### ### Mon Jun 7 08:20:23 EST 2004: ### /usr/pkg/bin/bmake bulk-package for glimmer-2.12 ### Current pkg count: 4 installed packages: digest-20021220 genesplicer-20030403 patch-2.5.4nb2 xpkgwedge-1.10 ### 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: digest-20021220 (pkgtools/digest) 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 /usr/pkg/sbin/pkg_delete -K /var/db/pkg -r xpkgwedge-1.10 pkg_delete: package 'xpkgwedge-1.10' doesn't have a prefix pkg_delete: package 'xpkgwedge-1.10' doesn't have a prefix 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 digest-20021220 (pkgtools/digest) is already installed /usr/pkg/bin/bmake package (glimmer-2.12) ===> Checking for vulnerabilities in glimmer-2.12 => Checksum OK for glimmer212.tar.gz. work -> /work/pkgbuild/biology/glimmer/work ===> Extracting for glimmer-2.12 ===> Required installed package patch>=2.2: patch-2.5.4nb2 found ===> 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 -c adjust.cc -o adjust.o CC -O -c delcher.cc -o delcher.o CC -o ./adjust adjust.o delcher.o -lm CC -O -c anomaly.cc -o anomaly.o CC -O -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 -c build-icm.c -o build-icm.o cc -O -c misc.c -o misc.o cc -o ./build-icm build-icm.o misc.o -lm CC -O -c check.cc -o check.o CC -o ./check check.o delcher.o -lm CC -O -c codon-usage.cc -o codon-usage.o CC -o ./codon-usage codon-usage.o delcher.o gene.o -lm CC -O -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 -c extract.cc -o extract.o CC -o ./extract extract.o delcher.o -lm CC -O -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 -c get-len.cc -o get-len.o CC -o ./get-len get-len.o delcher.o -lm CC -O -c get-putative.cc -o get-putative.o CC -o ./get-putative get-putative.o delcher.o -lm CC -O -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 -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/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 5986 Jun 7 08:22 .broken.html /usr/pkg/bin/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.mirror server hosted at Truenetwork, Russian Federation.