Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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’

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-27-2024, 06:37 PM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X