crazyhottommy / phantompeakqualtools

Automatically exported from code.google.com/p/phantompeakqualtools
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error installing spp package #8

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago
Hi,
is this tools still being maintained?  Suggestions for other tools if not?

I am having difficulty installing.  I am using R 3.2.1 and boost 1.48.0 on a 
Linux box.

R CMD INSTALL spp_1.10.1.tar.gz
* installing to library â/home/rsettlage/R/libraryâ
* installing *source* package âsppâ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for BZ2_bzDecompressInit in -lbz2... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/apps/packages/stats/R/3.2.1/lib64/R/include -DNDEBUG  
-I/usr/local/include   -I./ -D_FASTMAP -DMAQ_LONGREADS       -fpic  -g -O2  -c 
BGZF.cpp -o BGZF.o
g++ -I/apps/packages/stats/R/3.2.1/lib64/R/include -DNDEBUG  
-I/usr/local/include   -I./ -D_FASTMAP -DMAQ_LONGREADS       -fpic  -g -O2  -c 
BamAlignment.cpp -o BamAlignment.o
g++ -I/apps/packages/stats/R/3.2.1/lib64/R/include -DNDEBUG  
-I/usr/local/include   -I./ -D_FASTMAP -DMAQ_LONGREADS       -fpic  -g -O2  -c 
BamIndex.cpp -o BamIndex.o
In file included from BamIndex.cpp:13:0:
./BamIndex.h:77:23: error: âoff_tâ does not name a type
         virtual const off_t DataBeginOffset(void) const =0;
                       ^
In file included from ./BamIndex.h:15:0,
                 from BamIndex.cpp:13:
BamIndex.cpp: In member function âbool BamTools::BamIndex::Rewind()â:
BamIndex.cpp:149:53: error: âDataBeginOffsetâ was not declared in this scope
     return ( fseek64(m_indexStream, DataBeginOffset(), SEEK_SET) == 0 );
                                                     ^
./BamAux.h:30:41: note: in definition of macro âfseek64â
         #define fseek64(a,b,c) fseeko(a,b,c)
                                         ^
make: *** [BamIndex.o] Error 1
ERROR: compilation failed for package âsppâ
* removing â/home/rsettlage/R/library/sppâ

Original issue reported on code.google.com by bobsettl...@gmail.com on 19 Aug 2015 at 1:20

nataliesilmon commented 8 years ago

Hi did you resolve this issue? I am having a similar problem (R 3.2.2 and boost 1.59 on mac)