| Back to the "Multiple platform build/check report" |
This page was generated on 2016-10-08 19:30:14 -0700 (Sat, 08 Oct 2016).
| Package 144/293 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| IHWpaper 1.0.2 Nikos Ignatiadis
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | ||||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK |
| Package: IHWpaper |
| Version: 1.0.2 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IHWpaper_1.0.2.tar.gz |
| StartedAt: 2016-10-08 09:41:48 -0700 (Sat, 08 Oct 2016) |
| EndedAt: 2016-10-08 09:46:48 -0700 (Sat, 08 Oct 2016) |
| EllapsedTime: 299.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: IHWpaper.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IHWpaper_1.0.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.0.2’
* 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 10.684 0.016 10.73
* 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-3.3-data-experiment/meat/IHWpaper.Rcheck/00check.log’
for details.
testthat.Rout.fail:
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
IHWpaper.Rcheck/00install.out:
* installing *source* package ‘IHWpaper’ ... ** libs g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c ddhf.cpp -o ddhf.o g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o IHWpaper.so RcppExports.o ddhf.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.3-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)
IHWpaper.Rcheck/IHWpaper-Ex.timings:
| name | user | system | elapsed | |
| analyze_dataset | 10.684 | 0.016 | 10.730 | |
| bh | 0.065 | 0.000 | 0.064 | |
| bonf | 0.055 | 0.000 | 0.056 | |
| clfdr | 0.174 | 0.000 | 0.178 | |
| continuous_wrap | 0.157 | 0.000 | 0.157 | |
| ddhf | 3.681 | 0.012 | 3.694 | |
| du_ttest_sim | 0.050 | 0.004 | 0.058 | |
| gbh | 0.102 | 0.008 | 0.110 | |
| ihw_naive | 0.585 | 0.004 | 0.543 | |
| lsl_pi0_est | 0.059 | 0.000 | 0.060 | |
| null_sim | 0.003 | 0.000 | 0.002 | |
| pretty_legend | 0.506 | 0.000 | 0.519 | |
| run_evals | 2.286 | 0.004 | 2.363 | |
| storey_qvalue | 0.167 | 0.004 | 0.168 | |
| stratified_bh | 0.094 | 0.000 | 0.096 | |
| tst_pi0_est | 0.059 | 0.000 | 0.059 | |
| wasserman_normal_prds_sim | 0.009 | 0.000 | 0.008 | |
| wasserman_normal_sim | 0.008 | 0.000 | 0.007 | |