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Hi Gang Chen,<br>
<br>
It looks like you need to install samtools on your system (see
<a class="moz-txt-link-freetext" href="http://samtools.sourceforge.net/">http://samtools.sourceforge.net/</a>)<br>
You should also ensure you have zlib development package installed.<br>
<br>
Cheers,<br>
Nick<br>
<br>
<div class="moz-cite-prefix">On 16/02/2013 10:21, 陈岗 wrote:<br>
</div>
<blockquote
cite="mid:CABjKtWZBHk-EOy7Mwu2NsgXSiBnvuz3OmhaW=uS8N6hC_1jqWg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi All
<div><br>
</div>
<div>I've updated EnsemblGenomes to v17, however, I suffered
some problems that caused by new perl environment.</div>
<div><br>
</div>
<div><br clear="all">
<div>
<div>/usr/bin/perl
/usr/local/share/perl/5.10.1/ExtUtils/xsubpp -typemap
"/usr/share/perl/5.10/ExtUtils/typemap" bam_c184.xs >
bam_c184.xsc && mv bam_c184.xsc bam_c184.c</div>
<div>cc -c -I"/usr/local/ensembl_bacteria/conf"
-I/usr/local/ensembl_bacteria/samtools -D_REENTRANT
-D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.00\"
-DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.10/CORE"
bam_c184.c</div>
<div>bam_c184.xs:6:17: error: bam.h: No such file or
directory</div>
<div>bam_c184.xs: In function ?.re_filter_depth?.</div>
<div>bam_c184.xs:34: error: ?.am1_t?.undeclared (first use
in this function)</div>
<div>bam_c184.xs:34: error: (Each undeclared identifier is
reported only once</div>
<div>bam_c184.xs:34: error: for each function it appears
in.)</div>
<div>bam_c184.xs:34: error: ?.?.undeclared (first use in
this function)</div>
<div>bam_c184.xs:46: error: expected expression before
?.?.token</div>
<div>make: *** [bam_c184.o] Error 1</div>
<div><br>
</div>
<div>A problem was encountered while attempting to compile
and install your Inline</div>
<div>C code. The command that failed was:</div>
<div> make > out.make 2>&1</div>
<div><br>
</div>
<div>The build directory was:</div>
<div>/usr/local/ensembl_bacteria/cbuild/build/Bio/EnsEMBL/GlyphSet/bam_c184</div>
<div><br>
</div>
<div>To debug the problem, cd to the build directory, and
inspect the output files.</div>
<div><br>
</div>
<div> at
/usr/local/ensembl_bacteria/ensembl-draw/modules/Bio/EnsEMBL/GlyphSet/<a
moz-do-not-send="true" href="http://bam.pm">bam.pm</a>
line 388.</div>
<div><span class="" style="white-space:pre"> </span>...propagated
at /usr/local/share/perl/5.10.1/Inline/C.pm line 772.</div>
<div>BEGIN failed--compilation aborted at
/usr/local/ensembl_bacteria/ensembl-draw/modules/Bio/EnsEMBL/GlyphSet/<a
moz-do-not-send="true" href="http://bam.pm">bam.pm</a>
line 487.</div>
<div>Compilation failed in require at (eval 274) line 1.</div>
<div>Using a hash as a reference is deprecated at
/usr/local/ensembl_bacteria/eg-plugins/bacteria/modules/EnsEMBL/Web/Document/HTML/FTPtable.pm
line 55.</div>
</div>
<div><br>
</div>
<div style="">What is the problem? need some help, thanks.</div>
<div><br>
</div>
<div><font face="verdana, sans-serif" size="1">---Gang Chen</font></div>
<div><font face="verdana, sans-serif" size="1">TILSI</font></div>
<div><font face="verdana, sans-serif" size="1"><span
style="background-color:rgb(255,255,255)">Taicang
Institute For Life Science Information</span><br
style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">Address:
A2/162, Renmin South Road, Taicang, 215400, Jiangsu
Province, P.R.China</span><br
style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">Phone:
（+86）512-82782588</span></font></div>
</div>
</div>
<br>
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<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<br>
<br>
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