Ludovic Courtès <[email protected]> writes: > gnu/packages/audio.scm:272:12: calf-0.0.60: all the source URIs are > unreachable: > gnu/packages/audio.scm:272:12: calf-0.0.60: URI > http://prdownloads.sourceforge.net/calf/calf/0.0.60/calf-0.0.60.tar.gz not > reachable: 404 ("Not Found") > gnu/packages/audio.scm:272:12: calf-0.0.60: URI > http://heanet.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz > not reachable: 404 ("Not Found") > gnu/packages/audio.scm:272:12: calf-0.0.60: URI > http://surfnet.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz > unreachable: Network is unreachable > gnu/packages/audio.scm:272:12: calf-0.0.60: URI > http://dfn.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz > not reachable: 404 ("Not Found") > gnu/packages/audio.scm:272:12: calf-0.0.60: URI > http://mesh.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz > domain not found: Name or service not known > gnu/packages/audio.scm:272:12: calf-0.0.60: URI > http://ovh.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz > domain not found: Name or service not known > gnu/packages/audio.scm:272:12: calf-0.0.60: URI > http://osdn.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz > not reachable: 404 ("Not Found")
This has been fixed in commit 73cea74ddaf98f. > gnu/packages/bioinformatics.scm:1115:15: edirect-2.50: URI > http://www.ncbi.nlm.nih.gov/books/NBK179288 not reachable: 303 ("See Other") I can reach it, but it seems to redirect to URL + “/”. I’ll add the trailing slash. > gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: all the source > URIs are unreachable: > gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: URI > https://github.com/ncbi/sra-tools/archive/2.4.5-5.tar.gz not reachable: 404 > ("Not Found") The tarball has been removed. I’ll update it to the latest version. > gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: all the source URIs > are unreachable: > gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: URI > https://github.com/ncbi/ncbi-vdb /archive/2.4.5-5.tar.gz not > reachable: 404 ("Not Found") Same here. The tarball was removed. There are new versions out already, so I’ll take the opportunity to update it. > gnu/packages/bioinformatics.scm:2570:12: preseq-1.0.2: all the source URIs > are unreachable: > gnu/packages/bioinformatics.scm:2570:12: preseq-1.0.2: URI > http://smithlabresearch.org/downloads/preseq-1.0.2.tar.bz2 not reachable: 404 > ("Not Found") Version 2.0 has been released and the old tarball has been removed. The location for 2.0 is this: https://github.com/smithlabcode/preseq/archive/v2.0.tar.gz Attached are two patches to update our recipe. A new package was added to deal with the fact that bundled sources have been removed from the tarball.
>From 01d547a6eedfb28d19551042f581e588dcc56fb5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <[email protected]> Date: Fri, 20 Nov 2015 11:14:00 +0100 Subject: [PATCH 1/2] gnu: Add smithlab-cpp. * gnu/packages/bioinformatics.scm (smithlab-cpp): New variable. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e0c1944..90a3c51 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2662,6 +2662,59 @@ subsequent visualization, annotation and storage of results.") ;; LGPLv2.1+ (license (list license:gpl2 license:lgpl2.1+)))) +(define-public smithlab-cpp + (let ((revision "1") + (commit "728a097")) + (package + (name "smithlab-cpp") + (version (string-append "0." revision "." commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/smithlab_cpp.git";) + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74")))) + (build-system gnu-build-system) + (arguments + `(#:modules ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-26)) + #:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-samtools-headers + (lambda _ + (substitute* '("SAM.cpp" + "SAM.hpp") + (("sam.h") "samtools/sam.h")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (include (string-append out "/include/smithlab-cpp"))) + (mkdir-p lib) + (mkdir-p include) + (for-each (cut install-file <> lib) + (find-files "." "\\.o$")) + (for-each (cut install-file <> include) + (find-files "." "\\.hpp$"))) + #t)) + (delete 'configure)))) + (inputs + `(("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "https://github.com/smithlabcode/smithlab_cpp";) + (synopsis "C++ helper library for functions used in Smith lab projects") + (description + "Smithlab CPP is a C++ library that includes functions used in many of +the Smith lab bioinformatics projects, such as a wrapper around Samtools data +structures, classes for genomic regions, mapped sequencing reads, etc.") + (license license:gpl3+)))) + (define-public preseq (package (name "preseq") -- 2.1.0
>From 534d7b73cda92b982f1338b1c9db420767d78066 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <[email protected]> Date: Fri, 20 Nov 2015 11:14:48 +0100 Subject: [PATCH 2/2] gnu: preseq: Update to 2.0. * gnu/packages/bioinformatics.scm (preseq): Update to 2.0. [source]: Add file-name field, remove patches. [arguments]: Remove unused build phases, add make flags. [inputs]: Add smithlab-cpp. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove them. --- gnu-system.am | 2 - gnu/packages/bioinformatics.scm | 43 +++++++++------------- .../patches/preseq-1.0.2-install-to-PREFIX.patch | 37 ------------------- .../patches/preseq-1.0.2-link-with-libbam.patch | 33 ----------------- 4 files changed, 18 insertions(+), 97 deletions(-) delete mode 100644 gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch delete mode 100644 gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch diff --git a/gnu-system.am b/gnu-system.am index 9d41c49..7d9afba 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -625,8 +625,6 @@ dist_patch_DATA = \ gnu/packages/patches/plotutils-libpng-jmpbuf.patch \ gnu/packages/patches/polkit-drop-test.patch \ gnu/packages/patches/portaudio-audacity-compat.patch \ - gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch \ - gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch \ gnu/packages/patches/procps-make-3.82.patch \ gnu/packages/patches/pt-scotch-build-parallelism.patch \ gnu/packages/patches/pulseaudio-fix-mult-test.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 90a3c51..d66c6ab 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2718,46 +2718,39 @@ structures, classes for genomic regions, mapped sequencing reads, etc.") (define-public preseq (package (name "preseq") - (version "1.0.2") + (version "2.0") (source (origin (method url-fetch) - (uri - (string-append "http://smithlabresearch.org/downloads/preseq-"; - version ".tar.bz2")) + (uri (string-append "https://github.com/smithlabcode/"; + "preseq/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc")) - (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch") - (search-patch "preseq-1.0.2-link-with-libbam.patch"))) + (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) (modules '((guix build utils))) (snippet ;; Remove bundled samtools. - '(delete-file-recursively "preseq-master/samtools")))) + '(delete-file-recursively "samtools")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target #:phases (modify-phases %standard-phases - (add-after - 'unpack 'enter-dir - (lambda _ - (chdir "preseq-master") - #t)) - (add-after - 'enter-dir 'use-samtools-headers - (lambda _ - (substitute* '("smithlab_cpp/SAM.cpp" - "smithlab_cpp/SAM.hpp") - (("sam.h") "samtools/sam.h")) - #t)) (delete 'configure)) - #:make-flags (list (string-append "PREFIX=" - (assoc-ref %outputs "out")) - (string-append "LIBBAM=" - (assoc-ref %build-inputs "samtools") - "/lib/libbam.a")))) + #:make-flags + (list (string-append "PREFIX=" + (assoc-ref %outputs "out")) + (string-append "LIBBAM=" + (assoc-ref %build-inputs "samtools") + "/lib/libbam.a") + (string-append "SMITHLAB_CPP=" + (assoc-ref %build-inputs "smithlab-cpp") + "/lib") + "PROGS=preseq" + "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) (inputs `(("gsl" ,gsl) ("samtools" ,samtools-0.1) + ("smithlab-cpp" ,smithlab-cpp) ("zlib" ,zlib))) (home-page "http://smithlabresearch.org/software/preseq/";) (synopsis "Program for analyzing library complexity") diff --git a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch deleted file mode 100644 index f8318ae..0000000 --- a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch +++ /dev/null @@ -1,37 +0,0 @@ -This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15 - -From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001 -From: Ricardo Wurmus <[email protected]> -Date: Thu, 25 Jun 2015 15:01:53 +0200 -Subject: [PATCH] Install to PREFIX - ---- - Makefile | 8 ++++++-- - 1 file changed, 6 insertions(+), 2 deletions(-) - -diff --git a/Makefile b/Makefile -index 4d0367a..e334f2f 100644 ---- a/preseq-master/Makefile -+++ b/preseq-master/Makefile -@@ -22,6 +22,10 @@ ifndef ROOT - ROOT = $(shell pwd) - endif - -+ifndef PREFIX -+PREFIX = $(ROOT) -+endif -+ - ifndef SMITHLAB_CPP - SMITHLAB_CPP=$(ROOT)/smithlab_cpp/ - endif -@@ -91,8 +95,8 @@ endif - $(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS) - - install: $(PROGS) -- @mkdir -p $(ROOT)/bin -- @install -m 755 $(PROGS) $(ROOT)/bin -+ @mkdir -p $(PREFIX)/bin -+ @install -m 755 $(PROGS) $(PREFIX)/bin - - clean: - @-rm -f $(PROGS) *.o *~ diff --git a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch deleted file mode 100644 index 035a3b1..0000000 --- a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch +++ /dev/null @@ -1,33 +0,0 @@ -This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15 - -From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001 -From: Ricardo Wurmus <[email protected]> -Date: Thu, 25 Jun 2015 15:02:35 +0200 -Subject: [PATCH] Link with libbam.a if provided via LIBBAM - ---- - Makefile | 7 +++++++ - 1 file changed, 7 insertions(+) - -diff --git a/Makefile b/Makefile -index e334f2f..de310e4 100644 ---- a/preseq-master/Makefile -+++ b/preseq-master/Makefile -@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \ - preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o - - ifdef SAMTOOLS_DIR -+ifdef LIBBAM -+LIBS += -pthread -+bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \ -+ $(LIBBAM) -+else - bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \ - $(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \ - faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o) - endif -+endif # SAMTOOLS_DIR -+ - - %.o: %.cpp %.hpp - $(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS) -- 2.1.0
> gnu/packages/java.scm:139:12: ant-1.9.4: all the source URIs are unreachable: > gnu/packages/java.scm:139:12: ant-1.9.4: URI > https://www.apache.org/dist/ant/source/apache-ant-1.9.4-src.tar.gz not > reachable: 404 ("Not Found") I don’t know why people do this but here again the tarballs have been removed and replaced with those for version 1.9.6. Here’s another patch to update our ant package:
>From 212e56286c946b7a34d03819c20faa473cc42a9d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <[email protected]> Date: Fri, 20 Nov 2015 11:23:18 +0100 Subject: [PATCH] gnu: ant: Update to 1.9.6. * gnu/packages/java.scm (ant): Update to 1.9.6. --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 6d34460..f00a3d7 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -135,7 +135,7 @@ is implemented.") (define-public ant (package (name "ant") - (version "1.9.4") + (version "1.9.6") (source (origin (method url-fetch) (uri (string-append @@ -143,7 +143,7 @@ is implemented.") version "-src.tar.gz")) (sha256 (base32 - "09kf5s1ir0rdrclsy174bsvbdcbajza9fja490w4mmvcpkw3zpak")))) + "1396wflczyxjxl603dhxjvd559f289lha9y2f04f71c7hapjl3am")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target -- 2.1.0
> gnu/packages/messaging.scm:413:15: python2-nbxmpp-0.5.3: URI > http://python-nbxmpp.gajim.org not reachable: 500 ("Internal Server Error") > gnu/packages/messaging.scm:413:15: python-nbxmpp-0.5.3: URI > http://python-nbxmpp.gajim.org not reachable: 500 ("Internal Server Error") There are some problems with the project’s homepage (self-signed cert and trac configuration issues), but I don’t see a 500 error. ~~ Ricardo
