Package: icetea

Version: 1.1.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:icetea.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings icetea_1.1.1.tar.gz

StartedAt: 2019-04-09 01:18:07 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:23:49 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 342.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: icetea.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:icetea.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings icetea_1.1.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/icetea.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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   12.856  1.703  13.877
annotateTSS 10.079  0.084  10.254
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/icetea.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL icetea
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-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(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	10.079	0.084	10.254
demultiplexFASTQ	1.649	0.017	1.725
detectDiffTSS	0	0	0
detectTSS	12.856	1.703	13.877
exampleCSobject	0.163	0.020	0.183
exportTSS	0.263	0.012	0.275
filterDuplicates	1.400	0.120	1.527
fitDiffTSS	0	0	0
getGeneCounts	1.560	0.028	1.587
getNormFactors	0.789	0.156	1.091
mapCaps	0	0	0
newCapSet	0.555	0.484	0.072
plotReadStats	0.371	0.008	0.380
plotTSSprecision	2.128	0.044	2.172
sampleInfo	0.103	0.000	0.102
splitBAM_byIndex	0.232	0.068	0.300
splitBAM_byRepindex	0.203	0.068	0.272