BioC experimental data: CHECK report for IHWpaper on zin1

Package: IHWpaper

Version: 1.1.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IHWpaper_1.1.2.tar.gz

StartedAt: 2016-09-17 11:50:43 -0700 (Sat, 17 Sep 2016)

EndedAt: 2016-09-17 11:55:40 -0700 (Sat, 17 Sep 2016)

EllapsedTime: 297.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: IHWpaper.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IHWpaper_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/IHWpaper.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IHWpaper/DESCRIPTION’ ... OK
* this is package ‘IHWpaper’ version ‘1.1.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IHWpaper’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   9.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scott_fdrreg: no visible global function definition for ‘FDRreg’
scott_fdrreg: no visible global function definition for ‘getFDR’
sim_fun_eval: no visible binding for global variable ‘fdr_method’
sim_fun_eval: no visible binding for global variable ‘fdr_pars’
sim_fun_eval: no visible binding for global variable ‘FDP’
sim_fun_eval: no visible binding for global variable ‘power’
sim_fun_eval: no visible binding for global variable ‘rj_ratio’
sim_fun_eval: no visible binding for global variable ‘FPR’
sim_fun_eval: no visible global function definition for ‘sd’
sim_fun_eval: no visible binding for global variable ‘FWER’
Undefined global functions or variables:
  FDP FDRreg FPR FWER fdr_method fdr_pars getFDR power rj_ratio sd
Consider adding
  importFrom("stats", "power", "sd")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
analyze_dataset 10.672  0.052  11.562
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "TST GBH"
  [1] "SBH"
  [1] "Clfdr"
  [1] "Greedy Indep. Filt."
  [1] "IHW"
  [1] "IHW-Bonferroni E3"
  [1] "Bonferroni"
  [1] "qvalue"
  Error: incompatible size (20), expecting 2 (the group size) or 1
  In addition: There were 47 warnings (use warnings() to see them)
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-data-experiment/meat/IHWpaper.Rcheck/00check.log’
for details.

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(IHWpaper)
Loading required package: IHW
> 
> test_check("IHWpaper")
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 11 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "BH"
[1] "LSL GBH"
[1] "TST GBH"
[1] "SBH"
[1] "Clfdr"
[1] "Greedy Indep. Filt."
[1] "IHW"
[1] "IHW-Bonferroni E3"
[1] "Bonferroni"
[1] "qvalue"
Error: incompatible size (20), expecting 2 (the group size) or 1
In addition: There were 47 warnings (use warnings() to see them)
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted

* installing *source* package ‘IHWpaper’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c ddhf.cpp -o ddhf.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o IHWpaper.so RcppExports.o ddhf.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-data-experiment/meat/IHWpaper.Rcheck/IHWpaper/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IHWpaper)

name	user	system	elapsed
analyze_dataset	10.672	0.052	11.562
bh	0.068	0.000	0.068
bonf	0.064	0.000	0.061
clfdr	0.168	0.000	0.168
continuous_wrap	0.156	0.000	0.155
ddhf	2.988	0.000	2.989
du_ttest_sim	0.064	0.000	0.064
gbh	0.112	0.000	0.111
ihw_naive	0.860	0.000	0.676
lsl_pi0_est	0.060	0.004	0.064
null_sim	0.000	0.000	0.002
pretty_legend	0.452	0.004	0.463
run_evals	1.652	0.000	1.697
storey_qvalue	0.164	0.000	0.166
stratified_bh	0.104	0.000	0.105
tst_pi0_est	0.064	0.000	0.065
wasserman_normal_prds_sim	0.008	0.000	0.009
wasserman_normal_sim	0.008	0.000	0.008