[BioPython] installing on Mandriva Linux
tim
timmcilveen at talktalk.net
Wed Apr 11 14:15:52 UTC 2007
Hi,
I am getting lots of errors during python setup using biopython setup.py
install. I am running python 2.4.3. on Linux and have mxtextools,
numeric and headers etc. installed. The installation is definately not
working as i get errors when i type some of the test code such as:
from Bio.Seq import Seq
I get a traceback error.
Can anyone help. I'm new to biopython and Linux. I have everything
working fine under Windows.
I get problems from this point onwards in the install, with lots of
Bio/Cluster/clustermodule errors:
Do you want to continue this installation? (Y/n) Y
*** Bio.KDTree *** NOT built by default
The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
which in turn, depends on C++ code that does not compile cleanly on
all platforms. Hence, Bio.KDTree is not built by default.
Would you like to build Bio.KDTree ? (y/N) y
creating build/temp.linux-i686-2.4/Bio/Cluster
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fomit-frame-pointer -march=i586
-mtune=pentiumpro -fasynchronous-unwind-tables -g -fPIC -IBio/Cluster
-I/usr/include/python2.4 -c Bio/Cluster/clustermodule.c -o
build/temp.linux-i686-2.4/Bio/Cluster/clustermodule.o
Bio/Cluster/clustermodule.c:2:33: error: Numeric/arrayobject.h: No such
file or directory
Bio/Cluster/clustermodule.c:20: error: expected declaration specifiers
or ‘...’ before ‘PyArrayObject’
Bio/Cluster/clustermodule.c: In function ‘parse_data’:
Bio/Cluster/clustermodule.c:27: error: ‘array’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:27: error: (Each undeclared identifier is
reported only once
Bio/Cluster/clustermodule.c:27: error: for each function it appears in.)
Bio/Cluster/clustermodule.c:27: error: ‘PyArrayObject’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:27: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:35: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:44: error: ‘PyArray_DOUBLE’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:45: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:84: error: expected ‘)’ before ‘*’ token
Bio/Cluster/clustermodule.c:98: error: expected declaration specifiers
or ‘...’ before ‘PyArrayObject’
Bio/Cluster/clustermodule.c: In function ‘parse_mask’:
Bio/Cluster/clustermodule.c:109: error: ‘array’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:113: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:113: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:121: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:128: error: ‘PyArray_INT’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:130: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:178: error: expected ‘)’ before ‘*’ token
Bio/Cluster/clustermodule.c:191: error: expected declaration specifiers
or ‘...’ before ‘PyArrayObject’
Bio/Cluster/clustermodule.c: In function ‘parse_weight’:
Bio/Cluster/clustermodule.c:197: error: ‘array’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:201: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:201: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:209: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:210: error: ‘PyArray_DOUBLE’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:212: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:255: error: expected ‘)’ before ‘*’ token
Bio/Cluster/clustermodule.c:265: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘*’ token
Bio/Cluster/clustermodule.c:372: error: expected declaration specifiers
or ‘...’ before ‘PyArrayObject’
Bio/Cluster/clustermodule.c: In function ‘parse_clusterid’:
Bio/Cluster/clustermodule.c:383: error: ‘array’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:389: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:389: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:397: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:399: error: ‘PyArray_INT’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:401: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:471: error: expected ‘)’ before ‘*’ token
Bio/Cluster/clustermodule.c:482: error: expected declaration specifiers
or ‘...’ before ‘PyArrayObject’
Bio/Cluster/clustermodule.c: In function ‘free_distances’:
Bio/Cluster/clustermodule.c:485: error: ‘array’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:489: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:489: error: ‘a’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:489: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:515: error: expected declaration specifiers
or ‘...’ before ‘PyArrayObject’
Bio/Cluster/clustermodule.c: In function ‘parse_distance’:
Bio/Cluster/clustermodule.c:522: error: ‘array’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:522: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:522: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:545: error: ‘a’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:545: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:557: error: ‘PyArray_DOUBLE’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:576: warning: assignment makes pointer from
integer without a cast
Bio/Cluster/clustermodule.c:584: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:601: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:628: warning: passing argument 3 of
‘free_distances’ makes integer from pointer without a cast
Bio/Cluster/clustermodule.c:628: error: too many arguments to function
‘free_distances’
Bio/Cluster/clustermodule.c:637: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:640: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:716: error: expected declaration specifiers
or ‘...’ before ‘PyArrayObject’
Bio/Cluster/clustermodule.c: In function ‘create_celldata’:
Bio/Cluster/clustermodule.c:725: error: ‘array’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:725: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:725: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:753: error: expected declaration specifiers
or ‘...’ before ‘PyArrayObject’
Bio/Cluster/clustermodule.c: In function ‘parse_index’:
Bio/Cluster/clustermodule.c:757: error: ‘array’ undeclared (first use in
this function)
Bio/Cluster/clustermodule.c:766: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:766: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:776: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:778: error: ‘PyArray_INT’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:780: warning: assignment makes pointer from
integer without a cast
Bio/Cluster/clustermodule.c:787: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:803: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:818: error: expected ‘)’ before ‘*’ token
Bio/Cluster/clustermodule.c: In function ‘PyTree_cut’:
Bio/Cluster/clustermodule.c:1165: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:1165: error: ‘aCLUSTERID’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:1165: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:1181: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:1187: error: ‘clusterid’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:1197: warning: return makes pointer from
integer without a cast
Bio/Cluster/clustermodule.c: In function ‘py_kcluster’:
Bio/Cluster/clustermodule.c:1312: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:1312: error: ‘aDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1315: error: ‘aMASK’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1318: error: ‘aWEIGHT’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1325: error: ‘aCLUSTERID’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:1379: error: too many arguments to function
‘parse_data’
Bio/Cluster/clustermodule.c:1384: error: too many arguments to function
‘parse_mask’
Bio/Cluster/clustermodule.c:1416: error: too many arguments to function
‘parse_weight’
Bio/Cluster/clustermodule.c: In function ‘py_kmedoids’:
Bio/Cluster/clustermodule.c:1501: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:1501: error: ‘aDISTANCES’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:1504: error: ‘aCLUSTERID’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:1533: error: too many arguments to function
‘parse_distance’
Bio/Cluster/clustermodule.c:1538: warning: passing argument 3 of
‘free_distances’ makes integer from pointer without a cast
Bio/Cluster/clustermodule.c:1538: error: too many arguments to function
‘free_distances’
Bio/Cluster/clustermodule.c:1545: warning: passing argument 3 of
‘free_distances’ makes integer from pointer without a cast
Bio/Cluster/clustermodule.c:1545: error: too many arguments to function
‘free_distances’
Bio/Cluster/clustermodule.c:1552: warning: passing argument 3 of
‘free_distances’ makes integer from pointer without a cast
Bio/Cluster/clustermodule.c:1552: error: too many arguments to function
‘free_distances’
Bio/Cluster/clustermodule.c:1565: warning: passing argument 3 of
‘free_distances’ makes integer from pointer without a cast
Bio/Cluster/clustermodule.c:1565: error: too many arguments to function
‘free_distances’
Bio/Cluster/clustermodule.c: In function ‘py_treecluster’:
Bio/Cluster/clustermodule.c:1706: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:1706: error: ‘aDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1707: error: ‘aMASK’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1708: error: ‘aWEIGHT’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1726: error: too many arguments to function
‘parse_data’
Bio/Cluster/clustermodule.c:1733: error: too many arguments to function
‘parse_mask’
Bio/Cluster/clustermodule.c:1739: error: too many arguments to function
‘parse_weight’
Bio/Cluster/clustermodule.c:1762: error: ‘aDISTANCEMATRIX’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:1770: error: too many arguments to function
‘parse_distance’
Bio/Cluster/clustermodule.c:1783: warning: passing argument 3 of
‘free_distances’ makes integer from pointer without a cast
Bio/Cluster/clustermodule.c:1783: error: too many arguments to function
‘free_distances’
Bio/Cluster/clustermodule.c: In function ‘py_somcluster’:
Bio/Cluster/clustermodule.c:1849: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:1849: error: ‘aDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1852: error: ‘aMASK’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1855: error: ‘aWEIGHT’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:1863: error: ‘aCELLDATA’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:1865: error: ‘aCLUSTERID’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:1922: error: too many arguments to function
‘parse_data’
Bio/Cluster/clustermodule.c:1929: error: too many arguments to function
‘parse_mask’
Bio/Cluster/clustermodule.c:1935: error: too many arguments to function
‘parse_weight’
Bio/Cluster/clustermodule.c:1944: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:1954: error: too many arguments to function
‘create_celldata’
Bio/Cluster/clustermodule.c: In function ‘py_median’:
Bio/Cluster/clustermodule.c:1996: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:1996: error: ‘aDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2007: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:2015: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:2018: error: ‘PyArray_DOUBLE’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:2019: warning: initialization makes pointer
from integer without a cast
Bio/Cluster/clustermodule.c:2021: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:2037: warning: initialization makes pointer
from integer without a cast
Bio/Cluster/clustermodule.c:2043: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: In function ‘py_mean’:
Bio/Cluster/clustermodule.c:2062: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:2062: error: ‘aDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2073: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:2081: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:2084: error: ‘PyArray_DOUBLE’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:2085: warning: initialization makes pointer
from integer without a cast
Bio/Cluster/clustermodule.c:2087: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:2103: warning: initialization makes pointer
from integer without a cast
Bio/Cluster/clustermodule.c:2109: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: In function ‘py_clusterdistance’:
Bio/Cluster/clustermodule.c:2167: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:2167: error: ‘aDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2170: error: ‘aMASK’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2173: error: ‘aWEIGHT’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2181: error: ‘aINDEX1’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2184: error: ‘aINDEX2’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2216: error: too many arguments to function
‘parse_data’
Bio/Cluster/clustermodule.c:2222: error: too many arguments to function
‘parse_mask’
Bio/Cluster/clustermodule.c:2228: error: too many arguments to function
‘parse_weight’
Bio/Cluster/clustermodule.c:2235: error: too many arguments to function
‘parse_index’
Bio/Cluster/clustermodule.c:2242: error: too many arguments to function
‘parse_index’
Bio/Cluster/clustermodule.c: In function ‘py_clustercentroids’:
Bio/Cluster/clustermodule.c:2312: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:2312: error: ‘aDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2315: error: ‘aMASK’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2318: error: ‘aCLUSTERID’ undeclared (first
use in this function)
Bio/Cluster/clustermodule.c:2322: error: ‘aCDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2324: error: ‘aCMASK’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2350: error: too many arguments to function
‘parse_data’
Bio/Cluster/clustermodule.c:2356: error: too many arguments to function
‘parse_mask’
Bio/Cluster/clustermodule.c:2362: warning: passing argument 3 of
‘parse_clusterid’ makes pointer from integer without a cast
Bio/Cluster/clustermodule.c:2362: error: too many arguments to function
‘parse_clusterid’
Bio/Cluster/clustermodule.c:2371: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c:2384: error: expected expression before ‘)’
token
Bio/Cluster/clustermodule.c: In function ‘py_distancematrix’:
Bio/Cluster/clustermodule.c:2466: error: ‘PyArrayObject’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:2466: error: ‘aDATA’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2469: error: ‘aMASK’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2472: error: ‘aWEIGHT’ undeclared (first use
in this function)
Bio/Cluster/clustermodule.c:2507: error: too many arguments to function
‘parse_data’
Bio/Cluster/clustermodule.c:2514: error: too many arguments to function
‘parse_mask’
Bio/Cluster/clustermodule.c:2520: error: too many arguments to function
‘parse_weight’
Bio/Cluster/clustermodule.c:2542: error: ‘PyArray_DOUBLE’ undeclared
(first use in this function)
Bio/Cluster/clustermodule.c:2542: warning: initialization makes pointer
from integer without a cast
Bio/Cluster/clustermodule.c:2548: error: expected expression before ‘)’
token
error: command 'gcc' failed with exit status 1
[tim at localhost biopython-1.43]$
[tim at localhost biopython-1.43]$
Thanks,
Tim
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