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Old 12-08-2015, 09:36 AM   #1
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Angry SPP ChIP-seq peak caller installation problems


I am trying to install SPP version 1.10.1 (mac OS 10.9.5, R 3.3.2, Boost 1.55) and am having some problems. I also tried SPP version 1.11 and get the same problem but can't work out what the issue is. I'd really appreciate any clues!

Code I'm running:

R CMD INSTALL spp_1.11.tar.gz

And the result (truncated):

* installing to library ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’
* installing *source* package ‘spp’ ...
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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fPIC -Wall -mtune=core2 -g -O2 -c BGZF.cpp -o BGZF.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fPIC -Wall -mtune=core2 -g -O2 -c BamAlignment.cpp -o BamAlignment.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fPIC -Wall -mtune=core2 -g -O2 -c BamIndex.cpp -o BamIndex.o
In file included from BamIndex.cpp:15:
./BGZF.h:75:1: warning: 'BgzfData' defined as a struct here but previously declared as a class [-Wmismatched-tags]
struct API_EXPORT BgzfData {
./BamIndex.h:23:1: note: did you mean struct here?
class BgzfData;
In file included from BamIndex.cpp:16:
./BamStandardIndex_p.h:32:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
./BamAlignment.h:29:19: note: previous use is here
struct API_EXPORT BamAlignment {
./BamStandardIndex_p.h:32:1: note: did you mean struct here?
class BamAlignment;
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fPIC -Wall -mtune=core2 -g -O2 -c BamMultiReader.cpp -o BamMultiReader.o


make: *** [bamread.o] Error 1
ERROR: compilation failed for package ‘spp’
nataliesilmon is offline   Reply With Quote

bioinformatics, chip-seq, nextgen

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