###
### Fri Jan 23 13:16:25 EST 2004:
### bmake bulk-package for glimmer-2.12
### Current pkg count:  4 installed packages: digest-20021220 genesplicer-20030403 patch-2.5.4nb2 xpkgwedge-1.9
###
BULK> Full rebuild in progress...
BULK> Cleaning package and its depends
===> Cleaning for glimmer-2.12
===> Cleaning for patch-2.5.4nb2
BULK> Removing installed packages which are not needed to build glimmer-2.12
BULK> Keeping BULK_PREREQ: xpkgwedge-1.9 (pkgtools/xpkgwedge)
BULK> glimmer-2.12 requires installed package digest-20021220 (pkgtools/digest
pkgtools/rdigest) to build.
BULK> glimmer-2.12 requires installed package patch-2.5.4nb2 (devel/patch) to build.
/usr/pkg/sbin/pkg_delete -K /var/db/pkg -r genesplicer-20030403
BULK> Installing packages which are required to build glimmer-2.12.
BULK> Required package patch-2.5.4nb2 (devel/patch) is already installed
BULK> Required package xpkgwedge-1.9 (pkgtools/xpkgwedge) is already installed
BULK> Required package digest-20021220 (pkgtools/digest) is already installed
bmake package (glimmer-2.12)
===> Checking for vulnerabilities in glimmer-2.12
=> glimmer212.tar.gz doesn't seem to exist on this system.
=> Attempting to fetch glimmer212.tar.gz from ftp://ftp.tigr.org/pub/software/Glimmer/.
=> [79431 bytes]
=> Checksum OK for glimmer212.tar.gz.
work.sol9 -> /work/pkgbuild/biology/glimmer/work.sol9
===> Extracting for glimmer-2.12
===> Patching for glimmer-2.12
===> Applying pkgsrc patches for glimmer-2.12
===> Overriding tools for glimmer-2.12
===> Buildlinking for glimmer-2.12
===> Configuring for glimmer-2.12
===> Building for glimmer-2.12
CC -O -I/usr/pkg/include -c adjust.cc -o adjust.o
CC -O -I/usr/pkg/include -c delcher.cc -o delcher.o
CC -o ./adjust adjust.o delcher.o -lm
CC -O -I/usr/pkg/include -c anomaly.cc -o anomaly.o
CC -O -I/usr/pkg/include -c gene.cc -o gene.o
"gene.cc", line 505: Warning: String literal converted to char* in initialization.
1 Warning(s) detected.
CC -o ./anomaly anomaly.o delcher.o gene.o -lm
cc -O -I/usr/pkg/include -c build-icm.c -o build-icm.o
cc -O -I/usr/pkg/include -c misc.c -o misc.o
cc -o ./build-icm build-icm.o misc.o -lm
CC -O -I/usr/pkg/include -c check.cc -o check.o
CC -o ./check check.o delcher.o -lm
CC -O -I/usr/pkg/include -c codon-usage.cc -o codon-usage.o
CC -o ./codon-usage codon-usage.o delcher.o gene.o -lm
CC -O -I/usr/pkg/include -c compare-lists.cc -o compare-lists.o
"compare-lists.cc", line 80: Warning (Anachronism): Formal argument 4 of type extern "C" int(*)(const void*,const void*) in call to std::qsort(void*, unsigned, unsigned, extern "C" int(*)(const void*,const void*)) is being passed int(*)(const void*,const void*).
"compare-lists.cc", line 91: Warning (Anachronism): Formal argument 4 of type extern "C" int(*)(const void*,const void*) in call to std::qsort(void*, unsigned, unsigned, extern "C" int(*)(const void*,const void*)) is being passed int(*)(const void*,const void*).
2 Warning(s) detected.
CC -o ./compare-lists compare-lists.o delcher.o -lm
CC -O -I/usr/pkg/include -c extract.cc -o extract.o
CC -o ./extract extract.o delcher.o -lm
CC -O -I/usr/pkg/include -c generate.cc -o generate.o
"generate.cc", line 117: Warning: String literal converted to char* in formal argument s in call to Partial_Window_Prob_Dist(char*, int, Model*).
"generate.cc", line 121: Warning: String literal converted to char* in formal argument s in call to Partial_Window_Prob_Dist(char*, int, Model*).
"generate.cc", line 125: Warning: String literal converted to char* in formal argument s in call to Partial_Window_Prob_Dist(char*, int, Model*).
3 Warning(s) detected.
CC -o ./generate generate.o delcher.o gene.o -lm
CC -O -I/usr/pkg/include -c get-len.cc -o get-len.o
CC -o ./get-len get-len.o delcher.o -lm
CC -O -I/usr/pkg/include -c get-putative.cc -o get-putative.o
CC -o ./get-putative get-putative.o delcher.o -lm
CC -O -I/usr/pkg/include -c glimmer2.cc -o glimmer2.o
"glimmer2.cc", line 795: Warning (Anachronism): Formal argument 4 of type extern "C" int(*)(const void*,const void*) in call to std::qsort(void*, unsigned, unsigned, extern "C" int(*)(const void*,const void*)) is being passed int(*)(const void*,const void*).
"glimmer2.cc", line 815: Warning (Anachronism): Formal argument 4 of type extern "C" int(*)(const void*,const void*) in call to std::qsort(void*, unsigned, unsigned, extern "C" int(*)(const void*,const void*)) is being passed int(*)(const void*,const void*).
"glimmer2.cc", line 832: Warning (Anachronism): Formal argument 4 of type extern "C" int(*)(const void*,const void*) in call to std::qsort(void*, unsigned, unsigned, extern "C" int(*)(const void*,const void*)) is being passed int(*)(const void*,const void*).
"glimmer2.cc", line 2684: Warning (Anachronism): Formal argument 4 of type extern "C" int(*)(const void*,const void*) in call to std::qsort(void*, unsigned, unsigned, extern "C" int(*)(const void*,const void*)) is being passed int(*)(const void*,const void*).
4 Warning(s) detected.
CC -O -I/usr/pkg/include -c rnabin.cc -o rnabin.o
"rnabin.cc", line 29: Error: An integer constant expression is required within the array subscript operator.
"rnabin.cc", line 30: Error: An integer constant expression is required within the array subscript operator.
"rnabin.cc", line 31: Error: An integer constant expression is required within the array subscript operator.
"rnabin.cc", line 32: Error: An integer constant expression is required within the array subscript operator.
"rnabin.cc", line 36: Error: An integer constant expression is required within the array subscript operator.
"rnabin.cc", line 37: Error: An integer constant expression is required within the array subscript operator.
"rnabin.cc", line 170: Error: An integer constant expression is required within the array subscript operator.
"rnabin.cc", line 416: Warning (Anachronism): Formal argument 4 of type extern "C" int(*)(const void*,const void*) in call to std::qsort(void*, unsigned, unsigned, extern "C" int(*)(const void*,const void*)) is being passed int(*)(const void*,const void*).
7 Error(s) and 1 Warning(s) detected.
*** Error code 7

Stop.
bmake: stopped in /work/pkgbuild/biology/glimmer/work.sol9/glimmer2.12
*** Error code 1

Stop.
bmake: stopped in /usr/pkgsrc/biology/glimmer
*** Error code 1

Stop.
bmake: stopped in /usr/pkgsrc/biology/glimmer
BULK> glimmer-2.12 was marked as broken:
-rw-r--r--   1 root     other       6370 Jan 23 13:18 .broken.html
bmake deinstall
===> Deinstalling for glimmer
BULK> Marking all packages which depend upon glimmer-2.12 as broken:
BULK> Build for glimmer-2.12 was not successful, aborting.