diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioconductor.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/gd.scm | 11 | ||||
| -rw-r--r-- | gnu/packages/patches/gd-CVE-2018-1000222.patch | 87 | ||||
| -rw-r--r-- | gnu/packages/php.scm | 3 | ||||
| -rw-r--r-- | gnu/packages/statistics.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/tex.scm | 8 | ||||
| -rw-r--r-- | gnu/packages/tls.scm | 8 |
9 files changed, 115 insertions, 15 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) |