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Re: Broken URLs
|
From: |
Ricardo Wurmus |
|
Subject: |
Re: Broken URLs |
|
Date: |
Fri, 20 Nov 2015 11:24:36 +0100 |
Ludovic Courtès <address@hidden> 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 <address@hidden>
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 <address@hidden>
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 <address@hidden>
-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 <address@hidden>
-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 <address@hidden>
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
- Broken URLs, Ludovic Courtès, 2015/11/12
- Re: Broken URLs,
Ricardo Wurmus <=