On 2020-04-06, at 20:32:12 +0200, Andreas Tille wrote: > 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 Patch attached. J.
From d3b5c1358bcf8463719c0175d759f74819e74f8e Mon Sep 17 00:00:00 2001
From: Jeremy Sowden <jeremy@azazel.net>
Date: Mon, 6 Apr 2020 20:41:54 +0100
Subject: [PATCH] The definition of DO_APPLY in src/config.h.in is clobbered by
autoheader, so add it in Gadem_Analysis.c where it is used.
---
src/Gadem_Analysis.c | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/src/Gadem_Analysis.c b/src/Gadem_Analysis.c
index a604afeb0479..0e868b56918a 100755
--- a/src/Gadem_Analysis.c
+++ b/src/Gadem_Analysis.c
@@ -25,6 +25,32 @@
#include "config.h"
+#ifdef HAVE_DISPATCH_DISPATCH_H
+ #include <dispatch/dispatch.h>
+ #define DO_APPLY(task, n_times, counter_name) \
+ R_CheckUserInterrupt(); \
+ dispatch_apply(n_times, \
+ dispatch_get_global_queue(DISPATCH_QUEUE_PRIORITY_DEFAULT, 0), \
+ ^(size_t counter_name) { task; });
+
+#else // not HAVE_DISPATCH_DISPATCH_H
+ #ifdef HAVE_OPENMP
+ #include <omp.h>
+ #define DO_APPLY(task, n_times, counter_name) \
+ R_CheckUserInterrupt(); \
+ _Pragma("omp parallel for") \
+ for (int counter_name = 0; counter_name < n_times; ++counter_name) { \
+ task; \
+ }
+ #else // not HAVE_OPENMP
+ #define DO_APPLY(task, n_times, counter_name) \
+ for (int counter_name = 0; counter_name < n_times; ++counter_name) { \
+ R_CheckUserInterrupt(); \
+ task; \
+ }
+ #endif // HAVE_OPENMP
+#endif // HAVE_DISPATCH_DISPATCH_H
+
/*---------------------------------------------------------------------------
// v1.3.1: last modifications 5/14/2011
// added user-input background model
--
2.25.1
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