rtfbs

Copyright: Copyright (c) 2002-2015 University of California, Cornell
University
Package: rtfbs
Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>
License: BSD_3_clause + file LICENSE
Title: Transcription Factor Binding Site Identification Tool
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Description: RTFBS identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Version: 0.3.4
URL: http://compgen.cshl.edu/rtfbs
Date: 2015-02-08
Imports: rphast
Depends: stats
Collate: 'tfbs.R'
Packaged: 2015-02-09 03:53:43 UTC; melissa
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-02-09 07:44:17

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'rtfbs' ...
** package 'rtfbs' successfully unpacked and MD5 sums checked
checking for CFLAGS...  -g 
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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
 -g 
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for ANSI C header files... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking pcre.h usability... yes
checking pcre.h presence... yes
checking for pcre.h... yes
checking for an ANSI C-conforming const... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for working strtod... yes
checking for vprintf... yes
checking for _doprnt... no
checking for atexit... yes
checking for bzero... yes
checking for floor... no
checking for gethostname... yes
checking for gettimeofday... yes
checking for memset... yes
checking for pow... no
checking for re_comp... yes
checking for regcomp... yes
checking for rint... no
checking for sqrt... no
checking for strcasecmp... yes
checking for strdup... yes
checking for strstr... yes
checking for strtol... yes
checking for library containing pcre_compile... -lpcre
checking for -fno-strict-aliasing... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars

- configuration summary:

    C preprocessor .................. : gcc -E
    C compiler ...................... : gcc
    C compiler flags ................ :  -g  -fno-strict-aliasing 
    Extra libraries ................. : -lpcre 

** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c genepred.c -o genepred.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c subst_mods.c -o subst_mods.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c category_map.c -o category_map.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c misc.c -o misc.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_tfbs.c -o rph_tfbs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c lists.c -o lists.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c dgamma.c -o dgamma.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c phylo_p.c -o phylo_p.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c complex_matrix.c -o complex_matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c tree_model.c -o tree_model.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c maf.c -o maf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_hmm.c -o rph_hmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_tree_model.c -o rph_tree_model.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_wig.c -o rph_wig.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c trees.c -o trees.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_util.c -o rph_util.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c phylo_fit.c -o phylo_fit.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_phyloFit.c -o rph_phyloFit.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_subst_mods.c -o rph_subst_mods.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c phylo_p_print.c -o phylo_p_print.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c fit_em.c -o fit_em.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c em.c -o em.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c eigen.c -o eigen.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c hashtable.c -o hashtable.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_category_map.c -o rph_category_map.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c tree_likelihoods.c -o tree_likelihoods.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c complex_vector.c -o complex_vector.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c prob_matrix.c -o prob_matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c markov_matrix.c -o markov_matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c wig.c -o wig.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c bgc_hmm.c -o bgc_hmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c local_alignment.c -o local_alignment.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c list_of_lists.c -o list_of_lists.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_phastCons.c -o rph_phastCons.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c numerical_opt.c -o numerical_opt.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c prob_vector.c -o prob_vector.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c fit_feature.c -o fit_feature.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_gff.c -o rph_gff.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c msa.c -o msa.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c maf_block.c -o maf_block.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_list_of_lists.c -o rph_list_of_lists.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c multi_msa.c -o multi_msa.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_init.c -o rph_init.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c fit_column.c -o fit_column.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c gap_patterns.c -o gap_patterns.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c hmm.c -o hmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c vector.c -o vector.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c tfbs.c -o tfbs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c motif.c -o motif.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_phyloP.c -o rph_phyloP.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c phylo_hmm.c -o phylo_hmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_trees.c -o rph_trees.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c bed.c -o bed.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c phast_cons.c -o phast_cons.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_bgc_hmm.c -o rph_bgc_hmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c sufficient_stats.c -o sufficient_stats.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_phylo_hmm.c -o rph_phylo_hmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c subst_distrib.c -o subst_distrib.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c matrix.c -o matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c indel_history.c -o indel_history.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c gff.c -o gff.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c memory_handler.c -o memory_handler.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c indel_mod.c -o indel_mod.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c stringsplus.c -o stringsplus.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I. -DHAVE_CONFIG_H -DPHAST_VERSION='"v1.3"' -DRPHAST -DSKIP_LAPACK -DUSE_PHAST_MEMORY_HANDLER     -g  -fno-strict-aliasing  -fpic  -g -O2  -c rph_msa.c -o rph_msa.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o rtfbs.so genepred.o subst_mods.o category_map.o misc.o rph_tfbs.o lists.o dgamma.o phylo_p.o complex_matrix.o tree_model.o maf.o rph_hmm.o rph_tree_model.o rph_wig.o trees.o rph_util.o phylo_fit.o rph_phyloFit.o rph_subst_mods.o phylo_p_print.o fit_em.o em.o eigen.o hashtable.o rph_category_map.o tree_likelihoods.o complex_vector.o prob_matrix.o markov_matrix.o wig.o bgc_hmm.o local_alignment.o list_of_lists.o rph_phastCons.o numerical_opt.o prob_vector.o fit_feature.o rph_gff.o msa.o maf_block.o rph_list_of_lists.o multi_msa.o rph_init.o fit_column.o gap_patterns.o hmm.o vector.o tfbs.o motif.o rph_phyloP.o phylo_hmm.o rph_trees.o bed.o phast_cons.o rph_bgc_hmm.o sufficient_stats.o rph_phylo_hmm.o subst_distrib.o matrix.o indel_history.o gff.o memory_handler.o indel_mod.o stringsplus.o rph_msa.o -lpcre -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/rtfbs/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'rtfbs'
    finding HTML links ... done
    as.pointer.ms                           html  
    build.mm                                html  
    calc.fdr                                html  
    concat.ms                               html  
    from.pointer.ms                         html  
    gcContent.ms                            html  
    groupByGC.ms                            html  
    is.pointer.ms                           html  
    label.matrix                            html  
    length.ms                               html  
    lengths.ms                              html  
    makeFdrPlot                             html  
    ms                                      html  
    names.ms                                html  
    offsets.ms                              html  
    open-brace.ms                           html  
    output.sites                            html  
    print.ms                                html  
    read.mm                                 html  
    read.ms                                 html  
    read.pwm                                html  
    rtfbs-package                           html  
    score.ms                                html  
    sequences.ms                            html  
    simulate.ms                             html  
    split.ms                                html  
    summary.ms                              html  
    write.mm                                html  
    write.ms                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtfbs)
Making 'packages.html' ... done