Bioperl-guts: Installing New PreRelease 0.05

Greg Colello gcolello@tdl.com
Mon, 22 Mar 1999 12:02:16 -0800


Hi!

I am getting (apparently harmless) error and warning messages during
install (some of these were in 0.04 also). The directions say to ignore
some of these, but it's really unnerving to get any error messages in an
install program.

I am installing in my own account using:

perl Makefile.PL
PREFIX=/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre

I got the following message:

Checking if your kit is complete...
Warning: the following files are missing in your kit:
        Compile/SW/libs/cdna.c
        Compile/SW/libs/cdna.h
        Compile/SW/libs/cdnadb.c
        Compile/SW/libs/cdnadb.h
        Compile/SW/libs/codonmapper.c
        Compile/SW/libs/codonmapper.h
        Compile/SW/libs/codonmatrix.c
        Compile/SW/libs/codonmatrix.h
        Compile/SW/libs/embl.c
        Compile/SW/libs/embl.h
        Compile/SW/libs/gene.c
        Compile/SW/libs/gene.h
        Compile/SW/libs/genomic.c
        Compile/SW/libs/genomic.h
        Compile/SW/libs/genomicdb.c
        Compile/SW/libs/genomicdb.h
        Compile/SW/libs/genomicregion.c
        Compile/SW/libs/genomicregion.h
        Compile/SW/libs/transcript.c
        Compile/SW/libs/transcript.h
        Compile/SW/libs/translation.c
        Compile/SW/libs/translation.h
Please inform the author.
Writing Makefile for Bio

-------------------------------------

I also get some errors with make (some of these were in 0.04 also):

make

[cut....]

Manifying ./blib/man3/Bio::Tools::Blast.3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 119 of
Bio/Tools/Blast.pm: head3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 125 of
Bio/Tools/Blast.pm: head3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 128 of
Bio/Tools/Blast.pm: head3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 136 of
Bio/Tools/Blast.pm: head3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 139 of
Bio/Tools/Blast.pm: head3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 148 of
Bio/Tools/Blast.pm: head3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 152 of
Bio/Tools/Blast.pm: head3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 155 of
Bio/Tools/Blast.pm: head3
Manifying ./blib/man3/Bio::SeqIO::Raw.3
Manifying ./blib/man3/Bio::Tools::Blast::Sbjct.3
Manifying ./blib/man3/Bio::Parse.3
/usr/bin/pod2man: bad option in paragraph 38 of Bio/Parse.pm: ``-c''
should be [CB]<-c>
Manifying ./blib/man3/Bio::Index::Abstract.3
Manifying ./blib/man3/Bio::Root::Err.3
Manifying ./blib/man3/Bio::Tools::Blast::Run::Webblast.3
Manifying ./blib/man3/Bio::UnivAln.3
/usr/bin/pod2man: bad option in paragraph 198 of Bio/UnivAln.pm:
``scalar($aln2->I<var_sites()'' should be
[LCI]<scalar($aln2->I<var_sites()>
Manifying ./blib/man3/Bio::SeqIO::GCG.3
Manifying ./blib/man3/Bio::SeqIO.3
Manifying ./blib/man3/Bio::Tools::AlignFactory.3
Manifying ./blib/man3/Bio::Tools::SeqAnal.3
Manifying ./blib/man3/Bio::Root::Vector.3
Manifying ./blib/man3/Bio::Tools::SeqPattern.3
Manifying ./blib/man3/Bio::Root::Xref.3
Manifying ./blib/man3/bioback.3
/usr/bin/pod2man: Unrecognized pod directive in paragraph 16 of
bioback.pod: end

[cut...]

--------------------------

What about these hash messages (also in 0.04)?

make test

PERL_DL_NONLAZY=1 /usr/local/bin/perl -I./blib/arch -I./blib/lib
-I/usr/lib/perl5/i386-linux/5.00401 -I/usr/lib/perl5 -e 'use
Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t

t/Blast.............Odd number of elements in hash list at
blib/lib/Bio/Root/Object.pm line 515.
ok
t/DB................ok
t/Fasta.............Odd number of elements in hash list at
blib/lib/Bio/Root/Object.pm line 515.
ok
t/HSP...............ok
t/HTML..............ok
t/Index.............ok
t/RestrictionEnzyme.ok
t/Sbjct.............ok
t/Seq...............ok
t/SeqAnal...........ok
t/SeqIO.............ok
t/Sigcleave.........ok
t/SimpleAlign.......ok
t/UnivAln...........ok
t/WWW...............ok
All tests successful.
Files=15,  Tests=80, 13 secs ( 6.64 cusr  0.66 csys =  7.30 cpu)

The same hash message also appears during execution of Blast parsing:

[gcolello@ls2 blast]$ perl parse_blast.pl out/blastx.2

Parsing Blast report file(s).
Odd number of elements in hash list at /hosts/kinetic/dust/users/gcolel
.
Query: YAL011W, Length = 1917
0 total hits with significance <= 1.0e+03

------------------------------------


Greg Colello
Science Business Software


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