Bug 368473

Summary:	sci-biology/hmmer-3.0 fails to build with "mpi.c:27:23: error: impl_dummy.: No such file or directory"
Product:	Gentoo Linux	Reporter:	Willard Dawson <wfdawson>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED WORKSFORME
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	AMD64
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	Emerge info Emerge -pqv Build log Ebuild environment

Description Willard Dawson 2011-05-23 15:57:37 UTC

I'm attempting to convert to hardened / selinux using the instructions at http://www.gentoo.org/proj/en/hardened/selinux/selinux-handbook.xml?part=2&chap=1. At "Code Listing 2.3: Update your Gentoo Linux system," `emerge -uDN world`:

mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c p7_oprofile.c
mpicc -std=gnu99 -march=native -O2 -pipe -pthread   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src -c mpi.c
mpi.c:27:23: error: impl_dummy.: No such file or directory
mpi.c: In function 'p7_oprofile_MPIRecv':
mpi.c:133: warning: passing argument 4 of 'p7_profile_MPIRecv' from incompatible pointer type
../hmmer.h:931: note: expected 'const struct ESL_ALPHABET *' but argument is of type 'struct ESL_ALPHABET **'
make[1]: *** [mpi.o] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/src/impl_dummy'
make: *** [impl_lib] Error 2
emake failed


Reproducible: Always

Steps to Reproduce:
1.emerge -uDN world
2.
3.



See attachments.

Comment 1 Willard Dawson 2011-05-23 15:58:00 UTC

Created attachment 274403 [details]
Emerge info

Comment 2 Willard Dawson 2011-05-23 15:58:17 UTC

Created attachment 274405 [details]
Emerge -pqv

Comment 3 Willard Dawson 2011-05-23 15:58:33 UTC

Created attachment 274407 [details]
Build log

Comment 4 Willard Dawson 2011-05-23 15:58:52 UTC

Created attachment 274409 [details]
Ebuild environment

Comment 5 Willard Dawson 2011-06-21 09:31:43 UTC

I gave up on making hardened profile work as a Virtualbox guest... too many
issues and not enough time on my part.

Comment 6 Willard Dawson 2014-03-29 14:45:19 UTC

OMG this is an old bug.  Close it, please, unless someone has it as a problem still...

Comment 7 Justin Lecher (RETIRED) gentoo-dev

2014-03-30 07:17:50 UTC

cannot reproduce it here.