[ensembl-dev] could not startup EnsemblGenomes

[陈岗]

Hi All

I've updated EnsemblGenomes to v17, however, I suffered some problems that
caused by new perl environment.


/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
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
bam_c184.xs:6:17: error: bam.h: No such file or directory
bam_c184.xs: In function ?.re_filter_depth?.
bam_c184.xs:34: error: ?.am1_t?.undeclared (first use in this function)
bam_c184.xs:34: error: (Each undeclared identifier is reported only once
bam_c184.xs:34: error: for each function it appears in.)
bam_c184.xs:34: error: ?.?.undeclared (first use in this function)
bam_c184.xs:46: error: expected expression before ?.?.token
make: *** [bam_c184.o] Error 1

A problem was encountered while attempting to compile and install your
Inline
C code. The command that failed was:
  make > out.make 2>&1

The build directory was:
/usr/local/ensembl_bacteria/cbuild/build/Bio/EnsEMBL/GlyphSet/bam_c184

To debug the problem, cd to the build directory, and inspect the output
files.

 at /usr/local/ensembl_bacteria/ensembl-draw/modules/Bio/EnsEMBL/GlyphSet/
bam.pm line 388.
...propagated at /usr/local/share/perl/5.10.1/Inline/C.pm line 772.
BEGIN failed--compilation aborted at
/usr/local/ensembl_bacteria/ensembl-draw/modules/Bio/EnsEMBL/GlyphSet/bam.pmline
487.
Compilation failed in require at (eval 274) line 1.
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.

What is the problem? need some help, thanks.

---Gang Chen
TILSI
Taicang Institute For Life Science Information
Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province,
P.R.China
Phone:（+86）512-82782588
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