Plink 1.9 fails to build with GCC 6

[daissi]

Hi,
GCC 6 has not been released yet, but it's expected that GCC 6 will become the default compiler for Debian Stretch (next release). As reported by Martin Michlmayr, plink 1.9 fails to build [1] with GCC 6:

sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux
...
make[2]: Entering directory '/<>'
g++ -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c -o plink -llapack -lcblas -latlas -lm -lpthread -ldl -lz
In file included from plink.c:19:0:
plink_common.h:62:19: error: expected unqualified-id before 'long'
#define int64_t long long
^

plink_common.h:62:19: error: expected ';' before 'long'
plink_common.h:62:24: error: declaration does not declare anything [-fpermissive]
#define int64_t long long
^

plink_common.h:61:20: error: expected unqualified-id before 'unsigned'
#define uint64_t unsigned long long
^

plink_common.h:61:20: error: expected ';' before 'unsigned'
plink_common.h:61:34: error: declaration does not declare anything [-fpermissive]
#define uint64_t unsigned long long
^

You can see the full build log here [2].

Best regards,
Dylan

[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811910
[2] https://launchpadlibrarian.net/233688889/buildlog_ubuntu-xenial-amd64.plink1.9_1.90~b3b-150117-1_BUILDING.txt.gz

[chrchang]

I checked in a change which might fix this problem; let me know if the build still fails.

[daissi]

Hi,
The build still fails. GCC6_build_log.txt

Best,
Dylan

[chrchang]

I've made another patch attempt, but I could really use some documentation on what GCC 6 changed w.r.t. uint64_t and int64_t...

[daissi]

I performed others tests for building plink1.9 with GCC6.
Plink1.9 (commit 0475ac) builds successfully with GCC6 if we add the argument "-std=c++98" to the compiler but it fails with "-std=c++11" or "-std=c++14" (which is the default c++ standard since GCC6).
Since your commit 33f794, plink1.9 builds successfully whatever the c++ std defines.

[chrchang]

Okay, good to know that it's a C++11 issue, and that the codebase is now valid gcc C++11.

[daissi]

Hi,
The problem reappears. GCC 6 is now the default builder in Debian unstable and the last plink1.9 (beta 3.40, 16 Aug) fails to build for some architectures (including i386) except *amd64 [1]. Please find bellow the errors and the full log [2]:

...
In file included from plink_rserve.c:6:0:
plink_common.h:115:24: error: expected unqualified-id before 'long'
       #define intptr_t long
                        ^
plink_common.h:115:24: error: expected ';' before 'long'
plink_common.h:115:24: error: declaration does not declare anything [-fpermissive]
plink_common.h:112:25: error: expected unqualified-id before 'unsigned'
       #define uintptr_t unsigned long
                         ^
plink_common.h:112:25: error: expected ';' before 'unsigned'
plink_common.h:112:34: error: declaration does not declare anything [-fpermissive]
       #define uintptr_t unsigned long
...

Best regards,
Dylan

[1] https://buildd.debian.org/status/package.php?p=plink1.9
[2] https://buildd.debian.org/status/fetch.php?pkg=plink1.9&arch=i386&ver=1.90%7Eb3.40-160816-1&stamp=1472371290

[chrchang]

Okay, I've posted an attempt at a fix; let me know if this still fails.

[daissi]

It is now ok for i386 build.

Thanks