/var/log/portage/sci-biology:mavid-2.0.4:20080708-203009.log

sci-biology:mavid-2.0.4:20080708-203009.log (text/plain), 14.75 KB, created by Marek Miller on 2008-07-08 20:31:09 UTC

>>> Unpacking source...
>>> Unpacking mavid-package-2.0.4.tar.gz to /tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work
>>> Source unpacked.
>>> Compiling source in /tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4 ...
for i in bioc mavid utils; do cd $i; make opt; cd ..; done;
make[1]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/bioc'
make[1]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
make bioc "CPP_OPTIONS =  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions" "LINK_OPTIONS = -lstdc++ -lm"
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/bioc'
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c fasta.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c file.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c alignments.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c seq.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c tree.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c matrices.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c axt.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c common.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c match.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c align.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c sufftree.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c wobble.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c anchor.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c malign.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c constraints.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c refine.cc
g++  -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -c prune.cc
ar r libbioc.a fasta.o file.o alignments.o seq.o tree.o matrices.o axt.o common.o match.o align.o sufftree.o wobble.o anchor.o malign.o constraints.o refine.o prune.o
ar: creating libbioc.a
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/bioc'
make[1]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/bioc'
make[1]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/mavid'
make[1]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
make mavid "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -I../bioc" "LINK_OPTIONS = -lstdc++ -L../bioc -lbioc -lm"
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/mavid'
g++ -I../bioc -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -I../bioc -c mavid.cc 
mavid.cc: In function 'int main(int, char**)':
mavid.cc:164: warning: deprecated conversion from string constant to 'char*'
mavid.cc:165: warning: deprecated conversion from string constant to 'char*'
g++ -I../bioc -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -I../bioc -c output.cc 
g++ -I../bioc -O2 -march=pentium-m -pipe -g -ggdb  -O4 -ffast-math -fexpensive-optimizations -finline-functions -I../bioc -o mavid mavid.o output.o -lstdc++ -L../bioc -lbioc -lm
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/mavid'
make[1]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/mavid'
make[1]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils'
make[1]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
for i in checkfasta cut_alignment extract_seq extract_tree fasta2phylip phylip2fasta project_alignment randtree root_tree tree_dists; do cd $i; make opt; cd ..; done;
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/checkfasta'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align" "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/checkfasta'
c++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c checkfasta.cc 
c++ -I../../bioc -o checkfasta checkfasta.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/checkfasta'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/checkfasta'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/cut_alignment'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions " "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/cut_alignment'
g++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions  -c cut_alignment.cc 
c++ -I../../bioc -o cut_alignment cut_alignment.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/cut_alignment'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/cut_alignment'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_seq'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align" "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_seq'
g++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c extract_seq.cc 
c++ -I../../bioc -o extract_seq extract_seq.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_seq'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_seq'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_tree'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align" "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_tree'
g++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c extract_tree.cc 
c++ -I../../bioc -o extract_tree extract_tree.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_tree'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_tree'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/fasta2phylip'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align" "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/fasta2phylip'
c++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c fasta2phylip.cc 
c++ -I../../bioc -o fasta2phylip fasta2phylip.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/fasta2phylip'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/fasta2phylip'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/phylip2fasta'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align" "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/phylip2fasta'
c++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c phylip2fasta.cc 
c++ -I../../bioc -o phylip2fasta phylip2fasta.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/phylip2fasta'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/phylip2fasta'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/project_alignment'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align" "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/project_alignment'
g++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c project_alignment.cc 
c++ -I../../bioc -o project_alignment project_alignment.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/project_alignment'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/project_alignment'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/randtree'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align" "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/randtree'
g++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c randtree.cc 
g++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c output.cc 
g++ -I../../bioc -o randtree randtree.o output.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/randtree'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/randtree'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/root_tree'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions " "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/root_tree'
g++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions  -c root_tree.cc 
c++ -I../../bioc -o root_tree root_tree.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/root_tree'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/root_tree'
make[2]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/tree_dists'
make main "CPP_OPTIONS = -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align" "LINK_OPTIONS = -lstdc++ -lbioc -L../../bioc"
make[3]: Entering directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/tree_dists'
g++ -I../../bioc -O2 -march=pentium-m -pipe -g -ggdb -O4 -ffast-math -fexpensive-optimizations -finline-functions -Wall -Wpointer-arith -Wcast-align -c tree_dists.cc 
c++ -I../../bioc -o tree_dists tree_dists.o -lstdc++ -lbioc -L../../bioc
make[3]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/tree_dists'
make[2]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/tree_dists'
make[1]: Leaving directory `/tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils'
>>> Source compiled.
>>> Test phase [not enabled]: sci-biology/mavid-2.0.4

>>> Install mavid-2.0.4 into /tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/image/ category sci-biology
>>> Completed installing mavid-2.0.4 into /tmp/portage/tmpdir/portage/sci-biology/mavid-2.0.4/image/

strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/bin/extract_seq
   usr/bin/checkfasta
   usr/bin/fasta2phylip
   usr/bin/cut_alignment
   usr/bin/project_alignment
   usr/bin/phylip2fasta
   usr/bin/extract_tree
   usr/bin/mavid
   usr/bin/randtree
   usr/bin/root_tree
   usr/bin/tree_dists