Hi Jeremy,
On Mon, Apr 06, 2020 at 05:34:23PM +0100, Jeremy Sowden wrote:
> On 2020-04-06, at 17:59:05 +0200, Andreas Tille wrote:
> > dh_autoreconf -O--buildsystem=R
> > autoheader: warning: missing template: HAVE_OPENMP
> > autoheader: Use AC_DEFINE([HAVE_OPENMP], [], [Description])
> > autoreconf: /usr/bin/autoheader failed with exit status: 1
> > dh_autoreconf: error: autoreconf -f -i returned exit code 1
> > make: *** [debian/rules:4: binary] Error 25
> > dpkg-buildpackage: error: debian/rules binary subprocess returned exit
> > status 2
>
> Similar to some of the problems with mpqc yesterday. Patch attached.
Thanks a lot for your patch (commited to Git[1]) which solved the
autoconf issue. Unfortunately there is another issue now:
ecking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... no
checking dispatch/dispatch.h presence... no
checking for dispatch/dispatch.h... no
checking whether OpenMP will work in a package... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
make[1]: Entering directory '/build/r-bioc-rgadem-2.34.1/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2
-fdebug-prefix-map=/build/r-base-j1tBvV/r-base-3.6.3=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:618:7: warning: implicit declaration of function 'DO_APPLY'
[-Wimplicit-function-declaration]
618 | DO_APPLY(populationCalculation(maxSeqLen, numEM, fitness+ii,
| ^~~~~~~~
Gadem_Analysis.c:618:16: error: invalid use of void expression
618 | DO_APPLY(populationCalculation(maxSeqLen, numEM, fitness+ii,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
619 | startPWMfound, minminSites,
maxpFactor[ii],
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
620 | numSeq, numSeqEM, seq, rseq,
seqLen, Iseq,
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
621 | bfreq0, posWeight, weightType,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
622 | pvalueCutoff, emSeqLen,
| ~~~~~~~~~~~~~~~~~~~~~~~
623 | pwm[ii], pwmLen[ii], epwm[ii],
opwm[ii],
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
624 | pwmConsensus[ii], scoreCutoff+ii,
sdyad[ii], ii),
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:168: Gadem_Analysis.o] Error 1
Thanks a lot for your help anyway
Andreas.
[1] https://salsa.debian.org/r-pkg-team/r-bioc-rgadem
--
http://fam-tille.de
