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This page was generated on 2017-03-04 16:53:31 -0500 (Sat, 04 Mar 2017).
| Package 1060/1339 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| regsplice 1.1.6 Lukas M. Weber
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | ||||||
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | OK |
| Package: regsplice |
| Version: 1.1.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regsplice_1.1.6.tar.gz |
| StartedAt: 2017-03-04 07:57:54 -0800 (Sat, 04 Mar 2017) |
| EndedAt: 2017-03-04 08:01:41 -0800 (Sat, 04 Mar 2017) |
| EllapsedTime: 227.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: regsplice.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regsplice_1.1.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/regsplice.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regsplice/DESCRIPTION’ ... OK
* this is package ‘regsplice’ version ‘1.1.6’
* 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 ‘regsplice’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... 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
LRTests 14.154 0.319 14.506
fitRegMultiple 13.203 0.155 13.372
summaryTable 12.867 0.155 13.024
regsplice 12.857 0.138 13.000
* 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:
7: stop(msg, ": ", errors, domain = NA)
2. Error: voom transformation and weights are calculated correctly (@test_voom.R#20)
Need at least two genes to fit a mean-variance trend
1: runVoom(rs_data) at testthat/test_voom.R:20
2: limma::voom(counts = counts, design = design, lib.size = lib_sizes)
3: stop("Need at least two genes to fit a mean-variance trend")
testthat results ================================================================
OK: 89 SKIPPED: 0 FAILED: 2
1. Error: glmnet error example passes (@test_glmnet_error_example.R#47)
2. Error: voom transformation and weights are calculated correctly (@test_voom.R#20)
Error: testthat unit tests failed
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
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/regsplice.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R Under development (unstable) (2017-02-15 r72177) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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(regsplice)
>
> test_check("regsplice")
1. Error: glmnet error example passes (@test_glmnet_error_example.R#47) --------
invalid class "RegspliceResults" object: invalid object for slot "gene_IDs" in class "RegspliceResults": got class "NULL", should be or extend class "character"
1: initializeResults(rs_data) at testthat/test_glmnet_error_example.R:47
2: RegspliceResults(gene_IDs)
3: new("RegspliceResults", gene_IDs = gene_IDs)
4: initialize(value, ...)
5: initialize(value, ...)
6: validObject(.Object)
7: stop(msg, ": ", errors, domain = NA)
2. Error: voom transformation and weights are calculated correctly (@test_voom.R#20)
Need at least two genes to fit a mean-variance trend
1: runVoom(rs_data) at testthat/test_voom.R:20
2: limma::voom(counts = counts, design = design, lib.size = lib_sizes)
3: stop("Need at least two genes to fit a mean-variance trend")
testthat results ================================================================
OK: 89 SKIPPED: 0 FAILED: 2
1. Error: glmnet error example passes (@test_glmnet_error_example.R#47)
2. Error: voom transformation and weights are calculated correctly (@test_voom.R#20)
Error: testthat unit tests failed
Execution halted
regsplice.Rcheck/00install.out:
* installing *source* package ‘regsplice’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (regsplice)
regsplice.Rcheck/regsplice-Ex.timings:
| name | user | system | elapsed | |
| LRTests | 14.154 | 0.319 | 14.506 | |
| RegspliceData | 0.330 | 0.003 | 0.333 | |
| RegspliceResults | 0.002 | 0.000 | 0.002 | |
| createDesignMatrix | 0.002 | 0.001 | 0.002 | |
| filterLowCounts | 0.075 | 0.000 | 0.076 | |
| filterZeros | 0.053 | 0.001 | 0.054 | |
| fitRegMultiple | 13.203 | 0.155 | 13.372 | |
| initializeResults | 0.140 | 0.002 | 0.143 | |
| regsplice | 12.857 | 0.138 | 13.000 | |
| runNormalization | 0.098 | 0.001 | 0.099 | |
| runVoom | 0.171 | 0.001 | 0.172 | |
| summaryTable | 12.867 | 0.155 | 13.024 | |