[Bioperl-l] error during installation

Du, Peng du at ibio.jp
Fri Jun 22 00:25:46 EDT 2012


Hi everybody,

I tried to install this on another machine and also failed. The error
message which  are the same for the two machines and the cpu
information for them are attached below.
So, could anybody help me figure out where this is wrong or, if there
is any  chance that the developers can do something with it?

Thank you very much.

Machine 0:
CPU info.
processor	: 0
vendor_id	: AuthenticAMD
cpu family	: 15
model		: 33
model name	: Dual Core AMD Opteron(tm) Processor 280
stepping	: 2
microcode	: 0x4d
cpu MHz		: 2405.233
cache size	: 1024 KB
physical id	: 0
siblings	: 2
core id		: 0
cpu cores	: 2
apicid		: 0
initial apicid	: 0
fpu		: yes
fpu_exception	: yes
cpuid level	: 1
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt lm
3dnowext 3dnow rep_good nopl pni lahf_lm cmp_legacy
bogomips	: 4810.46
TLB size	: 1024 4K pages
clflush size	: 64
cache_alignment	: 64
address sizes	: 40 bits physical, 48 bits virtual
power management: ts fid vid ttp

Machine 1
CPU info.

processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 26
model name      : Intel(R) Core(TM) i7 CPU         920  @ 2.67GHz
stepping        : 5
cpu MHz         : 1600.000
cache size      : 8192 KB
physical id     : 0
siblings        : 8
core id         : 0
cpu cores       : 4
apicid          : 0
initial apicid  : 0
fpu             : yes
fpu_exception   : yes
cpuid level     : 11
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology
nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3
cx16 xtpr pdcm sse4_1 sse4_2 popcnt lahf_lm ida tpr_shadow vnmi
flexpriority ept vpid
bogomips        : 5345.11
clflush size    : 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual
power management:

Error message for both
sudo make test
make[1]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \
	cd libs && make CC=cc libsw.a -e
make[2]: Entering directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \
	cd libs && make CC=cc libsw.a -e
make[2]: Entering directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so
rm: cannot remove `../blib/arch/auto/Bio/Ext/Align/Align.so': Permission denied
make[1]: *** [../blib/arch/auto/Bio/Ext/Align/Align.so] Error 1
make[1]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align'
make: *** [subdirs] Error 2
ibio at ibio-H8DAR-T:~/Downloads/bioperl-ext-1.4/Bio/Ext$ sudo make test
make[1]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \
	cd libs && make CC=cc libsw.a -e
make[2]: Entering directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \
	cd libs && make CC=cc libsw.a -e
make[2]: Entering directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so
cc  -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o  -o
../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a'	\
	   -lm  	\
	
chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so
make[1]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align'
make[1]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \
	cd libs && make CC=cc libsw.a -e
make[2]: Entering directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \
	cd libs && make CC=cc libsw.a -e
make[2]: Entering directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs'
rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so
cc  -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o  -o
../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a'	\
	   -lm  	\
	
chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..2
Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module
Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined
symbol: bp_sw_show_simple_PackAln at /usr/lib/perl/5.14/DynaLoader.pm
line 184.
 at test.pl line 10.
Compilation failed in require at test.pl line 10.
BEGIN failed--compilation aborted at test.pl line 10.
not ok 1
make[1]: *** [test_dynamic] Error 2
make[1]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align'
make: *** [subdirs-test] Error 2


	


Thanks again.

Peng

On Wed, Jun 20, 2012 at 11:20 AM, Peng Du <du at ibio.jp> wrote:
>
> Thanks for all your kind replies, based on my current knowledge, it might be worth making dpAlign at work even in the absence of BioPerl-ext package.
> Thank you.
>
> Peng
>
> On 2012/06/20, at 2:38, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
>
>> On Jun 19, 2012, at 12:21 PM, Leon Timmermans wrote:
>>
>>> On Tue, Jun 19, 2012 at 5:25 PM, Du, Peng <du at ibio.jp> wrote:
>>>> As to the Clustalw problem, it turned out that, I didn't install it in
>>>> the first place, I am very sorry for the stupid mistake. It is alright
>>>> now. But, as to dpAlign, I compared the alignment of non coding
>>>> regions of two species with dpAlign (in an Intel x86 but much slower
>>>> machine where dpAlign is good) and Clustalw respectively and checked
>>>> the output, I found that, each with default parameters, the alignments
>>>> by dpAlign were better than that by Clustalw, and there was a
>>>> tremendous difference in the outputs in terms of A<=>G, C<=>T, AG<=>CT
>>>> substitutional rate and divergence by Tamura-Nei Model between the two
>>>> alignments. The values are much smaller with dpAlign.  Since I am a
>>>> newbie, I don't quite understand why there was such a difference. Is
>>>> it might because of the Clustalw is designed for multiple alignment or
>>>> the default parameters are not appropriate?
>>>>
>>>> I am now investigating other tools available in the main distribution
>>>> of  BioPerl, but I have no idea whether there is a good substitution
>>>> of dpAlign in context of non coding region alignment.
>>>
>>> ClustalW uses a heuristic algorithm, it cannot produce a solution that
>>> is guaranteed to be optimal. dpAlign uses the Miller-Myers algorithm
>>> (a variant on Needleman-Wunch), that does make such guarantees. It
>>> should be slower but may produce a better alignment.
>>>
>>> Leon
>>
>> Agreed.  I think it would be worth pulling this out and releasing it on it's own, maybe including Bio::Tools::dpAlign with it as well.  The key problem is one of maintenance; this code was pretty much written by one developer.  I'll see if I can track Yee Man (the developer) down.
>>
>> chris



-- 

Peng Du
Graduate School of Information Science and Technology, Hokkaido University
Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
Email: du at ibio.jp Tel: +81 80 3268 9713



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