diff --git a/pkgs/applications/editors/emacs-modes/stratego/builder.sh b/pkgs/applications/editors/emacs-modes/stratego/builder.sh deleted file mode 100644 index 7d734ec0888..00000000000 --- a/pkgs/applications/editors/emacs-modes/stratego/builder.sh +++ /dev/null @@ -1,4 +0,0 @@ -source $stdenv/setup - -mkdir -p $out/share/emacs/site-lisp -cp $src $out/share/emacs/site-lisp/stratego.el diff --git a/pkgs/applications/editors/emacs-modes/stratego/default.nix b/pkgs/applications/editors/emacs-modes/stratego/default.nix deleted file mode 100644 index bb4078d2d2d..00000000000 --- a/pkgs/applications/editors/emacs-modes/stratego/default.nix +++ /dev/null @@ -1,10 +0,0 @@ -{stdenv, fetchsvn}: -stdenv.mkDerivation { - name = "stratego-mode"; - builder = ./builder.sh; - src = fetchsvn { - url = https://svn.strategoxt.org/repos/StrategoXT/stratego-editors/trunk/emacs/stratego.el; - rev = 12678; - sha256 = "4ab4ec587550233f29ca08b82fa0a9f7e5b33fc178348037e3ab1816bd60f538"; - }; -} diff --git a/pkgs/applications/networking/siproxd/cheaders.patch b/pkgs/applications/networking/siproxd/cheaders.patch index 53c4813cc33..69a3e328737 100644 --- a/pkgs/applications/networking/siproxd/cheaders.patch +++ b/pkgs/applications/networking/siproxd/cheaders.patch @@ -3,11 +3,12 @@ index 1904ab3..cb3624d 100644 --- a/src/dejitter.c +++ b/src/dejitter.c @@ -22,6 +22,8 @@ - + #include - + +#include +#include + #include #include #include #include diff --git a/pkgs/applications/networking/siproxd/default.nix b/pkgs/applications/networking/siproxd/default.nix index 69ebab78f94..14ed2587e63 100644 --- a/pkgs/applications/networking/siproxd/default.nix +++ b/pkgs/applications/networking/siproxd/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, libosip }: stdenv.mkDerivation rec { - name = "siproxd-0.8.1"; - + name = "siproxd-0.8.2"; + src = fetchurl { url = "mirror://sourceforge/siproxd/${name}.tar.gz"; - sha256 = "1bcxl0h5nc28m8lcdhpbl5yc93w98xm53mfzrf04knsvmx7z0bfz"; + sha256 = "1l6cyxxhra825jiiw9npa7jrbfgbyfpk4966cqkrw66cn28y8v2j"; }; patches = [ ./cheaders.patch ]; diff --git a/pkgs/applications/science/biology/pal2nal/default.nix b/pkgs/applications/science/biology/pal2nal/default.nix deleted file mode 100644 index 956f8b07e98..00000000000 --- a/pkgs/applications/science/biology/pal2nal/default.nix +++ /dev/null @@ -1,31 +0,0 @@ -{stdenv, fetchurl, perl, paml}: - -stdenv.mkDerivation { - name = "pal2nal-12"; - src = fetchurl { - url = http://coot.embl.de/pal2nal/distribution/pal2nal.v12.tar.gz; - sha256 = "1qj9sq5skpa7vyccl9gxc5ls85jwiq8j6mr8wvacz4yhyg0afy04"; - }; - - installPhase = '' - mkdir -p $out/bin - - cp -v pal2nal.pl $out/bin - - mkdir -p $out/doc - - cp -v README $out/doc - ''; - - meta = { - description = "Program for aligning nucleotide sequences based on an aminoacid alignment"; - longDescription = '' - PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment can further be subjected to the calculation of synonymous (KS) and non-synonymous (KA) substitution rates. - -If the input is a pair of sequences, PAL2NAL automatically calculates KS and KA by the codeml program in PAML. -''; - license = "non-commercial"; - homepage = http://coot.embl.de/pal2nal/; - pkgMaintainer = "Pjotr Prins"; - }; -} diff --git a/pkgs/applications/science/biology/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix index cec0aa7e5eb..589c2809a93 100644 --- a/pkgs/applications/science/biology/paml/default.nix +++ b/pkgs/applications/science/biology/paml/default.nix @@ -1,11 +1,11 @@ {stdenv, fetchurl}: stdenv.mkDerivation rec { - version = "4.2a"; + version = "4.9c"; name = "paml-${version}"; src = fetchurl { - url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tar.gz"; - sha256 = "0yywyrjgxrpavp50n00l01pl90b7pykgb2k53yrlykz9dnf583pb"; + url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz"; + sha256 = "18a1l47223l7jyjavm8a8la84q9k9kbxwmj7kz4z3pdx70qrl04j"; }; preBuild = '' @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { ''; installPhase = '' mkdir -pv $out/bin - cp -v codeml $out/bin + cp -v codeml $out/bin cp -v baseml $out/bin cp -v basemlg $out/bin cp -v chi2 $out/bin @@ -28,6 +28,6 @@ stdenv.mkDerivation rec { description = "Phylogenetic Analysis by Maximum Likelihood (PAML)"; longDescription = ''PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.''; license = "non-commercial"; - homepage = http://abacus.gene.ucl.ac.uk/software/paml.html; + homepage = http://abacus.gene.ucl.ac.uk/software/paml.html; }; } diff --git a/pkgs/development/compilers/abc/builder-binjar.sh b/pkgs/development/compilers/abc/builder-binjar.sh deleted file mode 100644 index a954c49aa3f..00000000000 --- a/pkgs/development/compilers/abc/builder-binjar.sh +++ /dev/null @@ -1,4 +0,0 @@ -source $stdenv/setup - -mkdir -p $out/jars -cp $src $out/jars/$jarname.jar diff --git a/pkgs/development/compilers/abc/builder.sh b/pkgs/development/compilers/abc/builder.sh deleted file mode 100644 index ba594023842..00000000000 --- a/pkgs/development/compilers/abc/builder.sh +++ /dev/null @@ -1,40 +0,0 @@ -source $stdenv/setup - -tar zxvf $src - -cd abc-* - -for p in $patches; do - echo "applying patch $p" - patch -p1 < $p -done - -cat > ant.settings < $out/bin/abc < build-tmp.xml -mv build-tmp.xml build.xml - -cat > ant.settings < ant.settings <> "$bin" << EOF - #!/bin/sh - exec ${jre}/bin/java -jar $out/lib/selenium-server-${version}/selenium-server.jar "\$@" - EOF - chmod +x "$bin" - ''; - */ - - # this snapshot version starts a firefox from a script file. It only issues a warning about it - # you still have to pass -DfirefoxDefaultPath=/home/marc/.nix-profile/bin/firefox or such.. - name = "selenium-remote-control-${version}-dist"; - # this dist file has been created using mvn package -Dmaven.test.skip=true based on svn rev 2450 - src = fetchurl { - url = "http://mawercer.de/~nix/selenium-server-1.0-SNAPSHOT-standalone.jar"; - sha256 = "1lqr72a3lmmww1psl19pzp91c9q1dm0314b7y7mz1gnfpwc49y38"; - }; - phases = "buildPhase"; - buildPhase = '' - mkdir -p $out/{bin,lib} - cp $src $out/lib/ - bin="$out/bin/selenium-remote-control" - cat >> "$bin" << EOF - #!/bin/sh - exec ${jre}/bin/java -jar "$out/lib/$(basename $src)" "\$@" - EOF - chmod +x "$bin" - ''; -} diff --git a/pkgs/games/tintin/default.nix b/pkgs/games/tintin/default.nix index c2bc9d37b4f..deb283c57c4 100644 --- a/pkgs/games/tintin/default.nix +++ b/pkgs/games/tintin/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, zlib, pcre }: stdenv.mkDerivation rec { - name = "tintin-2.00.9"; + name = "tintin-2.01.1"; src = fetchurl { url = "mirror://sourceforge/tintin/${name}.tar.gz"; - sha256 = "0x8jakxx7hh7b0z6vjcxyrda0afbz2s2yy7mvrbxjffyc2dyxzna"; + sha256 = "195wrfcys8yy953gdrl1gxryhjnx9lg1vqgxm3dyzm8bi18aa2yc"; }; buildInputs = [ zlib pcre ]; diff --git a/pkgs/os-specific/linux/cryopid/default.nix b/pkgs/os-specific/linux/cryopid/default.nix deleted file mode 100644 index 0cb64bcc975..00000000000 --- a/pkgs/os-specific/linux/cryopid/default.nix +++ /dev/null @@ -1,39 +0,0 @@ -{stdenv, fetchurl, zlibStatic}: - -let - - pname = "cryopid"; - version = "20090908"; - revision = "7da69201d50e"; - -in - -stdenv.mkDerivation rec { - name = "${pname}-${version}"; - - src = fetchurl { - url = "https://sharesource.org/hg/cryopid/archive/${revision}.tar.bz2"; - sha256 = "908a4b1cb26322ee25afe13ff59e0d86f669538cb4583766b15ca79fda6c69ca"; - }; - - buildInputs = [ zlibStatic ]; - - preBuild = "cd src"; - - installPhase = "mkdir -p $out/bin; cp cryopid $out/bin"; - - meta = { - description = "A process freezer for Linux"; - longDescription = '' - CryoPID allows you to capture the state of a running process in Linux - and save it to a file. This file can then be used to resume the process - later on, either after a reboot or even on another machines. - ''; - homepage = http://sharesource.org/project/cryopid; - license = '' - Modified BSD license (without advertising clause). CryoPID ships with - and links against the dietlibc library, which is distributed under the - GNU General Public Licence, version 2. - ''; - }; -} diff --git a/pkgs/os-specific/linux/ttysnoop/default.nix b/pkgs/os-specific/linux/ttysnoop/default.nix deleted file mode 100644 index 670c9608344..00000000000 --- a/pkgs/os-specific/linux/ttysnoop/default.nix +++ /dev/null @@ -1,38 +0,0 @@ -{stdenv, fetchurl}: -let - s = # Generated upstream information - rec { - baseName="ttysnoop"; - version="0.12d.k26"; - name="${baseName}-${version}"; - hash="0jb2zchaiqmmickj0la7wjw3sf9vy65qfhhs11yrzx4mmwkp0395"; - url="http://sysd.org/stas/files/active/0/ttysnoop-0.12d.k26.tar.gz"; - sha256="0jb2zchaiqmmickj0la7wjw3sf9vy65qfhhs11yrzx4mmwkp0395"; - }; - buildInputs = [ - ]; -in -stdenv.mkDerivation { - inherit (s) name version; - inherit buildInputs; - src = fetchurl { - inherit (s) url sha256; - }; - preBuild = '' - sed -e "s@/sbin@$out/sbin@g" -i Makefile - sed -e "s@/usr/man@$out/share/man@g" -i Makefile - mkdir -p "$out/share/man/man8" - mkdir -p "$out/sbin" - ''; - postInstall = '' - mkdir -p "$out/etc" - cp snooptab.dist "$out/etc/snooptab" - ''; - meta = { - inherit (s) version; - description = "A tool to clone input and output of another tty/pty to the current one"; - license = stdenv.lib.licenses.gpl2 ; - maintainers = [stdenv.lib.maintainers.raskin]; - platforms = stdenv.lib.platforms.linux; - }; -} diff --git a/pkgs/os-specific/linux/ttysnoop/default.upstream b/pkgs/os-specific/linux/ttysnoop/default.upstream deleted file mode 100644 index 905a639c31e..00000000000 --- a/pkgs/os-specific/linux/ttysnoop/default.upstream +++ /dev/null @@ -1,3 +0,0 @@ -url http://sysd.org/stas/node/35 -ensure_choice -version '.*-([0-9a-z.]+)[.]tar[.].*' '\1' diff --git a/pkgs/servers/felix/remoteshell.nix b/pkgs/servers/felix/remoteshell.nix index 6e8089d32e9..3ac3c98718f 100644 --- a/pkgs/servers/felix/remoteshell.nix +++ b/pkgs/servers/felix/remoteshell.nix @@ -1,14 +1,15 @@ {stdenv, fetchurl}: stdenv.mkDerivation rec { - name = "apache-felix-remoteshell-bundle-1.0.4"; + version = "1.1.2"; + name = "apache-felix-remoteshell-bundle-${version}"; src = fetchurl { - url = http://apache.proserve.nl/felix/org.apache.felix.shell.remote-1.0.4.jar; - sha256 = "1bgahzs9nnnvfr0yyh9s0r6h1zp2ls6533377rp8r1qk2a4s1gzb"; + url = "http://apache.proserve.nl/felix/org.apache.felix.shell.remote-${version}.jar"; + sha256 = "147zw5ppn98wfl3pr32isyb267xm3gwsvdfdvjr33m9g2v1z69aq"; }; - buildCommand = + buildCommand = '' mkdir -p $out/bundle - cp ${src} $out/bundle/org.apache.felix.shell.remote-1.0.4.jar + cp ${src} $out/bundle/org.apache.felix.shell.remote-${version}.jar ''; } diff --git a/pkgs/tools/filesystems/fuse-zip/default.nix b/pkgs/tools/filesystems/fuse-zip/default.nix deleted file mode 100644 index a5ac74fe47a..00000000000 --- a/pkgs/tools/filesystems/fuse-zip/default.nix +++ /dev/null @@ -1,23 +0,0 @@ -{ stdenv, fetchurl, pkgconfig, fuse, libzip, zlib }: - -stdenv.mkDerivation rec { - name = "fuse-zip-0.2.13"; - - src = fetchurl { - url = "http://fuse-zip.googlecode.com/files/${name}.tar.gz"; - sha1 = "9cfa00e38a59d4e06fd47bfaca75ad5e299ecc6b"; - }; - - patches = [ ./libzip.patch ]; # problems with new libzip; from Gentoo - - buildInputs = [ pkgconfig fuse libzip zlib ]; - - makeFlags = "INSTALLPREFIX=$(out)"; - - meta = { - homepage = http://code.google.com/p/fuse-zip/; - description = "A FUSE-based filesystem that allows read and write access to ZIP files"; - platforms = stdenv.lib.platforms.linux; - license = stdenv.lib.licenses.gpl3Plus; - }; -} diff --git a/pkgs/tools/filesystems/fuse-zip/libzip.patch b/pkgs/tools/filesystems/fuse-zip/libzip.patch deleted file mode 100644 index f2348e5f1ba..00000000000 --- a/pkgs/tools/filesystems/fuse-zip/libzip.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -ru fuse-zip-0.2.13/lib/bigBuffer.cpp fuse-zip-0.2.13.new//lib/bigBuffer.cpp ---- fuse-zip-0.2.13/lib/bigBuffer.cpp 2010-12-06 12:34:32.000000000 -0500 -+++ fuse-zip-0.2.13.new//lib/bigBuffer.cpp 2011-09-28 21:40:01.294946957 -0400 -@@ -236,7 +236,7 @@ - len = offset; - } - --ssize_t BigBuffer::zipUserFunctionCallback(void *state, void *data, size_t len, enum zip_source_cmd cmd) { -+zip_int64_t BigBuffer::zipUserFunctionCallback(void *state, void *data, zip_uint64_t len, enum zip_source_cmd cmd) { - CallBackStruct *b = (CallBackStruct*)state; - switch (cmd) { - case ZIP_SOURCE_OPEN: { -diff -ru fuse-zip-0.2.13/lib/bigBuffer.h fuse-zip-0.2.13.new//lib/bigBuffer.h ---- fuse-zip-0.2.13/lib/bigBuffer.h 2010-12-06 12:34:32.000000000 -0500 -+++ fuse-zip-0.2.13.new//lib/bigBuffer.h 2011-09-28 21:40:23.203719133 -0400 -@@ -52,7 +52,7 @@ - * never called because read() always successfull. - * See zip_source_function(3) for details. - */ -- static ssize_t zipUserFunctionCallback(void *state, void *data, size_t len, enum zip_source_cmd cmd); -+ static zip_int64_t zipUserFunctionCallback(void *state, void *data, zip_uint64_t len, enum zip_source_cmd cmd); - - /** - * Return number of chunks needed to keep 'offset' bytes. diff --git a/pkgs/tools/misc/cowsay/default.nix b/pkgs/tools/misc/cowsay/default.nix index a9bdf1b2b92..0a7b079445d 100644 --- a/pkgs/tools/misc/cowsay/default.nix +++ b/pkgs/tools/misc/cowsay/default.nix @@ -1,11 +1,12 @@ -{ stdenv, fetchurl, perl }: +{ stdenv, fetchgit, perl }: stdenv.mkDerivation { - name = "cowsay-3.03"; + name = "cowsay-3.03+dfsg1-16"; - src = fetchurl { - url = http://www.nog.net/~tony/warez/cowsay-3.03.tar.gz; - sha256 = "1s3c0g5vmsadicc4lrlkmkm8znm4y6wnxd8kyv9xgm676hban1il"; + src = fetchgit { + url = https://anonscm.debian.org/git/collab-maint/cowsay.git; + rev = "acb946c166fa3b9526b9c471ef1330f9f89f9c8b"; + sha256 = "1ji66nrdcc8sh79hwils3nbaj897s352r5wp7kzjwiym8bm2azk6"; }; buildInputs = [ perl ]; diff --git a/pkgs/tools/misc/g500-control/default.nix b/pkgs/tools/misc/g500-control/default.nix deleted file mode 100644 index 9d42c7d68d5..00000000000 --- a/pkgs/tools/misc/g500-control/default.nix +++ /dev/null @@ -1,34 +0,0 @@ -{ stdenv, fetchurl }: - -stdenv.mkDerivation { - name = "g500-control-0.0.1"; - - src = fetchurl { - url = "http://g500-control.googlecode.com/files/g500_control_0.0.1.tar.gz"; - sha256 = "1xlg9lpxnk3228k81y1i6jjh4df1p4jh64g54w969g6a6v6dazvb"; - }; - - unpackPhase = '' - mkdir -p g500-control - tar -C g500-control/ -xf $src - ''; - - buildPhase = '' - cd g500-control - gcc -o g500-control *.c - ''; - - installPhase = '' - mkdir -p $out/bin/ - cp g500-control $out/bin/ - ''; - - meta = { - homepage = http://code.google.com/p/g500-control/; - description = "Configure Logitech G500's internal profile under Linux"; - license = stdenv.lib.licenses.gpl2; - platforms = stdenv.lib.platforms.linux; - maintainers = with stdenv.lib.maintainers; [ the-kenny ]; - }; -} - diff --git a/pkgs/tools/misc/mcrl/default.nix b/pkgs/tools/misc/mcrl/default.nix deleted file mode 100644 index bf5043e8b63..00000000000 --- a/pkgs/tools/misc/mcrl/default.nix +++ /dev/null @@ -1,14 +0,0 @@ -{stdenv, fetchurl, coreutils}: - -stdenv.mkDerivation { - name = "mcrl-2.18.4"; - src = fetchurl { - url = http://homepages.cwi.nl/~mcrl/mcrl-2.18.4.tar.gz ; - sha256 = "0gld7x3cv3y0vwjr1snz24xzr818sj1l2dfn8qhirfyhc7dnnqfw"; - }; - - RMPROG = "${coreutils}/bin/rm -f"; -} - - - diff --git a/pkgs/tools/text/xml/jing/default.nix b/pkgs/tools/text/xml/jing/default.nix deleted file mode 100644 index 5737fff14f5..00000000000 --- a/pkgs/tools/text/xml/jing/default.nix +++ /dev/null @@ -1,22 +0,0 @@ -{ stdenv, fetchurl, unzip, jre }: - -stdenv.mkDerivation { - name = "jing-20091111"; - builder = ./unzip-builder.sh; - - src = fetchurl { - url = https://jing-trang.googlecode.com/files/jing-20091111.zip; - sha256 = "134h2r22r64v5yk4v8mhl6r893dlw5vzx9daf2sj2mbbma004sap"; - }; - - inherit unzip jre; - - meta = with stdenv.lib; { - description = "A RELAX NG validator in Java"; - # The homepage is www.thaiopensource.com, but it links to googlecode.com - # for downloads and call it the "project site". - homepage = http://www.thaiopensource.com/relaxng/jing.html; - platforms = platforms.linux; - maintainers = [ maintainers.bjornfor ]; - }; -} diff --git a/pkgs/tools/text/xml/jing/unzip-builder.sh b/pkgs/tools/text/xml/jing/unzip-builder.sh deleted file mode 100755 index c02920e5a69..00000000000 --- a/pkgs/tools/text/xml/jing/unzip-builder.sh +++ /dev/null @@ -1,14 +0,0 @@ -set -e -source $stdenv/setup - -$unzip/bin/unzip $src -mkdir -p $out -mv $name/* $out - -cat > "$out/bin/jing" <> $out/bin/trang <