-2.0 $out/lib/gtk-2.0/2.10.0/immodules/*.so > $out/lib/gtk-2.0/2.10.0/immodules.cache ''; # workaround for bug of nix-mode for Emacs */ ''; + inherit gdktarget; }; - meta = with stdenv.lib; { + meta = { description = "A multi-platform toolkit for creating graphical user interfaces"; homepage = http://www.gtk.org/; license = licenses.lgpl2Plus; diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 4d538e21d24..ba5358f1906 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -7488,6 +7488,8 @@ in gtk2 = callPackage ../development/libraries/gtk+/2.x.nix { cupsSupport = config.gtk2.cups or stdenv.isLinux; + gdktarget = if stdenv.isDarwin then "quartz" else "x11"; + inherit (darwin.apple_sdk.frameworks) AppKit Cocoa; }; gtk3 = callPackage ../development/libraries/gtk+/3.x.nix { }; From 8f7adffe4deefafc40f170194718e7837bf9208a Mon Sep 17 00:00:00 2001 From: Johannes Bornhold Date: Fri, 23 Dec 2016 22:20:30 +0100 Subject: [PATCH 82/94] pygtk: Add flag -ObjC for darwin Had to add this so that it was able to parse the headers from the frameworks. --- pkgs/development/python-modules/pygtk/default.nix | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pkgs/development/python-modules/pygtk/default.nix b/pkgs/development/python-modules/pygtk/default.nix index 7d0896c1fb8..0940ef00ac9 100644 --- a/pkgs/development/python-modules/pygtk/default.nix +++ b/pkgs/development/python-modules/pygtk/default.nix @@ -3,7 +3,7 @@ buildPythonPackage rec { name = "pygtk-2.24.0"; - + disabled = isPy3k; src = fetchurl { @@ -20,6 +20,8 @@ buildPythonPackage rec { buildPhase = "buildPhase"; + NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isDarwin "-ObjC"; + installPhase = "installPhase"; checkPhase = stdenv.lib.optionalString (libglade == null) From ef8fd815cc794b1f535a353bf1ce4573870fcbed Mon Sep 17 00:00:00 2001 From: florianjacob Date: Sat, 7 Jan 2017 17:28:11 +0100 Subject: [PATCH 83/94] update os-release manpage link the old manpage at 0pointer is still there, but does not seem to get updated --- nixos/modules/misc/version.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nixos/modules/misc/version.nix b/nixos/modules/misc/version.nix index ec423768296..70cd3fb9766 100644 --- a/nixos/modules/misc/version.nix +++ b/nixos/modules/misc/version.nix @@ -99,7 +99,7 @@ in }; # Generate /etc/os-release. See - # http://0pointer.de/public/systemd-man/os-release.html for the + # https://www.freedesktop.org/software/systemd/man/os-release.html for the # format. environment.etc."os-release".text = '' From 2ef6af7afdbf0e1f8647f96f9c86082cca8b76d9 Mon Sep 17 00:00:00 2001 From: Anmol Sethi Date: Fri, 6 Jan 2017 08:41:49 -0500 Subject: [PATCH 84/94] libtermkey: from 0.18 to 0.19 --- pkgs/development/libraries/libtermkey/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/libtermkey/default.nix b/pkgs/development/libraries/libtermkey/default.nix index 43c8292a200..97bc98b22d8 100644 --- a/pkgs/development/libraries/libtermkey/default.nix +++ b/pkgs/development/libraries/libtermkey/default.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { name = "libtermkey-${version}"; - version = "0.18"; + version = "0.19"; src = fetchzip { url = "http://www.leonerd.org.uk/code/libtermkey/libtermkey-${version}.tar.gz"; - sha256 = "0a0ih1a114phzmyq6jzgbp03x97463fwvrp1cgnl26awqw3f8sbf"; + sha256 = "0v85h0zacd5lqwkykl2ms4009x8mfidzb6jr4dsq4gh7kwm54w56"; }; makeFlags = [ "PREFIX=$(out)" ] From 96504cd75cde6b733385dcb44bcb18da7bf8d18a Mon Sep 17 00:00:00 2001 From: schneefux Date: Fri, 6 Jan 2017 16:13:53 +0100 Subject: [PATCH 85/94] pythonPackages.discordpy: 0.15.1 -> 0.16 --- pkgs/development/python-modules/discordpy/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/discordpy/default.nix b/pkgs/development/python-modules/discordpy/default.nix index cf01ec835a7..6025956261e 100644 --- a/pkgs/development/python-modules/discordpy/default.nix +++ b/pkgs/development/python-modules/discordpy/default.nix @@ -11,13 +11,13 @@ let pname = "discord.py"; - version = "0.15.1"; + version = "0.16.0"; in buildPythonPackage rec { name = "${pname}-${version}"; src = fetchurl { url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz"; - sha256 = "01lgidvnwwva1i65853gaplamllym2nsk0jis2r6f1rzbamgk1yj"; + sha256 = "0r3qqvx36vywjyjk1nh11ymmr8y81sb45nk63665kcjagx8qnmfx"; }; propagatedBuildInputs = [ asyncio aiohttp websockets pynacl ]; From 0f67005c4a2651ab0d9a48468a4873cff3551b8b Mon Sep 17 00:00:00 2001 From: Johannes Bornhold Date: Sat, 24 Dec 2016 01:11:19 +0100 Subject: [PATCH 86/94] cairo: Add ApplicationServices as propagatedBuildInput Noticed that it caused depending packages to fail, like librsvg, imagemagiv, graphviz. --- pkgs/development/libraries/cairo/default.nix | 4 +++- pkgs/development/libraries/librsvg/default.nix | 7 ++----- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/pkgs/development/libraries/cairo/default.nix b/pkgs/development/libraries/cairo/default.nix index 7df72bc0560..5b40f27674d 100644 --- a/pkgs/development/libraries/cairo/default.nix +++ b/pkgs/development/libraries/cairo/default.nix @@ -48,7 +48,6 @@ stdenv.mkDerivation rec { ] ++ libintlOrEmpty ++ optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ CoreGraphics CoreText - ApplicationServices Carbon ]); @@ -57,6 +56,9 @@ stdenv.mkDerivation rec { ++ optionals xcbSupport [ libxcb xcbutil ] ++ optional gobjectSupport glib ++ optional glSupport mesa_noglu + ++ optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ + ApplicationServices + ]) ; # TODO: maybe liblzo but what would it be for here? configureFlags = if stdenv.isDarwin then [ diff --git a/pkgs/development/libraries/librsvg/default.nix b/pkgs/development/libraries/librsvg/default.nix index ebd0f79cd47..409307fb52b 100644 --- a/pkgs/development/libraries/librsvg/default.nix +++ b/pkgs/development/libraries/librsvg/default.nix @@ -1,5 +1,5 @@ { lib, stdenv, fetchurl, pkgconfig, glib, gdk_pixbuf, pango, cairo, libxml2, libgsf -, bzip2, libcroco, libintlOrEmpty, darwin +, bzip2, libcroco, libintlOrEmpty , withGTK ? false, gtk3 ? null , gobjectIntrospection ? null, enableIntrospection ? false }: @@ -22,10 +22,7 @@ stdenv.mkDerivation rec { propagatedBuildInputs = [ glib gdk_pixbuf cairo ] ++ lib.optional withGTK gtk3; - nativeBuildInputs = [ pkgconfig ] - ++ lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ - ApplicationServices - ]); + nativeBuildInputs = [ pkgconfig ]; configureFlags = [ "--enable-introspection=auto" ] ++ stdenv.lib.optional stdenv.isDarwin "--disable-Bsymbolic"; From ea053cad7a3c54a8fcb29d697c5c07f1f31c0937 Mon Sep 17 00:00:00 2001 From: Matthew Bauer Date: Tue, 22 Nov 2016 23:09:17 -0600 Subject: [PATCH 87/94] gtk-mac-integration: init at 2.0.8 --- .../libraries/gtk-mac-integration/default.nix | 30 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 4 +++ 2 files changed, 34 insertions(+) create mode 100644 pkgs/development/libraries/gtk-mac-integration/default.nix diff --git a/pkgs/development/libraries/gtk-mac-integration/default.nix b/pkgs/development/libraries/gtk-mac-integration/default.nix new file mode 100644 index 00000000000..30ac8f2fe28 --- /dev/null +++ b/pkgs/development/libraries/gtk-mac-integration/default.nix @@ -0,0 +1,30 @@ +{ stdenv, lib, fetchFromGitHub, autoreconfHook, pkgconfig, glib, gtk_doc, gtk }: + +stdenv.mkDerivation rec { + name = "gtk-mac-integration-2.0.8"; + + src = fetchFromGitHub { + owner = "GNOME"; + repo = "gtk-mac-integration"; + rev = "79e708870cdeea24ecdb036c77b4630104ae1776"; + sha256 = "1fbhnvj0rqc3089ypvgnpkp6ad2rr37v5qk38008dgamb9h7f3qs"; + }; + + nativeBuildInputs = [ autoreconfHook pkgconfig gtk_doc ]; + buildInputs = [ glib gtk ]; + + preAutoreconf = '' + gtkdocize + ''; + + meta = with lib; { + description = "Provides integration for Gtk+ applications into the Mac desktop"; + + license = licenses.lgpl21; + + homepage = https://wiki.gnome.org/Projects/GTK+/OSX/Integration; + + maintainers = [ maintainers.matthewbauer ]; + platforms = platforms.darwin; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index ba5358f1906..0d79a295854 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -7515,6 +7515,10 @@ in gtk-sharp-beans = callPackage ../development/libraries/gtk-sharp-beans { }; + gtk-mac-integration = callPackage ../development/libraries/gtk-mac-integration { + gtk = gtk2; + }; + gtkspell2 = callPackage ../development/libraries/gtkspell { }; gtkspell3 = callPackage ../development/libraries/gtkspell/3.nix { }; From f025d2c1898a5697ca109d51412850375883db44 Mon Sep 17 00:00:00 2001 From: Johannes Bornhold Date: Sun, 25 Dec 2016 00:56:49 +0100 Subject: [PATCH 88/94] gtksourceview: Add gtk-mac-integration for darwin Had to pick two commits as patches from the repository which update the dependency ige-mac-integration to gtk-mac-integration. --- .../gnome-2/desktop/gtksourceview/default.nix | 34 ++++++++++++++++--- 1 file changed, 30 insertions(+), 4 deletions(-) diff --git a/pkgs/desktops/gnome-2/desktop/gtksourceview/default.nix b/pkgs/desktops/gnome-2/desktop/gtksourceview/default.nix index c69ee82fa26..7c9cd42a0e9 100644 --- a/pkgs/desktops/gnome-2/desktop/gtksourceview/default.nix +++ b/pkgs/desktops/gnome-2/desktop/gtksourceview/default.nix @@ -1,5 +1,8 @@ -{stdenv, fetchurl, pkgconfig, atk, cairo, glib, gtk, pango, - libxml2Python, perl, intltool, gettext}: +{stdenv, fetchpatch, fetchurl, autoreconfHook, pkgconfig, atk, cairo, glib +, gnome_common, gtk, pango +, libxml2Python, perl, intltool, gettext, gtk-mac-integration }: + +with stdenv.lib; stdenv.mkDerivation rec { name = "gtksourceview-${version}"; @@ -9,6 +12,29 @@ stdenv.mkDerivation rec { url = "mirror://gnome/sources/gtksourceview/2.10/${name}.tar.bz2"; sha256 = "c585773743b1df8a04b1be7f7d90eecdf22681490d6810be54c81a7ae152191e"; }; - buildInputs = [pkgconfig atk cairo glib gtk pango libxml2Python perl intltool - gettext]; + + patches = optionals stdenv.isDarwin [ + (fetchpatch { + name = "change-igemacintegration-to-gtkosxapplication.patch"; + url = "https://git.gnome.org/browse/gtksourceview/patch/?id=e88357c5f210a8796104505c090fb6a04c213902"; + sha256 = "0h5q79q9dqbg46zcyay71xn1pm4aji925gjd5j93v4wqn41wj5m7"; + }) + (fetchpatch { + name = "update-to-gtk-mac-integration-2.0-api.patch"; + url = "https://git.gnome.org/browse/gtksourceview/patch/?id=ab46e552e1d0dae73f72adac8d578e40bdadaf95"; + sha256 = "0qzrbv4hpa0v8qbmpi2vp575n13lkrvp3cgllwrd2pslw1v9q3aj"; + }) + ]; + + buildInputs = [ + pkgconfig atk cairo glib gtk + pango libxml2Python perl intltool + gettext + ] ++ optionals stdenv.isDarwin [ + autoreconfHook gnome_common gtk-mac-integration + ]; + + preConfigure = optionalString stdenv.isDarwin '' + intltoolize --force + ''; } From fdb5832d097afdb295b92e96dd7df37dd81d71e0 Mon Sep 17 00:00:00 2001 From: Jascha Geerds Date: Sat, 7 Jan 2017 19:48:38 +0100 Subject: [PATCH 89/94] pythonPackages.docker_compose: Add myself as a maintainer --- pkgs/top-level/python-packages.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index f1dc2bf86dc..6070971874d 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -11125,6 +11125,9 @@ in { homepage = "https://docs.docker.com/compose/"; description = "Multi-container orchestration for Docker"; license = licenses.asl20; + maintainers = with maintainers; [ + jgeerds + ]; }; }; From a5be4fe67abb315fb0d4cece735882214be7d4a2 Mon Sep 17 00:00:00 2001 From: Jascha Geerds Date: Sat, 7 Jan 2017 19:49:49 +0100 Subject: [PATCH 90/94] pythonPackages.docker_compose: Set meta.platforms to linux --- pkgs/top-level/python-packages.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 6070971874d..687889f0b14 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -11125,6 +11125,7 @@ in { homepage = "https://docs.docker.com/compose/"; description = "Multi-container orchestration for Docker"; license = licenses.asl20; + platforms = platforms.linux; maintainers = with maintainers; [ jgeerds ]; From 372e04f1894a86f2c1dfdd9e7b673f30a5f0dc39 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Domen=20Ko=C5=BEar?= Date: Sat, 7 Jan 2017 20:15:59 +0100 Subject: [PATCH 91/94] libpqxx: use gnused_422 --- pkgs/development/libraries/libpqxx/default.nix | 4 ++-- pkgs/top-level/all-packages.nix | 4 +++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/pkgs/development/libraries/libpqxx/default.nix b/pkgs/development/libraries/libpqxx/default.nix index e8a80497de3..51cb1c48e54 100644 --- a/pkgs/development/libraries/libpqxx/default.nix +++ b/pkgs/development/libraries/libpqxx/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, postgresql, python2 }: +{ lib, stdenv, fetchurl, postgresql, python2, gnused }: stdenv.mkDerivation rec { name = "libpqxx-4.0.1"; @@ -8,7 +8,7 @@ stdenv.mkDerivation rec { sha256 = "0f6wxspp6rx12fkasanb0z2g2gc8dhcfwnxagx8wwqbpg6ifsz09"; }; - buildInputs = [ postgresql python2 ]; + buildInputs = [ postgresql python2 gnused ]; preConfigure = '' patchShebangs . diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 4d538e21d24..546ea865228 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -8375,7 +8375,9 @@ in libpfm = callPackage ../development/libraries/libpfm { }; - libpqxx = callPackage ../development/libraries/libpqxx { }; + libpqxx = callPackage ../development/libraries/libpqxx { + gnused = gnused_422; + }; libproxy = callPackage ../development/libraries/libproxy { stdenv = if stdenv.isDarwin From 760710efd1b05f02b6c1b92493994fa1b058dcef Mon Sep 17 00:00:00 2001 From: Sarah Brofeldt Date: Sat, 7 Jan 2017 19:58:48 +0100 Subject: [PATCH 92/94] qualia: init at 1.0.0 tests disabled maintainer srhb --- lib/maintainers.nix | 1 + pkgs/tools/text/mir-qualia/default.nix | 21 +++++++++++++++++++++ pkgs/top-level/all-packages.nix | 4 ++++ 3 files changed, 26 insertions(+) create mode 100644 pkgs/tools/text/mir-qualia/default.nix diff --git a/lib/maintainers.nix b/lib/maintainers.nix index 721e63cd6a7..47c79abc284 100644 --- a/lib/maintainers.nix +++ b/lib/maintainers.nix @@ -444,6 +444,7 @@ spinus = "Tomasz Czyż "; sprock = "Roger Mason "; spwhitt = "Spencer Whitt "; + srhb = "Sarah Brofeldt "; SShrike = "Severen Redwood "; stephenmw = "Stephen Weinberg "; sternenseemann = "Lukas Epple "; diff --git a/pkgs/tools/text/mir-qualia/default.nix b/pkgs/tools/text/mir-qualia/default.nix new file mode 100644 index 00000000000..b22d5893915 --- /dev/null +++ b/pkgs/tools/text/mir-qualia/default.nix @@ -0,0 +1,21 @@ +{ lib, pythonPackages, fetchurl }: + +pythonPackages.buildPythonApplication rec { + name = "mir.qualia-${version}"; + version = "1.0.0"; + doCheck = false; # 1.0.0-released pytests are broken + + buildInputs = with pythonPackages; [ pytest ]; + + src = fetchurl { + url = "mirror://pypi/m/mir.qualia/mir.qualia-${version}.tar.gz"; + sha256 = "1g0nwncwk4nq7b7zszqi1q4d2bdga1q50g9nkxigdaq647wqdf7x"; + }; + + meta = { + description = "Dynamically enable sections of config files"; + homepage = https://github.com/darkfeline/mir.qualia; + license = lib.licenses.asl20; + maintainers = [ lib.maintainers.srhb ] ; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 4d538e21d24..69f7c70dd38 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -2818,6 +2818,10 @@ in minixml = callPackage ../development/libraries/minixml { }; + mir-qualia = callPackage ../tools/text/mir-qualia { + pythonPackages = python3Packages; + }; + miredo = callPackage ../tools/networking/miredo { }; mitmproxy = callPackage ../tools/networking/mitmproxy { }; From 3dc8b5d904803853946e5c6637ab703edf764c89 Mon Sep 17 00:00:00 2001 From: Jay Mundrawala Date: Sun, 8 Jan 2017 01:53:44 -0800 Subject: [PATCH 93/94] rustUnstableBin.rustc: Run patchelf on bin/rustdoc (#21746) Cargo seems to run rustdoc and produces an annoying error when it tries to run. --- pkgs/development/compilers/rust/nightlyBin.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/development/compilers/rust/nightlyBin.nix b/pkgs/development/compilers/rust/nightlyBin.nix index 6f7cca9aff2..bac35c790d0 100644 --- a/pkgs/development/compilers/rust/nightlyBin.nix +++ b/pkgs/development/compilers/rust/nightlyBin.nix @@ -49,6 +49,9 @@ rec { patchelf \ --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \ "$out/bin/rustc" + patchelf \ + --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \ + "$out/bin/rustdoc" ''} ''; From 9653be493a961dd0fdef863385b00130eb57646f Mon Sep 17 00:00:00 2001 From: Michael Raskin <7c6f434c@mail.ru> Date: Sun, 8 Jan 2017 13:58:07 +0100 Subject: [PATCH 94/94] firejail: 0.9.44.2 -> 0.9.44.4 --- pkgs/os-specific/linux/firejail/default.nix | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/os-specific/linux/firejail/default.nix b/pkgs/os-specific/linux/firejail/default.nix index 6b3afc1d63c..74486843b92 100644 --- a/pkgs/os-specific/linux/firejail/default.nix +++ b/pkgs/os-specific/linux/firejail/default.nix @@ -3,11 +3,11 @@ let s = # Generated upstream information rec { baseName="firejail"; - version="0.9.44.2"; + version="0.9.44.4"; name="${baseName}-${version}"; - hash="0lc8vq6lj0669q4vx08m3dzqjayhl0cmm7n3qi4k18ys8ccyzbf5"; - url="https://kent.dl.sourceforge.net/project/firejail/firejail/firejail-0.9.44.2.tar.xz"; - sha256="0lc8vq6lj0669q4vx08m3dzqjayhl0cmm7n3qi4k18ys8ccyzbf5"; + hash="03y1xc70w5xr6jynmj305fmgniz2cq21q85s5q7dnda8ap6s4w1d"; + url="https://netcologne.dl.sourceforge.net/project/firejail/firejail/firejail-0.9.44.4.tar.xz"; + sha256="03y1xc70w5xr6jynmj305fmgniz2cq21q85s5q7dnda8ap6s4w1d"; }; buildInputs = [ which