From 5d8549328483978bf04dd2c710ef6a06614d4776 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel 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 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 . - (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 - ;; ). - (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 . - (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 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 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: + ;; + ,@(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 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