[BioC] installing genefilter
Denise Mauldin
dmauldin at systemsbiology.org
Wed Nov 4 02:57:12 CET 2009
Hello,
I'm trying to install the genefilter package. It's not compiling
because it can't find the c++config.h (among others). These are
present in an architecture specific subdirectory from where it's
looking. If I run the compile command manually it works, but I can't
figure out how to provide the include path to the R CMD INSTALL.
ie: R CMD INSTALL runs
g++ -I/tools/lib64/R/include -I/usr/local/include -fpic -g -O2 -c
half_range_mode.cpp -o half_range_mode.o
which fails.
The following command works:
g++ -I/tools/lib64/R/include -I/usr/local/include
-I/usr/include/c++/3.2.3/i386-redhat-linux -fpic -g -O2 -c
half_range_mode.cpp -o half_range_mode.o
# R
> sessionInfo()
R version 2.9.1 (2009-06-26)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
# R CMD INSTALL --version
R add-on package installer: 2.9.1 (r48839)
Copyright (C) 2000-2009 The R Core Development Team.
This is free software; see the GNU General Public License version 2
or later for copying conditions. There is NO warranty.
Thanks,
Denise
Full install error:
# R CMD INSTALL genefilter
* Installing to library /tools/lib64/R/library
* Installing *source* package genefilter ...
** libs
g++ -I/jdrf_tools/lib64/R/include -I/usr/local/include -fpic -g
-O2 -c half_range_mode.cpp -o half_range_mode.o
In file included from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/stl_algobase.h:64:28: bits/c++config.h: No
such file or directory
In file included from /usr/include/c++/3.2.3/bits/stl_algobase.h:67,
from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/cstdlib:49:28: bits/c++config.h: No such file
or directory
In file included from /usr/include/c++/3.2.3/bits/stl_algobase.h:70,
from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/iosfwd:44:28: bits/c++config.h: No such file or directory
In file included from /usr/include/c++/3.2.3/iosfwd:45,
from /usr/include/c++/3.2.3/bits/stl_algobase.h:70,
from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/stringfwd.h:44:28: bits/c++config.h: No
such file or directory
In file included from /usr/include/c++/3.2.3/iosfwd:46,
from /usr/include/c++/3.2.3/bits/stl_algobase.h:70,
from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/fpos.h:44:24: bits/c++io.h: No such file
or directory
In file included from /usr/include/c++/3.2.3/bits/fpos.h:45,
from /usr/include/c++/3.2.3/iosfwd:46,
from /usr/include/c++/3.2.3/bits/stl_algobase.h:70,
from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/cwchar:49:28: bits/c++config.h: No such file or directory
In file included from /usr/include/c++/3.2.3/iosfwd:46,
from /usr/include/c++/3.2.3/bits/stl_algobase.h:70,
from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/fpos.h:60: 'streamoff' is used as a type, but is
not defined as a type.
/usr/include/c++/3.2.3/bits/fpos.h:74: syntax error before `__off'
/usr/include/c++/3.2.3/bits/fpos.h:75: missing ';' before right brace
/usr/include/c++/3.2.3/bits/fpos.h:77: semicolon missing after declaration of `
std::fpos<_StateT>'
/usr/include/c++/3.2.3/bits/fpos.h: In constructor
`std::fpos<_StateT>::fpos()':
/usr/include/c++/3.2.3/bits/fpos.h:72: class `std::fpos<_StateT>' does not have
any field named `_M_off'
/usr/include/c++/3.2.3/bits/fpos.h: At global scope:
/usr/include/c++/3.2.3/bits/fpos.h:77: syntax error before `(' token
/usr/include/c++/3.2.3/bits/fpos.h:77: ISO C++ forbids defining types within
return type
/usr/include/c++/3.2.3/bits/fpos.h:77: syntax error before `(' token
/usr/include/c++/3.2.3/bits/fpos.h:77: non-member function `int
std::streamoff()' cannot have `const' method qualifier
/usr/include/c++/3.2.3/bits/fpos.h: In function `int std::streamoff()':
/usr/include/c++/3.2.3/bits/fpos.h:77: `_M_off' undeclared (first use this
function)
/usr/include/c++/3.2.3/bits/fpos.h:77: (Each undeclared identifier is reported
only once for each function it appears in.)
/usr/include/c++/3.2.3/bits/fpos.h: At global scope:
/usr/include/c++/3.2.3/bits/fpos.h:79: syntax error before `&' token
/usr/include/c++/3.2.3/bits/fpos.h:82: syntax error before `&' token
/usr/include/c++/3.2.3/bits/fpos.h:86: syntax error before `operator'
/usr/include/c++/3.2.3/bits/fpos.h:89: syntax error before `+=' token
/usr/include/c++/3.2.3/bits/fpos.h:94: syntax error before `operator'
/usr/include/c++/3.2.3/bits/fpos.h:97: syntax error before `-=' token
/usr/include/c++/3.2.3/bits/fpos.h:102: syntax error before `&' token
/usr/include/c++/3.2.3/bits/fpos.h:103: non-member function `bool
operator==(...)' cannot have `const' method qualifier
/usr/include/c++/3.2.3/bits/fpos.h:103: `bool operator==(...)' must have an
argument of class or enumerated type
/usr/include/c++/3.2.3/bits/fpos.h:103: `bool operator==(...)' must take
exactly two arguments
/usr/include/c++/3.2.3/bits/fpos.h: In function `bool operator==(...)':
/usr/include/c++/3.2.3/bits/fpos.h:103: `_M_off' undeclared (first use this
function)
/usr/include/c++/3.2.3/bits/fpos.h:103: `__pos' undeclared (first use this
function)
/usr/include/c++/3.2.3/bits/fpos.h: At global scope:
/usr/include/c++/3.2.3/bits/fpos.h:106: syntax error before `&' token
/usr/include/c++/3.2.3/bits/fpos.h:107: non-member function `bool
operator!=(...)' cannot have `const' method qualifier
/usr/include/c++/3.2.3/bits/fpos.h:107: `bool operator!=(...)' must have an
argument of class or enumerated type
/usr/include/c++/3.2.3/bits/fpos.h:107: `bool operator!=(...)' must take
exactly two arguments
/usr/include/c++/3.2.3/bits/fpos.h:110: syntax error before `)' token
/usr/include/c++/3.2.3/bits/fpos.h:113: `streamoff' was not declared in this
scope
/usr/include/c++/3.2.3/bits/fpos.h:113: syntax error before `)' token
/usr/include/c++/3.2.3/bits/fpos.h: In function `void _M_position(...)':
/usr/include/c++/3.2.3/bits/fpos.h:113: `__off' undeclared (first use this
function)
/usr/include/c++/3.2.3/bits/fpos.h: At global scope:
/usr/include/c++/3.2.3/bits/fpos.h:114: syntax error before `}' token
/usr/include/c++/3.2.3/bits/fpos.h:117: syntax error before `;' token
In file included from /usr/include/c++/3.2.3/bits/stl_algobase.h:72,
from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/type_traits.h:54:28: bits/c++config.h: No
such file or directory
In file included from /usr/include/c++/3.2.3/bits/stl_iterator_base_funcs.h:68,
from /usr/include/c++/3.2.3/bits/stl_algobase.h:74,
from /usr/include/c++/3.2.3/vector:67,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/concept_check.h:40:28: bits/c++config.h:
No such file or directory
In file included from /usr/include/c++/3.2.3/bits/stl_alloc.h:90,
from /usr/include/c++/3.2.3/vector:68,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/stl_threads.h:52:23: bits/gthr.h: No such
file or directory
In file included from /usr/include/c++/3.2.3/bits/stl_alloc.h:90,
from /usr/include/c++/3.2.3/vector:68,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/stl_threads.h:69: '__gthread_mutex_t' is used as a
type, but is not defined as a type.
/usr/include/c++/3.2.3/bits/stl_threads.h:79:2: #error
__GTHREAD_MUTEX_INIT or __GTHREAD_MUTEX_INIT_FUNCTION should be
defined by gthr.h abstraction layer, report problem to
libstdc++ at gcc.gnu.org.
/usr/include/c++/3.2.3/bits/stl_threads.h: In member function `void
std::_Refcount_Base::_M_incr()':
/usr/include/c++/3.2.3/bits/stl_threads.h:86: `_M_ref_count_lock' undeclared
(first use this function)
/usr/include/c++/3.2.3/bits/stl_threads.h:86: `__gthread_mutex_lock' undeclared
(first use this function)
/usr/include/c++/3.2.3/bits/stl_threads.h:88: `__gthread_mutex_unlock'
undeclared (first use this function)
/usr/include/c++/3.2.3/bits/stl_threads.h: At global scope:
/usr/include/c++/3.2.3/bits/stl_threads.h:158: '__gthread_mutex_t' is used as a
type, but is not defined as a type.
/usr/include/c++/3.2.3/bits/stl_threads.h: In member function `void
std::_STL_mutex_lock::_M_acquire_lock()':
/usr/include/c++/3.2.3/bits/stl_threads.h:192: `_M_lock' undeclared (first use
this function)
In file included from /usr/include/c++/3.2.3/vector:68,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/stl_alloc.h:92:28: bits/atomicity.h: No
such file or directory
In file included from /usr/include/c++/3.2.3/vector:68,
from half_range_mode.cpp:3:
/usr/include/c++/3.2.3/bits/stl_alloc.h: At global scope:
/usr/include/c++/3.2.3/bits/stl_alloc.h:390: syntax error before `;' token
/usr/include/c++/3.2.3/bits/stl_alloc.h:463: syntax error before `<' token
/usr/include/c++/3.2.3/bits/stl_alloc.h:463: `__threads' was not declared in
this scope
/usr/include/c++/3.2.3/bits/stl_alloc.h:463: `__inst' was not declared in this
scope
/usr/include/c++/3.2.3/bits/stl_alloc.h:463: template argument 1 is invalid
/usr/include/c++/3.2.3/bits/stl_alloc.h:463: template argument 2 is invalid
/usr/include/c++/3.2.3/bits/stl_alloc.h:614: syntax error before `;' token
/usr/include/c++/3.2.3/bits/stl_alloc.h:614: confused by earlier
errors, bailing out
make: *** [half_range_mode.o] Error 1
ERROR: compilation failed for package genefilter
* Removing /jdrf_tools/lib64/R/library/genefilter
* Restoring previous /jdrf_tools/lib64/R/library/genefilter
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