Multiple platform build/check report for BioC 3.9 - CHECK report for icetea on celaya2

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 02:47:25 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:55:19 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 474.3 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) (2019-03-18 r76245)
* 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   18.939  4.676  22.345
annotateTSS 14.997  0.906  16.471
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (icetea)


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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	14.997	0.906	16.471
demultiplexFASTQ	2.650	0.178	2.840
detectDiffTSS	0.000	0.001	0.001
detectTSS	18.939	4.676	22.345
exampleCSobject	0.156	0.034	0.190
exportTSS	0.383	0.078	0.462
filterDuplicates	2.292	0.503	2.794
fitDiffTSS	0.000	0.000	0.001
getGeneCounts	2.643	0.259	2.901
getNormFactors	2.459	1.303	2.145
mapCaps	0.001	0.000	0.001
newCapSet	0.132	0.043	0.176
plotReadStats	0.943	0.177	1.121
plotTSSprecision	4.279	0.617	4.857
sampleInfo	0.129	0.006	0.135
splitBAM_byIndex	0.270	0.020	0.291
splitBAM_byRepindex	0.349	0.039	0.389

CHECK report for icetea on celaya2

Summary

Command output

Installation output

Tests output

Example timings