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-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioconductor.scm4
-rw-r--r--gnu/packages/bioinformatics.scm4
-rw-r--r--gnu/packages/gd.scm11
-rw-r--r--gnu/packages/patches/gd-CVE-2018-1000222.patch87
-rw-r--r--gnu/packages/php.scm3
-rw-r--r--gnu/packages/statistics.scm4
-rw-r--r--gnu/packages/tex.scm8
-rw-r--r--gnu/packages/tls.scm8
-rw-r--r--guix/scripts/build.scm2
-rw-r--r--guix/scripts/package.scm39
-rw-r--r--guix/ui.scm162
12 files changed, 300 insertions, 33 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index 39cd55f105..b3bd208212 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -721,6 +721,7 @@ dist_patch_DATA = \
%D%/packages/patches/gcr-disable-failing-tests.patch \
%D%/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch \
%D%/packages/patches/gd-CVE-2018-5711.patch \
+ %D%/packages/patches/gd-CVE-2018-1000222.patch \
%D%/packages/patches/gd-fix-tests-on-i686.patch \
%D%/packages/patches/gd-freetype-test-failure.patch \
%D%/packages/patches/gdm-CVE-2018-14424.patch \
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a47a5aad05..108f3c398f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -410,14 +410,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.14.1")
+ (version "3.14.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1cn1hfc3nvsf2n3563lkmvwjxfbiygx7f84zk683p89gy7zi1gyj"))))
+ "13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2d5ec6d170..6580cac531 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9866,14 +9866,14 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-annotationhub
(package
(name "r-annotationhub")
- (version "2.12.0")
+ (version "2.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
- "11gh7qkgazs90czdqgv74gh2hz26xrmdp6wsz9x5pygbxls8xdw3"))))
+ "02ls279k1qlch147vw8kwvlhcqyzvi495bgv110m0xnnbpgbln6g"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/gd.scm b/gnu/packages/gd.scm
index c374695524..327a1f1545 100644
--- a/gnu/packages/gd.scm
+++ b/gnu/packages/gd.scm
@@ -39,6 +39,7 @@
(define-public gd
(package
(name "gd")
+ (replacement gd/fixed)
;; Note: With libgd.org now pointing to github.com, genuine old
;; tarballs are no longer available. Notably, versions 2.0.x are
;; missing.
@@ -91,6 +92,16 @@ most common applications of GD involve website development.")
"See COPYING file in the distribution."))
(properties '((cpe-name . "libgd")))))
+(define-public gd/fixed
+ (hidden-package
+ (package
+ (inherit gd)
+ (source (origin
+ (inherit (package-source gd))
+ (patches (append (origin-patches (package-source gd))
+ (search-patches "gd-CVE-2018-5711.patch"
+ "gd-CVE-2018-1000222.patch"))))))))
+
(define-public perl-gd
(package
(name "perl-gd")
diff --git a/gnu/packages/patches/gd-CVE-2018-1000222.patch b/gnu/packages/patches/gd-CVE-2018-1000222.patch
new file mode 100644
index 0000000000..7e94295bb6
--- /dev/null
+++ b/gnu/packages/patches/gd-CVE-2018-1000222.patch
@@ -0,0 +1,87 @@
+Fix CVE-2018-1000222:
+
+https://github.com/libgd/libgd/issues/447
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1000222
+
+Patch copied from upstream source repository:
+
+https://github.com/libgd/libgd/commit/4b1e18a00ce7c4b7e6919c3b3109a034393b805a
+
+From 4b1e18a00ce7c4b7e6919c3b3109a034393b805a Mon Sep 17 00:00:00 2001
+From: Mike Frysinger <vapier@gentoo.org>
+Date: Sat, 14 Jul 2018 13:54:08 -0400
+Subject: [PATCH] bmp: check return value in gdImageBmpPtr
+
+Closes #447.
+
+(cherry picked from commit ac16bdf2d41724b5a65255d4c28fb0ec46bc42f5)
+---
+ src/gd_bmp.c | 17 ++++++++++++++---
+ 1 file changed, 14 insertions(+), 3 deletions(-)
+
+diff --git a/src/gd_bmp.c b/src/gd_bmp.c
+index ccafdcd..d625da1 100644
+--- a/src/gd_bmp.c
++++ b/src/gd_bmp.c
+@@ -48,6 +48,8 @@ static int bmp_read_4bit(gdImagePtr im, gdIOCtxPtr infile, bmp_info_t *info, bmp
+ static int bmp_read_8bit(gdImagePtr im, gdIOCtxPtr infile, bmp_info_t *info, bmp_hdr_t *header);
+ static int bmp_read_rle(gdImagePtr im, gdIOCtxPtr infile, bmp_info_t *info);
+
++static int _gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression);
++
+ #define BMP_DEBUG(s)
+
+ static int gdBMPPutWord(gdIOCtx *out, int w)
+@@ -88,8 +90,10 @@ BGD_DECLARE(void *) gdImageBmpPtr(gdImagePtr im, int *size, int compression)
+ void *rv;
+ gdIOCtx *out = gdNewDynamicCtx(2048, NULL);
+ if (out == NULL) return NULL;
+- gdImageBmpCtx(im, out, compression);
+- rv = gdDPExtractData(out, size);
++ if (!_gdImageBmpCtx(im, out, compression))
++ rv = gdDPExtractData(out, size);
++ else
++ rv = NULL;
+ out->gd_free(out);
+ return rv;
+ }
+@@ -142,6 +146,11 @@ BGD_DECLARE(void) gdImageBmp(gdImagePtr im, FILE *outFile, int compression)
+ compression - whether to apply RLE or not.
+ */
+ BGD_DECLARE(void) gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression)
++{
++ _gdImageBmpCtx(im, out, compression);
++}
++
++static int _gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression)
+ {
+ int bitmap_size = 0, info_size, total_size, padding;
+ int i, row, xpos, pixel;
+@@ -149,6 +158,7 @@ BGD_DECLARE(void) gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression)
+ unsigned char *uncompressed_row = NULL, *uncompressed_row_start = NULL;
+ FILE *tmpfile_for_compression = NULL;
+ gdIOCtxPtr out_original = NULL;
++ int ret = 1;
+
+ /* No compression if its true colour or we don't support seek */
+ if (im->trueColor) {
+@@ -326,6 +336,7 @@ BGD_DECLARE(void) gdImageBmpCtx(gdImagePtr im, gdIOCtxPtr out, int compression)
+ out_original = NULL;
+ }
+
++ ret = 0;
+ cleanup:
+ if (tmpfile_for_compression) {
+ #ifdef _WIN32
+@@ -339,7 +350,7 @@ cleanup:
+ if (out_original) {
+ out_original->gd_free(out_original);
+ }
+- return;
++ return ret;
+ }
+
+ static int compress_row(unsigned char *row, int length)
+--
+2.18.0
+
diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index 121ffab767..4981c60554 100644
--- a/gnu/packages/php.scm
+++ b/gnu/packages/php.scm
@@ -57,7 +57,8 @@
(inherit (package-source gd))
(patches (search-patches "gd-fix-tests-on-i686.patch"
"gd-freetype-test-failure.patch"
- "gd-CVE-2018-5711.patch"))))))
+ "gd-CVE-2018-5711.patch"
+ "gd-CVE-2018-1000222.patch"))))))
(define-public php
(package
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6e915aa437..e2a673a4e6 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1749,13 +1749,13 @@ and density estimation.")
(define-public r-chron
(package
(name "r-chron")
- (version "2.3-52")
+ (version "2.3-53")
(source (origin
(method url-fetch)
(uri (cran-uri "chron" version))
(sha256
(base32
- "185lfp75cv3l4cavg64sccj8lgc5sivch13n6gkannv3pd5cyzy4"))))
+ "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/chron")
(synopsis "Chronological R objects which can handle dates and times")
diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index ed85950bb6..c62512b8d0 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4250,14 +4250,14 @@ PDF documents.")
(define-public texmaker
(package
(name "texmaker")
- (version "4.5")
+ (version "5.0.2")
(source (origin
(method url-fetch)
(uri (string-append "http://www.xm1math.net/texmaker/texmaker-"
version ".tar.bz2"))
(sha256
(base32
- "056njk6j8wma23mlp7xa3rgfaxx0q8ynwx8wkmj7iy0b85p9ds9c"))))
+ "0y81mjm89b99pr9svcwpaf4iz2q9pc9hjas5kiwd1pbgl5vqskm9"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@@ -4268,9 +4268,9 @@ PDF documents.")
(let ((out (assoc-ref outputs "out")))
(invoke "qmake"
(string-append "PREFIX=" out)
- (string-append "DESKTOPDIR=" out
- "/share/applications")
+ (string-append "DESKTOPDIR=" out "/share/applications")
(string-append "ICONDIR=" out "/share/pixmaps")
+ (string-append "METAINFODIR=" out "/share/metainfo")
"texmaker.pro")))))))
(inputs
`(("poppler-qt5" ,poppler-qt5)
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 22fcf6e96b..d4e403b64c 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -502,20 +502,20 @@ netcat implementation that supports TLS.")
(package
(name "python-acme")
;; Remember to update the hash of certbot when updating python-acme.
- (version "0.26.1")
+ (version "0.27.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "acme" version))
(sha256
(base32
- "1glhwqj6yyb11820lspgd0gl5dqdfljn43kcy4ar5caccpsbbrw6"))))
+ "142gynlfx7yv0sdba3gpdxlnhg9chhz7hpdxdrp630z17h1bk9ri"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'build 'build-documentation
(lambda _
- (zero? (system* "make" "-C" "docs" "man" "info"))))
+ (invoke "make" "-C" "docs" "man" "info")))
(add-after 'install 'install-documentation
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@@ -559,7 +559,7 @@ netcat implementation that supports TLS.")
(uri (pypi-uri name version))
(sha256
(base32
- "0rnayqhdabm0rljxh76blqd11h51dqnwlwvql0j6xwzpccym30s9"))))
+ "0anh3vjy9sif1bkp25nj76ii37xx8hh0igcx60ppag12xlabsw1m"))))
(build-system python-build-system)
(arguments
`(,@(substitute-keyword-arguments (package-arguments python-acme)
diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index 4dd4fbccdf..3fa3c2c20f 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -735,7 +735,7 @@ needed."
(parameterize ((current-build-output-port (if quiet?
(%make-void-port "w")
- (current-error-port))))
+ (build-output-port #:verbose? #t))))
(let* ((mode (assoc-ref opts 'build-mode))
(drv (options->derivations store opts))
(urls (map (cut string-append <> "/log")
diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm
index 97bcc699d9..73cbccba3b 100644
--- a/guix/scripts/package.scm
+++ b/guix/scripts/package.scm
@@ -329,7 +329,8 @@ ENTRIES, a list of manifest entries, in the context of PROFILE."
`((verbosity . 0)
(graft? . #t)
(substitutes? . #t)
- (build-hook? . #t)))
+ (build-hook? . #t)
+ (print-build-trace? . #t)))
(define (show-help)
(display (G_ "Usage: guix package [OPTION]...
@@ -930,18 +931,24 @@ processed, #f otherwise."
(arg-handler arg result)
(leave (G_ "~A: extraneous argument~%") arg)))
- (let ((opts (parse-command-line args %options (list %default-options #f)
- #:argument-handler handle-argument)))
- (with-error-handling
- (or (process-query opts)
- (parameterize ((%store (open-connection))
- (%graft? (assoc-ref opts 'graft?)))
- (set-build-options-from-command-line (%store) opts)
-
- (parameterize ((%guile-for-build
- (package-derivation
- (%store)
- (if (assoc-ref opts 'bootstrap?)
- %bootstrap-guile
- (canonical-package guile-2.2)))))
- (process-actions (%store) opts)))))))
+ (define opts
+ (parse-command-line args %options (list %default-options #f)
+ #:argument-handler handle-argument))
+ (define verbose?
+ (assoc-ref opts 'verbose?))
+
+ (with-error-handling
+ (or (process-query opts)
+ (parameterize ((%store (open-connection))
+ (%graft? (assoc-ref opts 'graft?)))
+ (set-build-options-from-command-line (%store) opts)
+
+ (parameterize ((%guile-for-build
+ (package-derivation
+ (%store)
+ (if (assoc-ref opts 'bootstrap?)
+ %bootstrap-guile
+ (canonical-package guile-2.2))))
+ (current-build-output-port
+ (build-output-port #:verbose? verbose?)))
+ (process-actions (%store) opts))))))
diff --git a/guix/ui.scm b/guix/ui.scm
index 29c0b2b9ce..1bbd37c255 100644
--- a/guix/ui.scm
+++ b/guix/ui.scm
@@ -10,6 +10,9 @@
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Benz Schenk <benz.schenk@uzh.ch>
;;; Copyright © 2018 Kyle Meyer <kyle@kyleam.com>
+;;; Copyright © 2013, 2014 Free Software Foundation, Inc.
+;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -115,7 +118,8 @@
guix-warning-port
warning
info
- guix-main))
+ guix-main
+ build-output-port))
;;; Commentary:
;;;
@@ -1622,4 +1626,160 @@ and signal handling has already been set up."
(initialize-guix)
(apply run-guix args))
+(define color-table
+ `((CLEAR . "0")
+ (RESET . "0")
+ (BOLD . "1")
+ (DARK . "2")
+ (UNDERLINE . "4")
+ (UNDERSCORE . "4")
+ (BLINK . "5")
+ (REVERSE . "6")
+ (CONCEALED . "8")
+ (BLACK . "30")
+ (RED . "31")
+ (GREEN . "32")
+ (YELLOW . "33")
+ (BLUE . "34")
+ (MAGENTA . "35")
+ (CYAN . "36")
+ (WHITE . "37")
+ (ON-BLACK . "40")
+ (ON-RED . "41")
+ (ON-GREEN . "42")
+ (ON-YELLOW . "43")
+ (ON-BLUE . "44")
+ (ON-MAGENTA . "45")
+ (ON-CYAN . "46")
+ (ON-WHITE . "47")))
+
+(define (color . lst)
+ "Return a string containing the ANSI escape sequence for producing the
+requested set of attributes in LST. Unknown attributes are ignored."
+ (let ((color-list
+ (remove not
+ (map (lambda (color) (assq-ref color-table color))
+ lst))))
+ (if (null? color-list)
+ ""
+ (string-append
+ (string #\esc #\[)
+ (string-join color-list ";" 'infix)
+ "m"))))
+
+(define (colorize-string str . color-list)
+ "Return a copy of STR colorized using ANSI escape sequences according to the
+attributes STR. At the end of the returned string, the color attributes will
+be reset such that subsequent output will not have any colors in effect."
+ (string-append
+ (apply color color-list)
+ str
+ (color 'RESET)))
+
+(define* (build-output-port #:key
+ (colorize? #t)
+ verbose?
+ (port (current-error-port)))
+ "Return a soft port that processes build output. By default it colorizes
+phase announcements and replaces any other output with a spinner."
+ (define spun? #f)
+ (define spin!
+ (let ((steps (circular-list "\\" "|" "/" "-")))
+ (lambda ()
+ (match steps
+ ((first . rest)
+ (set! steps rest)
+ (set! spun? #t) ; remember to erase spinner
+ first)))))
+
+ (define use-color?
+ (and colorize?
+ (not (or (getenv "NO_COLOR")
+ (getenv "INSIDE_EMACS")
+ (not (isatty? port))))))
+
+ (define handle-string
+ (let* ((proc (if use-color?
+ colorize-string
+ (lambda (s . _) s)))
+ (rules `(("^(@ build-started) (.*) (.*)"
+ #:transform
+ ,(lambda (m)
+ (string-append
+ (proc "Building " 'BLUE 'BOLD)
+ (match:substring m 2) "\n")))
+ ("^(@ build-failed) (.*) (.*)"
+ #:transform
+ ,(lambda (m)
+ (string-append
+ (proc "Build failed: " 'RED 'BOLD)
+ (match:substring m 2) "\n")))
+ ("^(@ build-succeeded) (.*) (.*)"
+ #:transform
+ ,(lambda (m)
+ (string-append
+ (proc "Built " 'GREEN 'BOLD)
+ (match:substring m 2) "\n")))
+ ("^(@ substituter-started) (.*) (.*)"
+ #:transform
+ ,(lambda (m)
+ (string-append
+ (proc "Substituting " 'BLUE 'BOLD)
+ (match:substring m 2) "\n")))
+ ("^(@ substituter-failed) (.*) (.*) (.*)"
+ #:transform
+ ,(lambda (m)
+ (string-append
+ (proc "Substituter failed: " 'RED 'BOLD)
+ (match:substring m 2) "\n"
+ (match:substring m 3) ": "
+ (match:substring m 4) "\n")))
+ ("^(@ substituter-succeeded) (.*)"
+ #:transform
+ ,(lambda (m)
+ (string-append
+ (proc "Substituted " 'GREEN 'BOLD)
+ (match:substring m 2) "\n")))
+ ("^(starting phase )(.*)"
+ BLUE GREEN)
+ ("^(phase)(.*)(succeeded after)(.*)(seconds)(.*)"
+ GREEN BLUE GREEN BLUE GREEN BLUE)
+ ("^(phase)(.*)(failed after)(.*)(seconds)(.*)"
+ RED BLUE RED BLUE RED BLUE))))
+ (lambda (str)
+ (let ((processed
+ (any (match-lambda
+ ((pattern #:transform transform)
+ (and=> (string-match pattern str)
+ transform))
+ ((pattern . colors)
+ (and=> (string-match pattern str)
+ (lambda (m)
+ (let ((substrings
+ (map (cut match:substring m <>)
+ (iota (- (match:count m) 1) 1))))
+ (string-join (map proc substrings colors) ""))))))
+ rules)))
+ (when spun?
+ (display (string #\backspace) port))
+ (if processed
+ (begin
+ (display processed port)
+ (set! spun? #f))
+ ;; Print unprocessed line, or replace with spinner
+ (display (if verbose? str (spin!)) port))))))
+ (make-soft-port
+ (vector
+ ;; procedure accepting one character for output
+ (cut write <> port)
+ ;; procedure accepting a string for output
+ handle-string
+ ;; thunk for flushing output
+ (lambda () (force-output port))
+ ;; thunk for getting one character
+ (const #t)
+ ;; thunk for closing port (not by garbage collection)
+ (lambda () (close port)))
+ "w"))
+
;;; ui.scm ends here
generated by cgit v1.2.3 (git 2.46.2) at 2024-11-10 06:57:24 +0000