XG does not compile with gcc7.1+matching glibc

[JervenBolleman]

As reported in gitter

deps/xg/src/xg.cpp: In member function ‘int xg::XG::min_distance_in_paths(int64_t, bool, size_t, int64_t, bool, size_t) const’:
deps/xg/src/xg.cpp:2348:22: error: call of overloaded ‘abs(long unsigned int&)’ is ambiguous
             if (abs(o) < abs(min_dist)) {

[cartoonist]

I also came here to report this. :)

Actually the type of o is size_t (a.k.a unsigned long int) which is unsigned and abs(o) does not make any sense. There are two ways for workaround:

1. Remove abs function call and replace it by simply o.

diff --git a/src/xg.cpp b/src/xg.cpp
index de702bf..78a6a32 100644
--- a/src/xg.cpp
+++ b/src/xg.cpp
@@ -2450,7 +2450,7 @@ int XG::min_distance_in_paths(int64_t id1, bool is_rev1, size_t offset1,
     int min_dist = std::numeric_limits<int>::max();
     for (auto& c : dist) {
         for (auto& o : c.second) {
-            if (abs(o) < abs(min_dist)) {
+            if (o < abs(min_dist)) {
                 min_dist = o;
             }
         }

2. or cast o to type std::intmax_t which is the largest possible integer type:

diff --git a/src/xg.cpp b/src/xg.cpp
index de702bf..78a6a32 100644
--- a/src/xg.cpp
+++ b/src/xg.cpp
@@ -2450,7 +2450,7 @@ int XG::min_distance_in_paths(int64_t id1, bool is_rev1, size_t offset1,
     int min_dist = std::numeric_limits<int>::max();
     for (auto& c : dist) {
         for (auto& o : c.second) {
-            if (abs(o) < abs(min_dist)) {
+            if (abs(static_cast<std::intmax_t>(o)) < abs(min_dist)) {
                 min_dist = o;
             }
         }

The latter ensures that the expression is always non-negative even if the type of o would change to a signed type in future.

[glennhickey]

This has been fixed. But please note that xg now lives in vg, so the current version is here:

https://github.com/vgteam/vg/blob/master/src/xg.cpp

On Tue, Sep 26, 2017 at 9:40 AM, Ali Ghaffaari [email protected] wrote:

I came here to report this. Actually the type of o is size_t (a.k.a unsigned long int) which is unsigned and abs(o) does not make any sense. There are two ways for workaround:

Make abs function call and replace it by simply o:

         if (o < abs(min_dist)) {

or cast it to std::intmax_t which is the largest possible integer type:

         if (abs(static_cast<std::intmax_t>(o)) < abs(min_dist)) {

The latter ensures the expression is always non-negative even if the type of o would change to a signed type in future.

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[cartoonist]

I didn't know that. Thanks for mentioning. How about 'libxg'?

[glennhickey]

Gone

On Tue, Sep 26, 2017 at 10:01 AM, Ali Ghaffaari [email protected] wrote:

I didn't know that. Thanks for mentioning. How about 'libxg'?

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