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Gentoo's Bugzilla – Attachment 265431 Details for
Bug 358195
sci-biology/recon _FORTIFY_SOURCE indicates presence of overflow
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Build log
recon-1.06:20110309-190647.log (text/plain), 6.90 KB, created by
Diego Elio Pettenò (RETIRED)
on 2011-03-10 10:15:57 UTC
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Description:
Build log
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Creator:
Diego Elio Pettenò (RETIRED)
Created:
2011-03-10 10:15:57 UTC
Size:
6.90 KB
patch
obsolete
> * Package: sci-biology/recon-1.06 > * Repository: gentoo > * Maintainer: weaver@gentoo.org sci-biology@gentoo.org > * USE: elibc_glibc kernel_linux test userland_GNU x86 > * FEATURES: sandbox test userpriv usersandbox >>>> Unpacking source... >>>> Unpacking RECON1.06.tar.gz to /var/tmp/portage/sci-biology/recon-1.06/work >>>> Source unpacked in /var/tmp/portage/sci-biology/recon-1.06/work >>>> Preparing source in /var/tmp/portage/sci-biology/recon-1.06/work/RECON1.06 ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/recon-1.06/work/RECON1.06 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/recon-1.06/work/RECON1.06 ... >make -j14 -C src >make: Entering directory `/var/tmp/portage/sci-biology/recon-1.06/work/RECON1.06/src' >gcc -O -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu imagespread.c -o imagespread >gcc -O -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu eledef.c -o eledef >gcc -O -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu eleredef.c -o eleredef >gcc -O -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu edgeredef.c -o edgeredef >gcc -O -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu famdef.c -o famdef >In file included from eledef.c:1:0: >msps.h: In function âscan_mspâ: >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 3 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 5 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 6 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 8 has type âint32_t *âIn file included from ele.h:1:0, > from famdef.c:1: >msps.h: In function âscan_mspâ: > >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 9 has type âint32_t *â >In file included from ele.h:1:0, > from edgeredef.c:1: >msps.h: In function âscan_mspâ:msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 3 has type âint32_t *â > >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 3 has type âint32_t *âmsps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 5 has type âint32_t *â > >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 6 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 5 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 8 has type âint32_t *âmsps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 6 has type âint32_t *â > >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 8 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 9 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 9 has type âint32_t *â >In file included from ele.h:1:0, > from eleredef.c:5: >msps.h: In function âscan_mspâ: >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 3 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 5 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 6 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 8 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 9 has type âint32_t *â >In file included from imagespread.c:2:0: >msps.h: In function âscan_mspâ: >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 3 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 5 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 6 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 8 has type âint32_t *â >msps.h:116:5: warning: format â%ldâ expects type âlong int *â, but argument 9 has type âint32_t *â >imagespread.c: In function âGetSeqNamesâ: >seqlist.h:19:8: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result >eledef.c: In function âmainâ: >eledef.c:246:7: warning: ignoring return value of âfreopenâ, declared with attribute warn_unused_result >eledef.c:253:5: warning: ignoring return value of âfreopenâ, declared with attribute warn_unused_result >eledef.c: In function âGetSeqNamesâ: >seqlist.h:19:8: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result >edgeredef.c: In function âgeneral_edge_redefâ: >edgeredef.c:196:11: warning: ignoring return value of âsystemâ, declared with attribute warn_unused_result >famdef.c: In function âGetSeqNamesâ: >seqlist.h:19:8: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result >edgeredef.c: In function âGetSeqNamesâ: >seqlist.h:19:8: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result >eleredef.c: In function âGetSeqNamesâ: >seqlist.h:19:8: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result >In file included from /usr/include/stdio.h:930:0, > from bolts.h:3, > from msps.h:3, > from eledef.c:1: >In function âfgetsâ, > inlined from âimg_chargeâ at eledef.c:393:15: >/usr/include/bits/stdio2.h:253:2: warning: call to â__fgets_chk_warnâ declared with attribute warning: fgets called with bigger size than length of destination buffer >make: Leaving directory `/var/tmp/portage/sci-biology/recon-1.06/work/RECON1.06/src' >>>> Source compiled. >>>> Test phase [none]: sci-biology/recon-1.06 > >>>> Install recon-1.06 into /var/tmp/portage/sci-biology/recon-1.06/image/ category sci-biology >>>> Completed installing recon-1.06 into /var/tmp/portage/sci-biology/recon-1.06/image/ > >strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment > usr/libexec/recon/famdef > usr/libexec/recon/edgeredef > usr/libexec/recon/eledef > usr/libexec/recon/eleredef > usr/libexec/recon/imagespread > > * QA Notice: Package has poor programming practices which may compile > * fine but exhibit random runtime failures. > * /usr/include/bits/stdio2.h:253:2: warning: call to â__fgets_chk_warnâ declared with attribute warning: fgets called with bigger size than length of destination buffer > > * Please do not file a Gentoo bug and instead report the above QA > * issues directly to the upstream developers of this software. > * Homepage: http://selab.janelia.org/recon.html > * http://www.repeatmasker.org/RepeatModeler.html
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bug 358195
: 265431