diff options
4 files changed, 218 insertions, 6 deletions
diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog index df43290cf514..d25cf848f78c 100644 --- a/sci-biology/ncbi-tools/ChangeLog +++ b/sci-biology/ncbi-tools/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/ncbi-tools -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.96 2013/06/12 11:31:50 jlec Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.97 2015/03/02 14:09:51 jlec Exp $ + + 02 Mar 2015; Justin Lecher <jlec@gentoo.org> + +files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch, + +files/ncbi-tools-2.2.26-format-security.patch, ncbi-tools-2.2.26-r2.ebuild: + Fix format-security and SLOT operators 12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools-2.2.26-r2.ebuild, files/ncbirc: diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch new file mode 100644 index 000000000000..bbc4623609c8 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch @@ -0,0 +1,81 @@ + corelib/ncbilcl.beos | 2 +- + corelib/ncbilcl.hlx | 2 +- + corelib/ncbilcl.lnx | 4 ++-- + corelib/ncbilcl.plx | 2 +- + corelib/ncbilcl.qnx | 2 +- + 5 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos +index f720567..fe6346f 100644 +--- a/corelib/ncbilcl.beos ++++ b/corelib/ncbilcl.beos +@@ -77,7 +77,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx +index 1492f93..0e98fb6 100644 +--- a/corelib/ncbilcl.hlx ++++ b/corelib/ncbilcl.hlx +@@ -67,7 +67,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-/*#define _SVID_SOURCE 1 */ ++/*#define _DEFAULT_SOURCE 1 */ + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx +index 46e2978..b3256b3 100644 +--- a/corelib/ncbilcl.lnx ++++ b/corelib/ncbilcl.lnx +@@ -65,7 +65,7 @@ + * fixes for new RedHat6.2 + * + * Revision 6.3 2000/02/10 16:36:32 vakatov +-* Added _SVID_SOURCE ++* Added _DEFAULT_SOURCE + * + * Revision 6.2 1999/07/12 05:50:49 vakatov + * Avoid redefinition of #_REENTRANT +@@ -141,7 +141,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + #define _GNU_SOURCE 1 + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx +index bf5824c..f2b53e1 100644 +--- a/corelib/ncbilcl.plx ++++ b/corelib/ncbilcl.plx +@@ -68,7 +68,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-/*#define _SVID_SOURCE 1 */ ++/*#define _DEFAULT_SOURCE 1 */ + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx +index c3d1f0a..4b27bd1 100644 +--- a/corelib/ncbilcl.qnx ++++ b/corelib/ncbilcl.qnx +@@ -72,7 +72,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + + + diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch new file mode 100644 index 000000000000..c12feff51af1 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch @@ -0,0 +1,124 @@ + api/alignmgr2.c | 2 +- + api/pgppop.c | 2 +- + api/txalign.c | 10 +++++----- + desktop/seqpanel.c | 4 ++-- + tools/spidey.c | 4 ++-- + 5 files changed, 11 insertions(+), 11 deletions(-) + +diff --git a/api/alignmgr2.c b/api/alignmgr2.c +index 5b43ef3..4b9007e 100644 +--- a/api/alignmgr2.c ++++ b/api/alignmgr2.c +@@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap, Int4 linesize, Boolean isn + spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand, seqcode); + ctr = SeqPortRead(spp, (Uint1Ptr)buf, amp->to_row-amp->from_row+1); + buf[ctr] = '\0'; +- fprintf(ofp, buf); ++ fprintf(ofp, "%s", buf); + SeqPortFree(spp); + } + } +diff --git a/api/pgppop.c b/api/pgppop.c +index d16d79d..b359378 100644 +--- a/api/pgppop.c ++++ b/api/pgppop.c +@@ -2994,7 +2994,7 @@ Char DefLine[255]; + if (szSeq){ + if (!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL, + NULL,NULL)) continue; +- fprintf(fp,szSeq); ++ fprintf(fp, "%s", szSeq); + fprintf(fp,"\n"); + MemFree(szSeq); + } +diff --git a/api/txalign.c b/api/txalign.c +index 5877f9c..cb35fbc 100644 +--- a/api/txalign.c ++++ b/api/txalign.c +@@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ + Char checkboxBuf[200]; + sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb); +- sprintf(docbuf+pos,checkboxBuf); ++ sprintf(docbuf+pos,"%s", checkboxBuf); + + pos += StringLen(checkboxBuf); + } + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, +@@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + sprintf(HTML_buffer, "<a name = THC%ld></a><a href=\"http://www.tigr.org/docs/tigr-scripts/hgi_scripts/thc_report.spl?est=THC%ld&report_type=n\">", (long) oip->id, (long) oip->id); + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, + tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); +@@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + sprintf(HTML_buffer, "<a name = TI%ld></a><a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id, (long) oip->id); + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, + tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); +@@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ + Char checkboxBuf[200]; + sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb); +- sprintf(docbuf+pos,checkboxBuf); ++ sprintf(docbuf+pos,"%s",checkboxBuf); + + pos += StringLen(checkboxBuf); + } +diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c +index 2e78e13..c7538aa 100644 +--- a/desktop/seqpanel.c ++++ b/desktop/seqpanel.c +@@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx + seqbuf, alnbuf, &alnbuf_len, + show_substitutions); + MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len); +- fprintf (fp, printed_line); ++ fprintf (fp, "%s", printed_line); + } + fprintf (fp, "\n"); + start = stop + 1; +@@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile + seqbuf, alnbuf, &alnbuf_len, + show_substitutions); + MemCpy (printed_line, alnbuf, alnbuf_len); +- fprintf (fp, printed_line); ++ fprintf (fp, "%s", printed_line); + start = stop + 1; + stop += seq_chars_per_row; + } +diff --git a/tools/spidey.c b/tools/spidey.c +index d6ce62d..ac9f59a 100644 +--- a/tools/spidey.c ++++ b/tools/spidey.c +@@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2, SPI_RegionInfoPtr srip, Biose + fprintf(ofp2, " "); + ctr++; + } +- fprintf(ofp2, buf); ++ fprintf(ofp2, "%s", buf); + if (spp){ + SeqPortFree(spp); + } +@@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2, SPI_mRNAToHerdPtr herd, S + ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10); + if (ctr > 0) + buf[ctr] = '\0'; +- fprintf(ofp2, buf); ++ fprintf(ofp2, "%s", buf); + SeqPortFree(spp); + } + done = TRUE; diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild index 5a170d413b4b..5a3f1ca33f32 100644 --- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild +++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild,v 1.6 2013/06/12 11:31:50 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild,v 1.7 2015/03/02 14:09:51 jlec Exp $ EAPI=5 @@ -18,7 +18,7 @@ IUSE="doc static-libs X" RDEPEND=" app-shells/tcsh dev-lang/perl - media-libs/libpng + media-libs/libpng:0= X? ( x11-libs/motif:0 )" DEPEND="${RDEPEND}" @@ -39,7 +39,9 @@ pkg_setup() { src_prepare() { epatch \ "${FILESDIR}"/${PN}-extra_vib.patch \ - "${FILESDIR}"/${P}-bfr-overflow.patch + "${FILESDIR}"/${P}-bfr-overflow.patch \ + "${FILESDIR}"/${P}-format-security.patch \ + "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch if use ppc || use ppc64; then epatch "${FILESDIR}"/${PN}-lop.patch |