Sorry to be back with problems in this miserable but useful package. The ajax graphics routines that are used for some output do not work for any version currently in portage or science overlay. Raw data output, for example, fails. Portage versions die with a segfault, while the heavily-patched version in the science overlay does not recognize the data output device. Building the package outside of portage without the --enable-systemlibs configure flag works as expected. The package does not work with libpcre-8.13. The internal pcre version seems to be 7.9. I suspect this discrepancy will only get worse with time. There has also been a version bump to emboss-6.4.0 and upstream patches to that version. Reproducible: Always Steps to Reproduce: 1. dotpath a.faa b.faa -wordsize 4 -graph data Results depend on versions of libpcre and emboss installed. If dev-libs/libpcre-8.13 is installed, the result is: Draw a non-overlapping wordmatch dotplot of two sequences Error: Failed to compile regular expression '[.][.]' at position 0: POSIX collating elements are not supported Segmentation fault If libpcre-8.12 (the stable version) and emboss-6.3.1_p4 from portage is installed (test both with and without X mysql pdf png use flags), the result is: Draw a non-overlapping wordmatch dotplot of two sequences Segmentation fault With emboss-6.3.1_p4-r1 from science overlay: Draw a non-overlapping wordmatch dotplot of two sequences Requested device data not available ...[omitted list of plplot devices]... Enter device number or keyword:
commit 08fae0a30263fd06fe51ac5b75301d574be9e1be Author: Justin Lecher <jlec@gentoo.org> Date: Thu Aug 27 15:47:31 2015 +0200 sci-biology/emboss: Drop old obsolets multiple bugs Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=542274 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=534418 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521604 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=514014 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=493724 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=406279 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=393311 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=382321 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=378443 Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org> https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=08fae0a30263fd06fe51ac5b75301d574be9e1be
