diff options
| -rw-r--r-- | sci-libs/cctbx/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-libs/cctbx/Manifest | 35 | ||||
| -rw-r--r-- | sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild | 5 | ||||
| -rw-r--r-- | sci-libs/cctbx/files/2010.03.29.2334-format-security.patch | 117 |
4 files changed, 143 insertions, 20 deletions
diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog index b2e804aa050d..aabcf24fba51 100644 --- a/sci-libs/cctbx/ChangeLog +++ b/sci-libs/cctbx/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-libs/cctbx # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.38 2015/04/22 06:58:03 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.39 2015/08/06 13:05:31 jlec Exp $ + + 06 Aug 2015; Justin Lecher <jlec@gentoo.org> + +files/2010.03.29.2334-format-security.patch, cctbx-2010.03.29.2334-r7.ebuild: + Fix for format-security, bug #547082 22 Apr 2015; Justin Lecher <jlec@gentoo.org> -cctbx-2010.03.29.2334-r6.ebuild: Drop old diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest index 636148d875dc..2c4ed7077e9c 100644 --- a/sci-libs/cctbx/Manifest +++ b/sci-libs/cctbx/Manifest @@ -4,30 +4,31 @@ Hash: SHA512 AUX 2010.03.29.2334-boost.patch 18175 SHA256 f6a8a246dfd42e7981687802a0e00d933759d3c749c0344bfbfbfde12814f4d7 SHA512 e722312a878be229a24269471902bd1febe98c5510bfc50e1ba3a841c1a0228cdb7964e69703083850052e49e91899b229bc3543d90485ba50e79e7eceb11e2e WHIRLPOOL f87a78d93a94fb93fd243269fe1e5c0cfcc6beff02d936d2b609cece6ea9fbe08b5201c354f982df6ef5f09b84032a25b8a3cac357abf6279c6b5a5b2468e0e7 AUX 2010.03.29.2334-clipper.patch 2209 SHA256 e7c8bf813bedd3b67de5ce727d5f75e9635568769373f237e7b624ed143351b1 SHA512 cb3fc1f89d9a4008b4add3ef2ecf5b2aa8e875e41e169916859a8e508858bc9548023bb552d4cb3794c46788eaa325c75bb858c7c08799b87f2e31bef57cf69a WHIRLPOOL 84b427cfc9ddba9891197f8185123a8f5831e6a9beaafe58ced2f52ea3d492217cbb5264f3118ec9f27b12746141b788e9464a66b00c56f54b786bd3aada9351 AUX 2010.03.29.2334-flags.patch 3336 SHA256 769edb3e5dcb608b54ab4d33c5933b523f73ff62c6cb627c4eb4b1a2086e40b1 SHA512 63ccefc4303136c9fea854fecdbed39efe9d7f565000bc356addc2b268e042c34815da3416e9960200b9f6ac33b7c4bb7ce705a7b7939cd65ef4f925d56ced41 WHIRLPOOL 22e86a519b74e54d6655e85defb1c9bd66bf8535c3b44cd03e924fffc6ddd6b5cf6d9dd0c69a82d1970893f19671ddd46ae8883c52763d29e3e20bfbe7da9cdc +AUX 2010.03.29.2334-format-security.patch 4696 SHA256 fccc39e80b59d3b728b1611777a218ad1b349d60209cceefb7aea5339be8da6b SHA512 715c3b810c7c89864c8192dc9678cd8e758ba1bbb39782a2077f7ca598ddd2bc01114d4e5b58821c3246f1951d8b53b8ecdc085b3a03e2ebb5082a9dbf46a156 WHIRLPOOL 1d8d57955b326da2d2b46329cf5e6df11107e7761034763a58f4a35d28ec003783ae9e60eef9c5e7d38a95bdcfb4453d39ac3b69ef69cad8caa61a05d5feed84 AUX 2010.03.29.2334-gcc-4.6.patch 1059 SHA256 dad06be10e1ba3fefee9f9aa79a897635cb8362f5719c5c8c5e5c25d1bea6236 SHA512 25ad8471b1108549de6806752f886057e86e875dbcf78ad4f11095a54295d2234bf704b55559bf48ff50f0db64fb3d6a0367bcdc85e517a244abecdbbcabb2c1 WHIRLPOOL 5e1d0cc70b9501ffce3af51ffd921b8d3ab30c7bf690ac2f31a823fbcfd8dd38aa6bbe9e1304bfae9750a917df622391fb0b68da898bd662f838d172f1737721 AUX 2010.03.29.2334-gcc-4.7.patch 6747 SHA256 ab01875a97ece09e4d729bb435b67960eff6193c27454cc889f0dda0cd3c92a5 SHA512 17d557567ed135c3c095f3849f2643121f6c183573f8e5b63e056180c5ca6985cd1fcf482378787fbf37078eb185bd2502dfc42fb163e50fc1567588d7e3ef0e WHIRLPOOL fc41e5fb4400103999e7a178547e46ec18253241fe69b0074d29223be36fc38ec7be725c2db10481db4d48634972cc51e4c3352c2ab44c687995dd027f9ad383 AUX 2010.03.29.2334-soname.patch 5177 SHA256 dd4ea6dbf34c1b2d9572adec5a33fe6a73b1a99e8c4364123e69382bb161ce74 SHA512 3f62bc52c32c3573fbcd90fc49234498d7c28fc0dc7a68497041af35da46cbd9cb386b9b13ed2269a5728e87526987ac49179e38b2bcb6a355ee4c180e9f7861 WHIRLPOOL cdd533d510defea65388ccd25c63055fc2798edd4222d1aa1b0201671d2c074107a151edc5ba62b5677908d5c045f98f26cd5ae5574e9fc83919632c4258c77c AUX 2010.03.29.2334-tst_server.py.patch 774 SHA256 df058d16d2dc5beaac9f1a1fbf2e640994c7e881d449eb01ac338dadbfb15ac3 SHA512 490918c3139355ecb0430d908ccafc6d66cb25ec7df285cedbb983d80f3473425c72d0766262c557c0c783626479edd2528eaf83b1decdeba416dde193472d5a WHIRLPOOL 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/var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild,v 1.8 2015/08/06 13:05:31 jlec Exp $ EAPI=5 @@ -61,7 +61,8 @@ src_prepare() { "${FILESDIR}"/${PV}-flags.patch \ "${FILESDIR}"/${PV}-soname.patch \ "${FILESDIR}"/${PV}-gcc-4.6.patch \ - "${FILESDIR}"/${PV}-gcc-4.7.patch + "${FILESDIR}"/${PV}-gcc-4.7.patch \ + "${FILESDIR}"/${PV}-format-security.patch eprefixify "${MY_S}"/scitbx/libtbx_refresh.py diff --git a/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch b/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch new file mode 100644 index 000000000000..057c135f9953 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch @@ -0,0 +1,117 @@ + cctbx_sources/scitbx/lbfgsb/raw.h | 54 +++++++++++++++++++-------------------- + 1 file changed, 27 insertions(+), 27 deletions(-) + +diff --git a/cctbx_sources/scitbx/lbfgsb/raw.h b/cctbx_sources/scitbx/lbfgsb/raw.h +index 21afed7..5b15055 100644 +--- a/cctbx_sources/scitbx/lbfgsb/raw.h ++++ b/cctbx_sources/scitbx/lbfgsb/raw.h +@@ -853,7 +853,7 @@ namespace raw { + if (iprint >= 99) { + printf(" LINE SEARCH%12d times; norm of step = %.15G\n", + iback, xstep); +- printf(fmt_2001, iter,f,sbgnrm); ++ printf("%s %i %f %f", fmt_2001, iter,f,sbgnrm); + if (iprint > 100) { + write_ref1(" X =", x); + write_ref1(" G =", g); +@@ -862,7 +862,7 @@ namespace raw { + else if (iprint > 0) { + int imod = iter % iprint; + if (imod == 0) { +- printf(fmt_2001, iter,f,sbgnrm); ++ printf("%s %i %f %f", fmt_2001, iter,f,sbgnrm); + } + } + if (iprint >= 1) { +@@ -967,9 +967,9 @@ namespace raw { + " 2 rounding error dominate computation.\n"; + if (task.substr(0,5) == "ERROR") goto lbl_999; + if (iprint >= 0) { +- printf(fmt_3003); +- printf(fmt_3004); +- printf(fmt_3005, n,iter,nfgv,nintol,nskip,nact,sbgnrm,f); ++ printf("%s", fmt_3003); ++ printf("%s", fmt_3004); ++ printf("%s %i %i %i %i %i %i %f %f", fmt_3005, n,iter,nfgv,nintol,nskip,nact,sbgnrm,f); + if (iprint >= 100) { + write_ref1(" X =", x); + } +@@ -977,40 +977,40 @@ namespace raw { + } + lbl_999: + if (iprint >= 0) { +- printf(fmt_3009, task.c_str()); ++ printf("%s %s", fmt_3009, task.c_str()); + if (info != 0) { +- if (info == -1) printf(fmt_9011); +- if (info == -2) printf(fmt_9012); +- if (info == -3) printf(fmt_9013); +- if (info == -4) printf(fmt_9014); +- if (info == -5) printf(fmt_9015); ++ if (info == -1) printf("%s", fmt_9011); ++ if (info == -2) printf("%s", fmt_9012); ++ if (info == -3) printf("%s", fmt_9013); ++ if (info == -4) printf("%s", fmt_9014); ++ if (info == -5) printf("%s", fmt_9015); + if (info == -6) { + printf(" Input nbd(%12d) is invalid.\n", k); + } + if (info == -7) { + printf(" l(%12d) > u(%12d). No feasible solution.\n", k, k); + } +- if (info == -8) printf(fmt_9018); +- if (info == -9) printf(fmt_9019); ++ if (info == -8) printf("%s", fmt_9018); ++ if (info == -9) printf("%s", fmt_9019); + } +- if (iprint >= 1) printf(fmt_3007, cachyt,sbtime,lnscht); +- printf(fmt_3008, time); ++ if (iprint >= 1) printf("%s %f %f %f", fmt_3007, cachyt,sbtime,lnscht); ++ printf("%s %f", fmt_3008, time); + if (iprint >= 1) { + if (info == -4 || info == -9) { +- printf(fmt_3002, ++ printf("%s %i %i %i %i %s %i %f %f", fmt_3002, + iter,nfgv,nint,nact,word.c_str(),iback,stp,xstep); // itfile + } +- printf(fmt_3009, task.c_str()); // itfile ++ printf("%s %s", fmt_3009, task.c_str()); // itfile + if (info != 0) { +- if (info == -1) printf(fmt_9011); // itfile +- if (info == -2) printf(fmt_9012); // itfile +- if (info == -3) printf(fmt_9013); // itfile +- if (info == -4) printf(fmt_9014); // itfile +- if (info == -5) printf(fmt_9015); // itfile +- if (info == -8) printf(fmt_9018); // itfile +- if (info == -9) printf(fmt_9019); // itfile ++ if (info == -1) printf("%s", fmt_9011); // itfile ++ if (info == -2) printf("%s", fmt_9012); // itfile ++ if (info == -3) printf("%s", fmt_9013); // itfile ++ if (info == -4) printf("%s", fmt_9014); // itfile ++ if (info == -5) printf("%s", fmt_9015); // itfile ++ if (info == -8) printf("%s", fmt_9018); // itfile ++ if (info == -9) printf("%s", fmt_9019); // itfile + } +- printf(fmt_3008, time); // itfile ++ printf("%s %f", fmt_3008, time); // itfile + } + } + } +@@ -3902,7 +3902,7 @@ namespace raw { + " refresh the lbfgs memory and restart the iteration.\n"; + if (info != 0) { + // singular triangular system detected; refresh the lbfgs memory. +- if(iprint >= 1) printf(fmt_1005); ++ if(iprint >= 1) printf("%s", fmt_1005); + info = 0; + col = 0; + head = 1; +@@ -3968,7 +3968,7 @@ namespace raw { + if (info != 0) { + // singular triangular system detected; + // refresh the lbfgs memory and restart the iteration. +- if(iprint >= 1) printf(fmt_1005); ++ if(iprint >= 1) printf("%s", fmt_1005); + info = 0; + col = 0; + head = 1; |