Need to set old C++ standard on recent Debian platforms.

[charles-plessy]

Hello,

When compiling SlideSort on a recent Debian (9.1/Stretch) that uses GCC 6.3.0, I get the following error:

mstree.cpp:228:11: error: no match for ‘operator==’ (operand types are ‘std::ofstream {aka std::basic_ofstream<char>}’ and ‘long int’)
   if(dFile==NULL){
           ^

As a quick workaround, I could bypass it by using GCC's option -std=c++98 as follows:

diff --git a/SS_v2/Makefile.gcc b/SS_v2/Makefile.gcc
index 3bb22d6..b1b8546 100644
--- a/SS_v2/Makefile.gcc
+++ b/SS_v2/Makefile.gcc
@@ -10,7 +10,7 @@ objs = blockutil.o pssExecutor.o parallelslidesort.o pmscls.o box.o seq.o comlin
 CXX = g++
 AR = ar
 
-CFLAGS =  -O3 -fPIC -fopenmp
+CFLAGS =  -O3 -fPIC -fopenmp -std=c++98
 
 .SUFFIXES: .cpp .o
 
diff --git a/mst_v2/Makefile.gcc b/mst_v2/Makefile.gcc
index d38f34d..882a6d8 100644
--- a/mst_v2/Makefile.gcc
+++ b/mst_v2/Makefile.gcc
@@ -7,7 +7,7 @@ objs = tree.o mstree.o blockutil.o pssExecutor.o parallelslidesort.o box.o seq.o
 CXX = g++
 AR = ar
 
-CFLAGS = -O3 -fPIC -Wall -L./ -I./ -fopenmp
+CFLAGS = -O3 -fPIC -Wall -L./ -I./ -fopenmp -std=c++98
 
 .SUFFIXES: .cpp .o
 

Have a nice day,

--
Charles Plessy, RIKEN Yokohama, Japan.

[mcfrith]

I think this is the long-term fix:

if(!dFile){

[charles-plessy]

Thanks Martin,

with the following patch, the code compiles as well as with the previous patch.

diff --git a/mst_v1/mstree.cpp b/mst_v1/mstree.cpp
index d4b3254..7b2f6a8 100644
--- a/mst_v1/mstree.cpp
+++ b/mst_v1/mstree.cpp
@@ -217,7 +217,7 @@ Contact: shimizu-kana@aist.go.jp \n";
 
        if(isPairOut || isAlnOut){
                pFile.open(pairFname);
-               if(pFile==NULL){
+               if(!pFile){
                        cerr<<"ERROR: output file for alignment is not found\nPlease use -F filename\n";
                        exit(1);
                }
@@ -225,7 +225,7 @@ Contact: shimizu-kana@aist.go.jp \n";
 
        if(isDegreeOut){
                dFile.open(degreeFname);
-               if(dFile==NULL){
+               if(!dFile){
                        cerr<<"ERROR: output file for degree is not found\nPlease use -R filename\n";
                        exit(1);
                }

Unfortunately, in both cases the ssmt_v2 program segfaults in some corner case situations, for instance with the following data and commands:

cat > test.fa << _END_
>seq1:umi=TTAACTGG
TTAACTGGCATCCAGAACGAGCTATCGA
>seq2:umi=AGGTTATA
AGGTTATACATCCAGAACGAGCTATCGA
>seq3:umi=TGAGGTAA
TGAGGTAACATCCAGAACGAGCTATCGA
>seq4:umi=TTAAGACA
TTAAGACACATCCAGAACGAGCTATCGA
_END_
./mst_v2/ssmst_v2 -u -d 0 -g 0.5 -Z -U -i test.fa

The segmentation fault does not happen on a computer using GCC version 4.9.4, where the code could compile without patch.

Edit (25/12/2017): corrected the patch, which contained dFile==NULL, which compiled but was wrong. See StackOverflow for an explanation on Martin's suggestion to use if(!dFile).

[charles-plessy]

Here the output of valgrind, after patching the source as above plus as follows, and running the following test command:

valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes ./mst_v2/ssmst_v2 -u -d 0 -g 0.5 -Z -U -i test.fa

diff --git a/SS_v2/Makefile.gcc b/SS_v2/Makefile.gcc
index 3bb22d6..23068fd 100644
--- a/SS_v2/Makefile.gcc
+++ b/SS_v2/Makefile.gcc
@@ -10,7 +10,7 @@ objs = blockutil.o pssExecutor.o parallelslidesort.o pmscls.o box.o seq.o comlin
 CXX = g++
 AR = ar
 
-CFLAGS =  -O3 -fPIC -fopenmp
+CFLAGS =  -g -O0 -fPIC -fopenmp
 
 .SUFFIXES: .cpp .o
 
diff --git a/mst_v2/Makefile.gcc b/mst_v2/Makefile.gcc
index d38f34d..e75249d 100644
--- a/mst_v2/Makefile.gcc
+++ b/mst_v2/Makefile.gcc
@@ -7,7 +7,7 @@ objs = tree.o mstree.o blockutil.o pssExecutor.o parallelslidesort.o box.o seq.o
 CXX = g++
 AR = ar
 
-CFLAGS = -O3 -fPIC -Wall -L./ -I./ -fopenmp
+CFLAGS = -g -O0 -fPIC -Wall -L./ -I./ -fopenmp
 
 .SUFFIXES: .cpp .o
 

[charles-plessy]

Good news, no segfault after compiling with gcc 8.3.0!