Package: icetea

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:icetea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings icetea_1.1.1.tar.gz

StartedAt: 2019-04-09 01:34:25 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:40:35 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 369.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: icetea.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:icetea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings icetea_1.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/icetea.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘icetea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘icetea’ version ‘1.1.1’
* 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 ‘icetea’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
detectTSS   13.863  2.666  15.779
annotateTSS 11.766  0.566  12.709
* 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:
  > library(icetea)
  > 
  > test_check("icetea")
  ── 1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14)  ─
  annot$value not equal to `expected_vals`.
  2/7 mismatches (average diff: 5)
  [2]  7 - 12 == -5
  [3] 56 - 51 ==  5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 20 SKIPPED: 0 FAILED: 1
  1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14) 
  
  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-3.9-bioc/meat/icetea.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL icetea
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘icetea’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (icetea)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(icetea)
> 
> test_check("icetea")
── 1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14)  ─
annot$value not equal to `expected_vals`.
2/7 mismatches (average diff: 5)
[2]  7 - 12 == -5
[3] 56 - 51 ==  5

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 20 SKIPPED: 0 FAILED: 1
1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14) 

Error: testthat unit tests failed
Execution halted

name	user	system	elapsed
annotateTSS	11.766	0.566	12.709
demultiplexFASTQ	2.486	0.118	2.642
detectDiffTSS	0	0	0
detectTSS	13.863	2.666	15.779
exampleCSobject	0.132	0.025	0.158
exportTSS	0.281	0.039	0.322
filterDuplicates	1.353	0.246	1.650
fitDiffTSS	0	0	0
getGeneCounts	2.102	0.178	2.304
getNormFactors	1.758	0.638	1.506
mapCaps	0.000	0.001	0.001
newCapSet	0.072	0.021	0.093
plotReadStats	0.511	0.062	0.575
plotTSSprecision	3.231	0.356	3.544
sampleInfo	0.143	0.004	0.148
splitBAM_byIndex	0.277	0.012	0.289
splitBAM_byRepindex	0.245	0.006	0.253