SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SPP -- ChIP-seq program installation 2?? potatoo Bioinformatics 3 01-06-2016 06:20 AM
ODIN - A Differential Peak Caller for ChIP-seq data ManuelRWTHaices Bioinformatics 1 11-23-2015 10:31 AM
ChIP-seq peak caller that handles biological replicates AnnaE Bioinformatics 6 05-13-2015 12:49 PM
SPP -- ChIP-seq program installation?? ewilbanks Bioinformatics 10 06-19-2013 06:41 AM
ChIP-Seq: PeakRanger: A cloud-enabled peak caller for ChIP-seq data. Newsbot! Literature Watch 0 05-11-2011 03:40 AM

Reply
 
Thread Tools
Old 12-08-2015, 09:36 AM   #1
nataliesilmon
Junior Member
 
Location: New York

Join Date: Mar 2015
Posts: 2
Angry SPP ChIP-seq peak caller installation problems

Hi,

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;
^~~~~
struct
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;
^~~~~
struct
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
Reply

Tags
bioinformatics, chip-seq, nextgen

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:54 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO