edgeR 3.16.5
Yunshun Chen , Aaron Lun , Mark Robinson , Davis McCarthy , Gordon Smyth
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/edgeR | | Last Changed Rev: 125002 / Revision: 128728 | | Last Changed Date: 2016-12-11 19:42:43 -0500 (Sun, 11 Dec 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL edgeR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.4-bioc/R/library’
* installing *source* package ‘edgeR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_add_prior_count.cpp -o R_add_prior_count.o
In file included from matvec_check.h:1:0,
from R_add_prior_count.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_add_repeat_matrices.cpp -o R_add_repeat_matrices.o
In file included from matvec_check.h:1:0,
from R_add_repeat_matrices.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_calculate_cpm.cpp -o R_calculate_cpm.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_check_counts.cpp -o R_check_counts.o
In file included from matvec_check.h:1:0,
from R_check_counts.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
In file included from matvec_check.h:1:0,
from R_check_poisson_bound.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_compute_apl.cpp -o R_compute_apl.o
In file included from glm.h:5:0,
from R_compute_apl.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_compute_nbdev.cpp -o R_compute_nbdev.o
In file included from R_compute_nbdev.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
In file included from R_exact_test_by_deviance.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
In file included from glm.h:5:0,
from R_get_one_way_fitted.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
In file included from glm.h:5:0,
from R_initialize_levenberg.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_levenberg.cpp -o R_levenberg.o
In file included from glm.h:5:0,
from R_levenberg.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_loess_by_col.cpp -o R_loess_by_col.o
In file included from R_loess_by_col.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
In file included from R_maximize_interpolant.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_one_group.cpp -o R_one_group.o
In file included from glm.h:5:0,
from R_one_group.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_simple_good_turing.cpp -o R_simple_good_turing.o
In file included from R_simple_good_turing.cpp:9:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c add_prior.cpp -o add_prior.o
In file included from matvec_check.h:1:0,
from add_prior.h:3,
from add_prior.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c adj_coxreid.cpp -o adj_coxreid.o
In file included from glm.h:5:0,
from adj_coxreid.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fmm_spline.c -o fmm_spline.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glm_levenberg.cpp -o glm_levenberg.o
In file included from glm.h:5:0,
from glm_levenberg.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glm_one_group.cpp -o glm_one_group.o
In file included from glm.h:5:0,
from glm_one_group.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
In file included from init.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c interpolator.cpp -o interpolator.o
In file included from interpolator.h:4:0,
from interpolator.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c matvec_check.cpp -o matvec_check.o
In file included from matvec_check.h:1:0,
from matvec_check.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nbdev.cpp -o nbdev.o
In file included from glm.h:5:0,
from nbdev.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_add_repeat_matrices.o R_ave_log_cpm.o R_calculate_cpm.o R_check_counts.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_get_one_way_fitted.o R_initialize_levenberg.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/edgeR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘edgeR.Rnw’
** testing if installed package can be loaded
* DONE (edgeR)