multtest

Package: multtest
Title: Resampling-based multiple hypothesis testing
Version: 2.28.0
Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra
Taylor, Sandrine Dudoit
Description: Non-parametric bootstrap and permutation resampling-based
multiple testing procedures (including empirical Bayes methods)
for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the
proportion of false positives (TPPFP), and false discovery rate
(FDR). Several choices of bootstrap-based null distribution
are implemented (centered, centered and scaled,
quantile-transformed). Single-step and step-wise methods are
available. Tests based on a variety of t- and F-statistics
(including t-statistics based on regression parameters from
linear and survival models as well as those based on
correlation parameters) are included. When probing hypotheses
with t-statistics, users may also select a potentially faster
null distribution which is multivariate normal with mean zero
and variance covariance matrix derived from the vector
influence function. Results are reported in terms of adjusted
p-values, confidence regions and test statistic cutoffs. The
procedures are directly applicable to identifying
differentially expressed genes in DNA microarray experiments.
Maintainer: Katherine S. Pollard <katherine.pollard@gladstone.ucsf.edu>
Depends: R (>= 2.10), methods, BiocGenerics, Biobase
Imports: survival, MASS, stats4
Suggests: snow
License: LGPL
LazyLoad: yes
biocViews: Microarray, DifferentialExpression, MultipleComparison
NeedsCompilation: yes
Packaged: 2016-05-04 02:37:12 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'multtest' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c Rpack.c -o Rpack.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c VScount.c -o VScount.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c block_sampling_fixed.c -o block_sampling_fixed.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c bootloop.c -o bootloop.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c mt.c -o mt.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c pairt_sampling.c -o pairt_sampling.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c random.c -o random.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c sampling.c -o sampling.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c sampling_fixed.c -o sampling_fixed.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c stat_func.c -o stat_func.o
stat_func.c: In function 'read_infile':
stat_func.c:703:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fh, "%s", pdata->name);
   ^
stat_func.c:705:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fh, "%d", pdata->L+j);
     ^
stat_func.c:710:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fh, "%s", pdata->id[i]);
     ^
stat_func.c:714:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
       fscanf(fh, "%lg",&ftemp);
       ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2  -c stat_order.c -o stat_order.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/multtest/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'update' from package 'stats' in package 'multtest'
** help
*** installing help indices
  converting help for package 'multtest'
    finding HTML links ... done
    EBMTP-class                             html  
    EBMTP                                   html  
    Hsets                                   html  
    MTP-class                               html  
    MTP-methods                             html  
    MTP                                     html  
    boot.null                               html  
    corr.null                               html  
    fwer2gfwer                              html  
    get.index                               html  
    golub                                   html  
    meanX                                   html  
    mt.internal                             html  
    mt.maxT                                 html  
    mt.plot                                 html  
    mt.rawp2adjp                            html  
    mt.reject                               html  
    mt.sample.teststat                      html  
    mt.teststat                             html  
    ss.maxT                                 html  
    wapply                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (multtest)
Making 'packages.html' ... done