[Reproducible-builds] Bug#835074: clustalo: FTBFS: Makefile:448: recipe for target 'hhalign.lo' failed
Chris Lamb
lamby at debian.org
Mon Aug 22 07:20:02 UTC 2016
Source: clustalo
Version: 1.2.2-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org
Dear Maintainer,
clustalo fails to build from source in unstable/amd64:
[..]
^
hhhit-C.h:1697:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname=new(char*[t.n_display])(); // Call Compare only once with irep=1
^
hhhit-C.h:1698:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq =new(char*[t.n_display])(); // Call Compare only once with irep=1
^
hhhit-C.h:1731:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
this->i = new( int[i2+j2+2])();
^
hhhit-C.h:1732:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
this->j = new( int[i2+j2+2])();
^
hhhit-C.h:1733:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
states = new( char[i2+j2+2])();
^
In file included from hhalign.cpp:73:0:
hhhalfalignment-C.h: In constructor 'HalfAlignment::HalfAlignment(int)':
hhhalfalignment-C.h:67:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written
^
hhhalfalignment-C.h:68:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment
^
hhhalfalignment-C.h:69:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k
^
hhhalfalignment-C.h:70:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k]
^
In file included from hhalign.cpp:74:0:
hhfullalignment-C.h: In member function 'void FullAlignment::PrintHHR(FILE*, Hit&)':
hhfullalignment-C.h:360:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
lq = new(short unsigned int[qa->n+2]);
^
hhfullalignment-C.h:361:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
lt = new(short unsigned int[ta->n+2]);
^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
hhhitlist-C.h:1286:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:1289:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:1294:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:1297:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:1304:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:1305:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:1306:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:1307:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:1308:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:1309:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:1310:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:1311:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:1374:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1375:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1378:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1379:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:1454:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1457:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1471:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1472:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
hhhitlist-C.h:1651:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:1654:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:1659:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:1662:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:1669:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:1670:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:1671:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:1672:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:1673:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:1674:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:1675:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:1676:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:1740:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1741:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1744:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1745:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:1822:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1825:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1839:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1840:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
hhhitlist-C.h:2021:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:2024:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:2029:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:2032:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:2039:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:2040:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:2041:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:2042:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:2043:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:2044:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:2045:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:2046:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:2115:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2116:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:2119:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2120:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:2187:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2190:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2204:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:2205:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
hhhitlist-C.h:2386:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:2389:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:2394:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:2397:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:2404:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:2405:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:2406:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:2407:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:2408:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:2409:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:2410:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:2411:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:2473:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2476:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2539:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2542:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::InvertMatrix(double**, double**, int)':
hhhitlist-C.h:2841:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** V = new(double*[N]);
^
hhhitlist-C.h:2842:29: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double* s = new(double[N]);
^
hhhitlist-C.h:2843:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
for (k=0; k<N; k++) V[k] = new(double[N]);
^
hhhitlist-C.h: In member function 'void HitList::SVD(double**, int, double*, double**)':
hhhitlist-C.h:2926:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
rv1=new(double[n]);
^
Makefile:448: recipe for target 'hhalign.lo' failed
make[4]: *** [hhalign.lo] Error 1
make[4]: Leaving directory '/home/lamby/temp/cdt.20160822081140.i6usCoBoEm.db.clustalo/clustalo-1.2.2/src/hhalign'
Makefile:653: recipe for target 'all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory '/home/lamby/temp/cdt.20160822081140.i6usCoBoEm.db.clustalo/clustalo-1.2.2/src'
Makefile:427: recipe for target 'all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory '/home/lamby/temp/cdt.20160822081140.i6usCoBoEm.db.clustalo/clustalo-1.2.2/src'
Makefile:479: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/lamby/temp/cdt.20160822081140.i6usCoBoEm.db.clustalo/clustalo-1.2.2'
dh_auto_build: make -j1 returned exit code 2
debian/rules:10: recipe for target 'build' failed
make: *** [build] Error 2
[..]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` lamby at debian.org / chris-lamb.co.uk
`-
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