[covid-19] Autoconf solved but now there is a C issue (Was: Help with r-bioc-rgadem needed)

[Andreas Tille <andreas@an3as.eu>]

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

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