=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for plink-1.07nb1
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c plink.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c options.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c input.cpp
In file included from plink.cpp:35:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
input.cpp:2162:26: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if ( (!par::plink) && (!par::run_chr==0) )
^ ~~
input.cpp:2162:26: note: add parentheses after the '!' to evaluate the comparison first
if ( (!par::plink) && (!par::run_chr==0) )
^
( )
input.cpp:2162:26: note: add parentheses around left hand side expression to silence this warning
if ( (!par::plink) && (!par::run_chr==0) )
^
( )
input.cpp:2215:26: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
^ ~~
input.cpp:2215:26: note: add parentheses after the '!' to evaluate the comparison first
if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
^
( )
input.cpp:2215:26: note: add parentheses around left hand side expression to silence this warning
if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
^
( )
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c binput.cpp
binput.cpp:146:26: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if ( (!par::plink) && (!par::run_chr==0) )
^ ~~
binput.cpp:146:26: note: add parentheses after the '!' to evaluate the comparison first
if ( (!par::plink) && (!par::run_chr==0) )
^
( )
binput.cpp:146:26: note: add parentheses around left hand side expression to silence this warning
if ( (!par::plink) && (!par::run_chr==0) )
^
( )
binput.cpp:394:26: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if ( (!par::plink) && (!par::run_chr==0) )
^ ~~
binput.cpp:394:26: note: add parentheses after the '!' to evaluate the comparison first
if ( (!par::plink) && (!par::run_chr==0) )
^
( )
binput.cpp:394:26: note: add parentheses around left hand side expression to silence this warning
if ( (!par::plink) && (!par::run_chr==0) )
^
( )
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tinput.cpp
tinput.cpp:208:26: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if ( (!par::plink) && (!par::run_chr==0) )
^ ~~
tinput.cpp:208:26: note: add parentheses after the '!' to evaluate the comparison first
if ( (!par::plink) && (!par::run_chr==0) )
^
( )
tinput.cpp:208:26: note: add parentheses around left hand side expression to silence this warning
if ( (!par::plink) && (!par::run_chr==0) )
^
( )
tinput.cpp:261:26: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
^ ~~
tinput.cpp:261:26: note: add parentheses after the '!' to evaluate the comparison first
if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
^
( )
tinput.cpp:261:26: note: add parentheses around left hand side expression to silence this warning
if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
^
( )
2 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genome.cpp
2 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c helper.cpp
helper.cpp:219:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
helper.cpp:232:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
helper.cpp:244:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
helper.cpp:256:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
helper.cpp:380:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
helper.cpp:393:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
helper.cpp:407:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
2 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c stats.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c filters.cpp
7 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c locus.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c multi.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c crandom.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cluster.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mds.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c output.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c informative.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c assoc.cpp
In file included from assoc.cpp:29:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c epi.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c prephap.cpp
In file included from prephap.cpp:25:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c phase.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c trio.cpp
In file included from phase.cpp:27:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from phase.cpp:28:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from phase.cpp:29:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tdt.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sharing.cpp
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genepi.cpp
genepi.cpp:78:1: warning: non-void function does not return a value [-Wreturn-type]
}
^
genepi.cpp:169:1: warning: non-void function does not return a value [-Wreturn-type]
}
^
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sets.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c perm.cpp
In file included from sets.cpp:24:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
2 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mh.cpp
mh.cpp:1312:1: warning: non-void function does not return a value [-Wreturn-type]
}
^
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genedrop.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c gxe.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c merge.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c hotel.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c multiple.cpp
hotel.cpp:80:7: warning: add explicit braces to avoid dangling else [-Wdangling-else]
else
^
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploCC.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploTDT.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c poo.cpp
In file included from haploCC.cpp:25:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from haploTDT.cpp:25:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c webcheck.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c qfam.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c linear.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c bmerge.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c parse.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c mishap.cpp
In file included from mishap.cpp:20:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c legacy.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c homozyg.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c segment.cpp
homozyg.cpp:2155:20: warning: equality comparison result unused [-Wunused-comparison]
homozygWindows[l] == 0;
~~~~~~~~~~~~~~~~~~^~~~
homozyg.cpp:2155:20: note: use '=' to turn this equality comparison into an assignment
homozygWindows[l] == 0;
^~
=
segment.cpp:2378:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 1 )
~~~~~~~~~~~~~^~~
segment.cpp:2378:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 1 )
^
( )
segment.cpp:2378:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 1 )
^
==
segment.cpp:2380:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 2 )
~~~~~~~~~~~~~^~~
segment.cpp:2380:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 2 )
^
( )
segment.cpp:2380:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 2 )
^
==
segment.cpp:2382:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 3 )
~~~~~~~~~~~~~^~~
segment.cpp:2382:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 3 )
^
( )
segment.cpp:2382:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 3 )
^
==
segment.cpp:2412:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 1 )
~~~~~~~~~~~~~^~~
segment.cpp:2412:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 1 )
^
( )
segment.cpp:2412:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 1 )
^
==
segment.cpp:2414:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 2 )
~~~~~~~~~~~~~^~~
segment.cpp:2414:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 2 )
^
( )
segment.cpp:2414:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 2 )
^
==
segment.cpp:2416:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 3 )
~~~~~~~~~~~~~^~~
segment.cpp:2416:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 3 )
^
( )
segment.cpp:2416:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 3 )
^
==
segment.cpp:2443:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 1 )
~~~~~~~~~~~~~^~~
segment.cpp:2443:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 1 )
^
( )
segment.cpp:2443:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 1 )
^
==
segment.cpp:2445:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 2 )
~~~~~~~~~~~~~^~~
segment.cpp:2445:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 2 )
^
( )
segment.cpp:2445:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 2 )
^
==
segment.cpp:2447:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 3 )
~~~~~~~~~~~~~^~~
segment.cpp:2447:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 3 )
^
( )
segment.cpp:2447:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 3 )
^
==
segment.cpp:2474:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 1 )
~~~~~~~~~~~~~^~~
segment.cpp:2474:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 1 )
^
( )
segment.cpp:2474:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 1 )
^
==
segment.cpp:2476:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 2 )
~~~~~~~~~~~~~^~~
segment.cpp:2476:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 2 )
^
( )
segment.cpp:2476:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 2 )
^
==
segment.cpp:2478:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
else if ( par::cnv_col = 3 )
~~~~~~~~~~~~~^~~
segment.cpp:2478:27: note: place parentheses around the assignment to silence this warning
else if ( par::cnv_col = 3 )
^
( )
segment.cpp:2478:27: note: use '==' to turn this assignment into an equality comparison
else if ( par::cnv_col = 3 )
^
==
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c model.cpp
In file included from model.cpp:17:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
model.cpp:850:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
12 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c logistic.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c glm.cpp
In file included from glm.cpp:25:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
2 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dcdflib.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c elf.cpp
dcdflib.cpp:6025:23: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR");
^
dcdflib.cpp:6401:28: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR");
^
dcdflib.cpp:6782:29: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM");
^
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dfam.cpp
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c fisher.cpp
fisher.cpp:261:17: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(1, "NROW must be less than or equal to LDTABL.");
^
fisher.cpp:267:14: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(2, "All elements of TABLE must be positive.");
^
fisher.cpp:272:17: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(3, "All elements of TABLE are zero.\n"
^
fisher.cpp:448:15: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(1, "NROW must be less than or equal to LDTABL.");
^
fisher.cpp:450:15: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(4, "NCOL must be at least 2");
^
fisher.cpp:501:18: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(2, "All elements of TABLE must be positive.");
^
fisher.cpp:508:17: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(3, "All elements of TABLE are zero.\n"
^
fisher.cpp:559:17: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(5, "The hash table key cannot be computed because "
^
fisher.cpp:750:17: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(6, "LDKEY is too small for this problem.\n"
^
fisher.cpp:1538:17: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(6, "LDKEY is too small for this problem.\n"
^
fisher.cpp:1554:16: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(7, "LDSTP is too small for this problem.\n"
^
fisher.cpp:1596:17: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(7, "LDSTP is too small for this problem.\n"
^
fisher.cpp:2001:18: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(40, "Out of workspace.");
^
fisher.cpp:2078:18: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
prterr(20, "This should never occur.");
^
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c linput.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c sockets.cpp
14 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lookup.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c proxy.cpp
In file included from proxy.cpp:24:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c pdriver.cpp
In file included from pdriver.cpp:18:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haploQTL.cpp
In file included from haploQTL.cpp:25:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
1 warning generated.
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haplohelper.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c haplowindow.cpp
In file included from haplohelper.cpp:25:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from haplowindow.cpp:27:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from haplowindow.cpp:28:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from haplohelper.cpp:27:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from haplowindow.cpp:30:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
In file included from haplohelper.cpp:28:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genogroup.cpp
In file included from genogroup.cpp:24:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from genogroup.cpp:28:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from genogroup.cpp:29:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c nonfounderphasing.cpp
In file included from nonfounderphasing.cpp:27:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from nonfounderphasing.cpp:28:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from nonfounderphasing.cpp:29:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c clumpld.cpp
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c genoerr.cpp
In file included from clumpld.cpp:21:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from genoerr.cpp:27:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from genoerr.cpp:28:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from genoerr.cpp:29:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c em.cpp
In file included from em.cpp:27:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from em.cpp:28:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from em.cpp:29:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c impute.cpp
In file included from impute.cpp:27:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from impute.cpp:28:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from impute.cpp:29:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c metaem.cpp
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c profile.cpp
In file included from metaem.cpp:27:
./genogroup.h:14:9: warning: '__GENOGROUP_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __GENOGROUP_H_
^~~~~~~~~~~~~~
./genogroup.h:15:9: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'?
#define __GENOGROUP_H__
^~~~~~~~~~~~~~~
__GENOGROUP_H_
In file included from metaem.cpp:28:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
In file included from metaem.cpp:29:
./haplowindow.h:13:9: warning: '__HAPWINDOW_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPWINDOW_H_
^~~~~~~~~~~~~~
./haplowindow.h:14:9: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'?
#define __HAPWINDOW_H__
^~~~~~~~~~~~~~~
__HAPWINDOW_H_
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c nlist.cpp
3 warnings generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c whap.cpp
In file included from whap.cpp:25:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c simul.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c gvar.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cnv.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c step.cpp
cnv.cpp:2098:13: warning: equality comparison result unused [-Wunused-comparison]
noCovar == true;
~~~~~~~~^~~~~~~
cnv.cpp:2098:13: note: use '=' to turn this equality comparison into an assignment
noCovar == true;
^~
=
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c greport.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c flip.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c qualscores.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cnvqt.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c cfamily.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c setscreen.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c idhelp.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c tag.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c hapglm.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lookup2.cpp
In file included from hapglm.cpp:25:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c blox.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c zed.cpp
In file included from blox.cpp:23:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c dosage.cpp
In file included from dosage.cpp:23:
./phase.h:14:9: warning: '__HAPPHASE_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef __HAPPHASE_H_
^~~~~~~~~~~~~
./phase.h:15:9: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'?
#define __HAPPHASE_H__
^~~~~~~~~~~~~~
__HAPPHASE_H_
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c annot.cpp
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c metaanal.cpp
metaanal.cpp:203:18: warning: equality comparison result unused [-Wunused-comparison]
par::run_chr == -1;
~~~~~~~~~~~~~^~~~~
metaanal.cpp:203:18: note: use '=' to turn this equality comparison into an assignment
par::run_chr == -1;
^~
=
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c r.cpp
In file included from r.cpp:29:
./Rconnection.h:203:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
{ name=""; fix_content(); }
^
./Rconnection.h:206:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
{ name=""; fix_content(); }
^
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c Rconnection.cpp
In file included from Rconnection.cpp:30:
./Rconnection.h:203:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
{ name=""; fix_content(); }
^
./Rconnection.h:206:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
{ name=""; fix_content(); }
^
Rconnection.cpp:56:20: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */
^
1 warning generated.
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c zfstream.cpp
clang++ -pipe -Os -I/opt/pkg/include -Dfopen64=fopen -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -DWITH_LAPACK -c lapackf.cpp
3 warnings generated.
2 warnings generated.
lapackf.cpp:58:11: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
dgesdd_("A", &m, &n, &A[0] , &m, &S[0], &U[0], &m, &tV[0], &n, &optim_lwork, &lwork, &iwork[0], &info);
^
lapackf.cpp:63:11: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
dgesdd_("A", &m, &n, &A[0] , &m, &S[0], &U[0], &m, &tV[0], &n, &work[0], &lwork, &iwork[0], &info);
^
lapackf.cpp:113:11: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
dsyevx_("V" , // get eigenvalues and eigenvectors
^
lapackf.cpp:114:4: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"I" , // get interval of selected eigenvalues
^
lapackf.cpp:115:4: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"L" , // data stored as upper triangular
^
lapackf.cpp:139:11: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
dsyevx_("V" , // get eigenvalues and eigenvectors
^
lapackf.cpp:140:4: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"I" , // get interval of selected eigenvalues
^
lapackf.cpp:141:4: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"L" , // data stored as upper triangular
^
8 warnings generated.
clang++ -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o lapackf.o -lcrypt -lz -L/opt/pkg/lib -L/opt/pkg/lib -llapack -lblas -lf2c
ld: library 'crypt' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
gmake: *** [Makefile:154: plink] Error 1
*** Error code 2
Stop.
bmake[1]: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/plink
*** Error code 1
Stop.
bmake: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/plink