Your message dated Tue, 30 Aug 2016 10:19:33 +0000
with message-id <[email protected]>
and subject line Bug#835074: fixed in clustalo 1.2.3-1
has caused the Debian Bug report #835074,
regarding clustalo: FTBFS: Makefile:448: recipe for target 'hhalign.lo' failed
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
835074: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=835074
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: clustalo
Version: 1.2.2-1
Severity: serious
Justification: fails to build from source
User: [email protected]
Usertags: ftbfs
X-Debbugs-Cc: [email protected]
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
`. `'` [email protected] / chris-lamb.co.uk
`-
clustalo.1.2.2-1.unstable.amd64.log.txt.gz
Description: Binary data
--- End Message ---
--- Begin Message ---
Source: clustalo
Source-Version: 1.2.3-1
We believe that the bug you reported is fixed in the latest version of
clustalo, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated clustalo package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 30 Aug 2016 09:46:54 +0200
Source: clustalo
Binary: clustalo libclustalo-dev libclustalo-doc
Architecture: source amd64 all
Version: 1.2.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
clustalo - General purpose multiple sequence alignment program for proteins
libclustalo-dev - library to embed Clustal Omega
libclustalo-doc - API documentation for library to embed Clustal Omega
Closes: 835074 835740
Changes:
clustalo (1.2.3-1) unstable; urgency=medium
.
* New upstream version
* Remove duplicated definitions of log2
Closes: #835074, #835740
Checksums-Sha1:
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Files:
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clustalo_1.2.3.orig.tar.gz
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clustalo-dbgsym_1.2.3-1_amd64.deb
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clustalo_1.2.3-1_amd64.deb
d63e6005f156ba672a3817835f8af0b4 313368 libdevel optional
libclustalo-dev_1.2.3-1_amd64.deb
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libclustalo-doc_1.2.3-1_all.deb
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--- End Message ---
