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CHECK report for RiboProfiling on malbec1

This page was generated on 2018-04-12 13:14:12 -0400 (Thu, 12 Apr 2018).

Package 1177/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RiboProfiling 1.7.2
A. Popa
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/RiboProfiling
Branch: RELEASE_3_6
Last Commit: 6d6a1e4
Last Changed Date: 2017-12-13 09:58:53 -0400 (Wed, 13 Dec 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RiboProfiling
Version: 1.7.2
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RiboProfiling_1.7.2.tar.gz
StartedAt: 2018-04-12 02:26:43 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:36:22 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 578.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RiboProfiling.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RiboProfiling_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/RiboProfiling.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RiboProfiling/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboProfiling’ version ‘1.7.2’
* 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 ‘RiboProfiling’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
See ‘/home/biocbuild/bbs-3.6-bioc/meat/RiboProfiling.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 loading without being on the library search path ... 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
applyShiftFeature: no visible global function definition for 'is'
aroundPromoter: no visible global function definition for 'is'
codonInfo: no visible global function definition for 'is'
countShiftReads: no visible global function definition for 'is'
histMatchLength: no visible global function definition for 'is'
orfRelativePos: no visible global function definition for 'is'
plotSummarizedCov: no visible global function definition for 'is'
readStartCov: no visible global function definition for 'is'
readsToStartOrEnd: no visible global function definition for 'is'
riboSeqFromBAM: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
countsPlot        62.572  1.616  64.200
riboSeqFromBAM    56.136  1.412  57.482
orfRelativePos    34.404  0.296  34.771
codonInfo         28.216  0.296  28.491
countShiftReads   26.496  0.916  27.416
aroundPromoter     5.808  0.136   5.947
plotSummarizedCov  5.180  0.148   5.334
* 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-3.6-bioc/meat/RiboProfiling.Rcheck/00check.log’
for details.



Installation output

RiboProfiling.Rcheck/00install.out

* installing *source* package ‘RiboProfiling’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
* DONE (RiboProfiling)

Tests output

RiboProfiling.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(RiboProfiling)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling' 
> 
> test_check("RiboProfiling")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 12 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 83.728   1.044  85.518 

Example timings

RiboProfiling.Rcheck/RiboProfiling-Ex.timings

nameusersystemelapsed
aroundPromoter5.8080.1365.947
codonInfo28.216 0.29628.491
codonPCA3.0360.1243.141
countShiftReads26.496 0.91627.416
countsPlot62.572 1.61664.200
histMatchLength0.2680.0080.274
orfRelativePos34.404 0.29634.771
plotSummarizedCov5.1800.1485.334
printPCA1.9600.1002.052
readStartCov2.8520.0322.879
readsToStartOrEnd0.0640.0000.063
riboSeqFromBAM56.136 1.41257.482