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CHECK report for TCseq on malbec2

This page was generated on 2019-03-18 11:18:20 -0400 (Mon, 18 Mar 2019).

Package 1574/1676HostnameOS / ArchINSTALLBUILDCHECK
TCseq 1.7.1
Mengjun Wu
Snapshot Date: 2019-03-17 17:01:51 -0400 (Sun, 17 Mar 2019)
URL: https://git.bioconductor.org/packages/TCseq
Branch: master
Last Commit: 8de3bd7
Last Changed Date: 2019-01-04 13:52:19 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS 

Summary

Package: TCseq
Version: 1.7.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TCseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TCseq_1.7.1.tar.gz
StartedAt: 2019-03-18 05:04:46 -0400 (Mon, 18 Mar 2019)
EndedAt: 2019-03-18 05:08:27 -0400 (Mon, 18 Mar 2019)
EllapsedTime: 221.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: TCseq.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TCseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TCseq_1.7.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TCseq.Rcheck’
* using R Under development (unstable) (2019-01-21 r75999)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCseq’ version ‘1.7.1’
* 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 ‘TCseq’ can be installed ... WARNING
Found the following significant warnings:
    The prototype for class “TCA” has undefined slot(s): ''
See ‘/home/biocbuild/bbs-3.9-bioc/meat/TCseq.Rcheck/00install.out’ for details.
* 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 ... NOTE
DBresult: no visible global function definition for ‘as’
DBresult.cluster: no visible global function definition for ‘as’
TCA: no visible global function definition for ‘is’
TCA: no visible global function definition for ‘as’
TCAFromSummarizedExperiment: no visible global function definition for
  ‘is’
TCAFromSummarizedExperiment: no visible global function definition for
  ‘as’
countReads: no visible global function definition for
  ‘createAnnotationFile’
countReads: no visible global function definition for ‘featureCounts’
timeclustplot: no visible binding for global variable ‘group’
timecourseTable: no visible global function definition for ‘as’
Undefined global functions or variables:
  as createAnnotationFile featureCounts group is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/TCseq.Rcheck/00check.log’
for details.



Installation output

TCseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TCseq
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘TCseq’ ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses,  :
  The prototype for class “TCA” has undefined slot(s): ''
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCseq)

Tests output

TCseq.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-01-21 r75999) -- "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(TCseq)
> 
> test_check("TCseq")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 10.406   0.374  10.804 

Example timings

TCseq.Rcheck/TCseq-Ex.timings

nameusersystemelapsed
DBanalysis1.6580.0041.666
DBresult2.7500.0002.754
TCA0.0220.0000.022
TCA.accessors0.0890.0200.109
counts0.0710.0000.071
countsTable0.0010.0000.001
experiment0.0010.0000.001
experiment_BAMfile0.0010.0000.001
genomicIntervals0.0020.0000.001
peakreference0.0140.0000.014
tca_ATAC0.0010.0000.001
timeclust0.0290.0000.029
timeclustplot2.1610.0912.257
timecourseTable1.4990.0081.515