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

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TCseq
###
##############################################################################
##############################################################################


* 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)

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 

name	user	system	elapsed
DBanalysis	1.658	0.004	1.666
DBresult	2.750	0.000	2.754
TCA	0.022	0.000	0.022
TCA.accessors	0.089	0.020	0.109
counts	0.071	0.000	0.071
countsTable	0.001	0.000	0.001
experiment	0.001	0.000	0.001
experiment_BAMfile	0.001	0.000	0.001
genomicIntervals	0.002	0.000	0.001
peakreference	0.014	0.000	0.014
tca_ATAC	0.001	0.000	0.001
timeclust	0.029	0.000	0.029
timeclustplot	2.161	0.091	2.257
timecourseTable	1.499	0.008	1.515