From 5d8549328483978bf04dd2c710ef6a06614d4776 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Wed, 28 Sep 2016 13:18:19 +0200
Subject: gnu: Remove python-setuptools and python2-setuptools from inputs
(part 1b)
This patch contains the changes in all modules beside python.scm where
removing setuptools from the inputs could be achieved by removing complete
lines.
* gnu/packages/admin.scm (graphios, thefuck): Remove all [inputs],
[native-inputs] and [propagated-inputs] where python-setuptools or
python2-setuptools are the sole entries. Remove python-setuptools and
python2-setuptools listed on a line by its own from [inputs],
[native-inputs] and [propagated-inputs].
* gnu/packages/backup.scm (rdiff-backup): Likewise.
* gnu/packages/bioinformatics.scm (htseq, macs, python2-pbcore, rseqc,
multiqc): Likewise.
* gnu/packages/django.scm (python-django, python2-django,
python-django-simple-math-captcha, python2-django-simple-math-captcha):
Likewise.
* gnu/packages/docker.scm (python-docker-py, docker-compose): Likewise.
* gnu/packages/game-development.scm (python-pygame): Likewise.
* gnu/packages/key-mon.scm (key-mon): Likewise.
* gnu/packages/mail.scm (khard): Likewise.
* gnu/packages/music.scm (beets, python2-pyechonest): Likewise.
* gnu/packages/openstack.scm (python-bandit, python2-bandit,
python-debtcollector, python2-debtcollector,
python-mox3, python2-mox3,
python-os-client-config, python2-os-client-config,
python-oslo.config, python2-oslo.config,
python-oslo.context, python2-oslo.context,
python-oslo.i18n, python2-oslo.i18n,
python-oslo.serialization, python2-oslo.serialization,
python-oslosphinx, python2-oslosphinx,
python-oslotest, python2-oslotest,
python-oslo.utils, python2-oslo.utils,
python-swiftclient, python2-swiftclient): Likewise.
* gnu/packages/pdf.scm (pdfposter): Likewise.
* gnu/packages/tls.scm (python-acme, python2-acme): Likewise.
---
gnu/packages/tls.scm | 1 -
1 file changed, 1 deletion(-)
(limited to 'gnu/packages/tls.scm')
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 74cc25bb67..608fd6a080 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -462,7 +462,6 @@ security, and applying best practice development processes.")
("python-sphinx" ,python-sphinx)
("python-sphinxcontrib-programoutput" ,python-sphinxcontrib-programoutput)
("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
- ("python-setuptools" ,python-setuptools)
("texinfo" ,texinfo)))
(propagated-inputs
`(("python-ndg-httpsclient" ,python-ndg-httpsclient)
--
cgit v1.2.3
From b41a05ce497d5ecc682cf46ce61aa2215193f9f6 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Wed, 28 Sep 2016 15:23:10 +0200
Subject: gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).
Bug 20765 is solved since we build all Python packages using
option "--single-version-externally-managed".
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove
configure-flags. (pepr): remove phase "disable-egg-generation".
* gnu/packages/pdf.scm (reportlab): Remove configure-flags.
* gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl,
python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove
configure-flags. (python-pillow) remove phase
"disable-egg-generation". (python-libarchive-c) Remove patching
setup.cfg.
* gnu/packages/statistics.scm (python-patsy): remove phase
"prevent-generation-of-egg-archive".
* gnu/packages/tls.scm (python-acme): remove phase
"disable-egg-compression".
* gnu/packages/tor.scm (onionshare): Remove configure-flags.
---
gnu/packages/bioinformatics.scm | 19 +----------------
gnu/packages/pdf.scm | 5 -----
gnu/packages/python.scm | 47 ++++-------------------------------------
gnu/packages/statistics.scm | 8 +------
gnu/packages/tls.scm | 9 --------
gnu/packages/tor.scm | 6 +-----
6 files changed, 7 insertions(+), 87 deletions(-)
(limited to 'gnu/packages/tls.scm')
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 481a2a3bcb..9872933693 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3563,11 +3563,6 @@ the phenotype as it models the data.")
(build-system python-build-system)
(arguments
`(#:python ,python-2
- ;; With standard flags, the install phase attempts to create a zip'd
- ;; egg file, and fails with an error: 'ZIP does not support timestamps
- ;; before 1980'
- #:configure-flags '("--single-version-externally-managed"
- "--record=pbtranscript-tofu.txt")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-directory
@@ -7576,19 +7571,7 @@ may optionally be provided to further inform the peak-calling process.")
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; python2 only
- #:tests? #f ; no tests included
- #:phases
- (modify-phases %standard-phases
- ;; When setuptools is used a ".egg" archive is generated and
- ;; installed. This makes it hard to actually run PePr. This issue
- ;; has been reported upstream:
- ;; https://github.com/shawnzhangyx/PePr/issues/9
- (add-after 'unpack 'disable-egg-generation
- (lambda _
- (substitute* "setup.py"
- (("from setuptools import setup")
- "from distutils.core import setup"))
- #t)))))
+ #:tests? #f)) ; no tests included
(propagated-inputs
`(("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index e447ef1603..b86f5efbfa 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -638,11 +638,6 @@ using a stylus.")
(base32
"0rz2pg04wnzjjm2f5a8ik9v8s54mv4xrjhv5liqjijqv6awh12gl"))))
(build-system python-build-system)
- (arguments
- ;; Prevent creation of the egg. Without this flag, various artifacts
- ;; from the build inputs end up in the final python3 output. It also
- ;; works around https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765 .
- `(#:configure-flags '("--single-version-externally-managed" "--root=/")))
(propagated-inputs
`(("python-pillow" ,python-pillow)))
(home-page "http://www.reportlab.com")
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f103706533..3fcd92dc83 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2800,12 +2800,6 @@ sources.")
(base32
"19nw3rn7awplcdrz63kg1njqwkbymfg9lwn7l2grhdyhyr2gaa8g"))))
(build-system python-build-system)
- (arguments
- `(;; With standard flags, the install phase attempts to create a zip'd
- ;; egg file, and fails with an error: 'ZIP does not support timestamps
- ;; before 1980'
- #:configure-flags '("--single-version-externally-managed"
- "--record=sphinx-rtd-theme.txt")))
(inputs
`(("python-docutils" ,python-docutils)
("python-sphinx" ,python-sphinx)))
@@ -3988,12 +3982,7 @@ Python's distutils.")
(arguments
;; incompatible with Python 3 (exception syntax)
`(#:python ,python-2
- #:tests? #f
- ;; With standard flags, the install phase attempts to create a zip'd
- ;; egg file, and fails with an error: 'ZIP does not support timestamps
- ;; before 1980'
- #:configure-flags '("--single-version-externally-managed"
- "--record=elib.txt")))
+ #:tests? #f))
(home-page "https://github.com/dieterv/elib.intl")
(synopsis "Enhanced internationalization for Python")
(description
@@ -4026,17 +4015,6 @@ services for your Python modules and applications.")
;; Note: setuptools used at runtime for pkg_resources
(arguments
`(#:phases (modify-phases %standard-phases
- (add-before
- 'install 'disable-egg-compression
- (lambda _
- ;; Leave the .egg uncompressed since compressing it would
- ;; prevent the GC from identifying run-time dependencies.
- ;; See <http://bugs.gnu.org/20765>.
- (let ((port (open-file "setup.cfg" "a")))
- (display "\n[easy_install]\nzip_ok = 0\n"
- port)
- (close-port port)
- #t)))
(add-after
'install 'check-installed
(lambda _
@@ -6520,15 +6498,7 @@ a hash value.")
(substitute* "libarchive/ffi.py"
(("find_library\\('archive'\\)")
(string-append "'" libarchive
- "/lib/libarchive.so'"))))
-
- ;; Do not make a compressed egg (see
- ;; <http://bugs.gnu.org/20765>).
- (let ((port (open-file "setup.cfg" "a")))
- (display "\n[easy_install]\nzip_ok = 0\n"
- port)
- (close-port port)
- #t))))))
+ "/lib/libarchive.so'")))))))))
(inputs
`(("libarchive" ,libarchive)))
(home-page "https://github.com/Changaco/python-libarchive-c")
@@ -9454,9 +9424,6 @@ CloudFront content delivery network.")
`(;; Tests fail with "ValueError: _type_ 'v' not supported" on Python 3,
;; and on Python 2 they need the dl module deprecated since Python 2.6.
#:tests? #f
- ;; Prevent creation of the egg. This works around
- ;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765 .
- #:configure-flags '("--single-version-externally-managed" "--root=/")
;; Hard-code the path to pkg-config.
#:phases
(modify-phases %standard-phases
@@ -10979,10 +10946,7 @@ failures.")
"06032agzhw1i9d9qlhfblnl3dw5hcyxhagn7b120zhrszbjzfbh3"))))
(build-system python-build-system)
(arguments
- `(#:tests? #f ; Fails with recent pytest and pep8. See upstream issues #8 and #12.
- ;; Prevent creation of the egg. This works around
- ;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765 .
- #:configure-flags '("--single-version-externally-managed" "--root=/")))
+ `(#:tests? #f)) ; Fails with recent pytest and pep8. See upstream issues #8 and #12.
(native-inputs
`(("python-pytest" ,python-pytest)))
(propagated-inputs
@@ -11007,10 +10971,7 @@ failures.")
"0flag3n33kbhyjrhzmq990rvg4yb8hhhl0i48q9hw0ll89jp28lw"))))
(build-system python-build-system)
(arguments
- `(;; Prevent creation of the egg. This works around
- ;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765 .
- #:configure-flags '("--single-version-externally-managed" "--root=/")
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(delete 'check)
(add-after 'install 'check
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 950c3ec64f..cca08d26a8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1394,13 +1394,7 @@ and fast file reading.")
(arguments
`(#:phases
(modify-phases %standard-phases
- (replace 'check (lambda _ (zero? (system* "nosetests" "-v"))))
- (add-after 'unpack 'prevent-generation-of-egg-archive
- (lambda _
- (substitute* "setup.py"
- (("from setuptools import setup")
- "from distutils.core import setup"))
- #t)))))
+ (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 608fd6a080..607fa33b27 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -437,15 +437,6 @@ security, and applying best practice development processes.")
(arguments
`(#:phases
(modify-phases %standard-phases
- (add-before 'install 'disable-egg-compression
- (lambda _
- ;; Do not compress the egg.
- ;; See <http://bugs.gnu.org/20765>.
- (let ((port (open-file "setup.cfg" "a")))
- (display "\n[easy_install]\nzip_ok = 0\n"
- port)
- (close-port port)
- #t)))
(add-after 'install 'docs
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index e6fbf6e005..fe079fb104 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -208,11 +208,7 @@ networks.")
;; After all the patching we run the tests after installing.
;; This is also a known issue:
;; https://github.com/micahflee/onionshare/issues/284
- (lambda _ (zero? (system* "nosetests" "test")))))
- ;; can't compress the egg because it expects to find all the resources
- ;; inside the egg as though it were a folder.
- #:configure-flags '("--single-version-externally-managed" "--root=/")
- ))
+ (lambda _ (zero? (system* "nosetests" "test")))))))
(native-inputs
`(("python-nose" ,python-nose)))
(inputs
--
cgit v1.2.3
From 4b569a4ff5b1db020d8b9be8a3b6fad2eebeb37b Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 3 Dec 2016 22:36:10 -0500
Subject: gnu: acme-client: Update to 0.1.15.
* gnu/packages/tls.scm (acme-client): Update to 0.1.15.
[native-inputs]: Add pkg-config.
---
gnu/packages/tls.scm | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
(limited to 'gnu/packages/tls.scm')
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 607fa33b27..854ba1cb47 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -671,7 +671,7 @@ number generator")
(define-public acme-client
(package
(name "acme-client")
- (version "0.1.14")
+ (version "0.1.15")
(source (origin
(method url-fetch)
(uri (string-append "https://kristaps.bsd.lv/" name "/"
@@ -679,7 +679,7 @@ number generator")
version ".tgz"))
(sha256
(base32
- "1qq4xk41pn65m3v7nnvkmxg96pr06vz6hzdrm0vcmlp3clzpbahl"))))
+ "07p723391whrswl4rir0l1k03l457sjscnj0cfaxr8mfnkx4y3wi"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; no test suite
@@ -689,6 +689,8 @@ number generator")
#:phases
(modify-phases %standard-phases
(delete 'configure)))) ; no './configure' script
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
(inputs
`(("libbsd" ,libbsd)
("libressl" ,libressl)))
--
cgit v1.2.3
From fc184fe2de60846b65636a1ca1d3e3af344f8c5f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 9 Dec 2016 09:48:38 +0100
Subject: gnu: openssl-next: Update to 1.1.0c [fixes CVE-{7053,7054,7055}].
* gnu/packages/tls.scm (openssl-next): Update to 1.1.0c.
[arguments]: Duplicate 'configure' to add rpath flag previously handled by
now-defunct 'patch-runpath' phase. Duplicate 'remove-miscellany' phase.
---
gnu/packages/tls.scm | 45 +++++++++++++++++++++++++++++++++++++--------
1 file changed, 37 insertions(+), 8 deletions(-)
(limited to 'gnu/packages/tls.scm')
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 854ba1cb47..f5ffe42b91 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -355,7 +355,7 @@ required structures.")
(package
(inherit openssl)
(name "openssl")
- (version "1.1.0b")
+ (version "1.1.0c")
(source (origin
(method url-fetch)
(uri (list (string-append "ftp://ftp.openssl.org/source/"
@@ -366,7 +366,7 @@ required structures.")
(patches (search-patches "openssl-1.1.0-c-rehash-in.patch"))
(sha256
(base32
- "1xznrqvb1dbngv2k2nb6da6fdw00c01sy2i36yjdxr4vpxrf0pd4"))))
+ "1xfn5ydl14myd9wgxm4nxy5a42cpp1g12ijf3g9m4mz0l90n8hzw"))))
(outputs '("out"
"doc" ;1.3MiB of man3 pages
"static")) ; 5.5MiB of .a files
@@ -377,13 +377,42 @@ required structures.")
(delete 'patch-tests) ; These two phases are not needed by
(delete 'patch-Makefile.org) ; OpenSSL 1.1.0.
- (add-after 'configure 'patch-runpath
+ ;; Override configure phase since -rpath is now a configure option.
+ (replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
- (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
- (substitute* "Makefile.shared"
- (("\\$\\$\\{SHAREDCMD\\} \\$\\$\\{SHAREDFLAGS\\}")
- (string-append "$${SHAREDCMD} $${SHAREDFLAGS}"
- " -Wl,-rpath," lib)))
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib")))
+ (zero?
+ (system* "./config"
+ "shared" ;build shared libraries
+ "--libdir=lib"
+
+ ;; The default for this catch-all directory is
+ ;; PREFIX/ssl. Change that to something more
+ ;; conventional.
+ (string-append "--openssldir=" out
+ "/share/openssl-" ,version)
+
+ (string-append "--prefix=" out)
+ (string-append "-Wl,-rpath," lib)
+
+ ;; XXX FIXME: Work around a code generation bug in GCC
+ ;; 4.9.3 on ARM when compiled with -mfpu=neon. See:
+ ;; <https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66917>
+ ,@(if (and (not (%current-target-system))
+ (string-prefix? "armhf" (%current-system)))
+ '("-mfpu=vfpv3")
+ '()))))))
+
+ ;; XXX: Duplicate this phase to make sure 'version' evaluates
+ ;; in the current scope and not the inherited one.
+ (replace 'remove-miscellany
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; The 'misc' directory contains random undocumented shell and Perl
+ ;; scripts. Remove them to avoid retaining a reference on Perl.
+ (let ((out (assoc-ref outputs "out")))
+ (delete-file-recursively (string-append out "/share/openssl-"
+ ,version "/misc"))
#t)))))))))
(define-public libressl
--
cgit v1.2.3
From 7c1a7bf484cb6078798e132f16d1600b9a36349f Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Mon, 12 Dec 2016 21:04:43 -0500
Subject: gnu: acme-client: Provide path to certificates.
* gnu/packages/tls.scm (acme-client)[arguments]: Add 'patch-paths' phase.
---
gnu/packages/tls.scm | 7 +++++++
1 file changed, 7 insertions(+)
(limited to 'gnu/packages/tls.scm')
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index f5ffe42b91..e577421fac 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -717,6 +717,13 @@ number generator")
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'patch-paths
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((pem (string-append (assoc-ref inputs "libressl")
+ "/etc/ssl/cert.pem")))
+ (substitute* "http.c"
+ (("/etc/ssl/cert.pem") pem))
+ #t)))
(delete 'configure)))) ; no './configure' script
(native-inputs
`(("pkg-config" ,pkg-config)))
--
cgit v1.2.3