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Compilling SOAPdenovo2 failed on Debian11/gcc10.2 for r242 as well as from git.
Attached is patch that fixes this issue
commit 56fbd4afe3134a84346353e3bb8b0d5f7415d228 Author: Alois SCHLOEGL <alois.schloegl@ist.ac.at> Date: Mon Oct 10 12:49:50 2022 +0200 fix compilation for Debian11 diff --git a/Makefile b/Makefile index f46b30d..6418443 100644 --- a/Makefile +++ b/Makefile @@ -10,7 +10,7 @@ SUBDIRS = sparsePregraph standardPregraph fusion PROG= SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -LIBPATH= -L./sparsePregraph/inc -L./standardPregraph/inc -L/lib64 -L/usr/lib64 +LIBPATH= -L./sparsePregraph/inc -L./standardPregraph/inc -L/usr/lib LIBS= -pthread -lz -lm EXTRA_FLAGS= diff --git a/fusion/inc/def.h b/fusion/inc/def.h index 9ed70e4..813df4c 100644 --- a/fusion/inc/def.h +++ b/fusion/inc/def.h @@ -18,7 +18,7 @@ #define int2compbase(seq) "TGAC"[seq] #define int_comp(seq) (char)(seq^0x02) //(char)((0x4E>>((seq)<<1))&0x03) -int b_ban; +extern int b_ban; typedef unsigned long long Kmer; diff --git a/sparsePregraph/inc/libbam.a b/sparsePregraph/inc/libbam.a deleted file mode 100644 index d86ebe0..0000000 Binary files a/sparsePregraph/inc/libbam.a and /dev/null differ diff --git a/standardPregraph/contig.c b/standardPregraph/contig.c index 7fd39d5..32f005b 100644 --- a/standardPregraph/contig.c +++ b/standardPregraph/contig.c @@ -27,7 +27,7 @@ #include "extvab.h" static void initenv ( int argc, char **argv ); static void display_contig_usage (); -char shortrdsfile[256], graphfile[256]; +extern char shortrdsfile[256], graphfile[256]; static boolean repeatSolve; //whether solve repeat or not //static boolean keepReadFile = 0; //whether keep tmp selected reads file or not static boolean iter = 0; //whether use multikmer or not diff --git a/standardPregraph/inc/def.h b/standardPregraph/inc/def.h index f5819f0..c714ddc 100644 --- a/standardPregraph/inc/def.h +++ b/standardPregraph/inc/def.h @@ -41,7 +41,7 @@ #define int2compbase(seq) "TGAC"[seq] //int 0123 => base TGAC complement of ACTG #define int_comp(seq) (char)(seq^0x02) //(char)((0x4E>>((seq)<<1))&0x03) -int b_ban; +extern int b_ban; #ifdef MER127 typedef struct kmer diff --git a/standardPregraph/inc/libbam.a b/standardPregraph/inc/libbam.a deleted file mode 100644 index d86ebe0..0000000 Binary files a/standardPregraph/inc/libbam.a and /dev/null differ diff --git a/standardPregraph/read2edge.c b/standardPregraph/read2edge.c index 373eeb4..b93fc76 100644 --- a/standardPregraph/read2edge.c +++ b/standardPregraph/read2edge.c @@ -110,7 +110,7 @@ struct preArc_array_t //arc array struct preArc_array_t arc_arr; -pthread_mutex_t *locks; +extern pthread_mutex_t *locks; /************************************************* Function:
You can also pull the changes from here https://git.ist.ac.at/alois.schloegl/SOAPdenovo2
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Compilling SOAPdenovo2 failed on Debian11/gcc10.2 for r242 as well as from git.
Attached is patch that fixes this issue
You can also pull the changes from here https://git.ist.ac.at/alois.schloegl/SOAPdenovo2
The text was updated successfully, but these errors were encountered: