Merge branch 'master' into core-updates

8 files changed, 114 insertions, 15 deletions

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)