[BioC] installing genefilter
Martin Morgan
mtmorgan at fhcrc.org
Wed Nov 4 04:13:35 CET 2009
Hi Denise --
Denise Mauldin wrote:
> 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
Try
PKG_CXXFLAGS=-I/usr/include/c++/3.2.3/i386-redhat-linux R CMD INSTALL
genefilter
or the like, or editing R_HOME/etc/Makeconf. But probably this is an
issue that should have been discovered / configured when R was
installed, see ./configure --help in the R source tree.
Martin
>
> # 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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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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