Package: riboSeqR

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:riboSeqR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings riboSeqR_1.14.0.tar.gz

StartedAt: 2018-10-16 23:42:34 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:44:56 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 142.6 seconds

RetCode: 0

Status:  OK

CheckDir: riboSeqR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:riboSeqR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings riboSeqR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/riboSeqR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘riboSeqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘riboSeqR’ version ‘1.14.0’
* 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 ‘riboSeqR’ 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 ... NOTE
.readAlignments : <anonymous>: no visible global function definition
  for ‘read.delim’
filterHits : <anonymous> : <anonymous>: no visible global function
  definition for ‘chisq.test’
frameCounting : getHits: no visible global function definition for
  ‘queryHits’
frameCounting : getHits: no visible global function definition for
  ‘subjectHits’
lengthDist: no visible global function definition for ‘modifyList’
lengthDist: no visible global function definition for ‘rainbow’
lengthDist: no visible binding for global variable ‘lines’
plotCDS: no visible global function definition for ‘dev.list’
plotCDS: no visible global function definition for ‘par’
plotCDS : <anonymous> : <anonymous> : makeMatz: no visible binding for
  global variable ‘weighted.mean’
plotCDS : <anonymous> : <anonymous>: no visible global function
  definition for ‘barplot’
plotCDS : <anonymous> : <anonymous>: no visible global function
  definition for ‘rainbow’
plotCDS : <anonymous> : <anonymous>: no visible global function
  definition for ‘axis’
plotFS: no visible global function definition for ‘barplot’
plotFS: no visible global function definition for ‘rainbow’
plotTranscript: no visible global function definition for ‘dev.list’
plotTranscript: no visible global function definition for ‘par’
plotTranscript: no visible global function definition for ‘plot’
plotTranscript: no visible global function definition for ‘barplot’
plotTranscript: no visible global function definition for ‘axis’
plotTranscript: no visible global function definition for ‘rect’
plotTranscript: no visible global function definition for ‘text’
plotTranscript: no visible global function definition for ‘rgb’
plotTranscript: no visible global function definition for ‘segments’
rnaCounts : <anonymous>: no visible global function definition for
  ‘subjectHits’
Undefined global functions or variables:
  axis barplot chisq.test dev.list lines modifyList par plot queryHits
  rainbow read.delim rect rgb segments subjectHits text weighted.mean
Consider adding
  importFrom("grDevices", "dev.list", "rainbow", "rgb")
  importFrom("graphics", "axis", "barplot", "lines", "par", "plot",
             "rect", "segments", "text")
  importFrom("stats", "chisq.test", "weighted.mean")
  importFrom("utils", "modifyList", "read.delim")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/riboSeqR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL riboSeqR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘riboSeqR’ ...
** 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
* DONE (riboSeqR)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.

> BiocGenerics:::testPackage("riboSeqR")

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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


Attaching package: 'S4Vectors'

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

    expand.grid



RUNIT TEST PROTOCOL -- Tue Oct 16 23:44:51 2018 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
riboSeqR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  4.941   0.316   5.291 

name	user	system	elapsed
filterHits	2.872	0.098	3.011
findCDS	0.339	0.001	0.344
frameCounting	2.180	0.075	2.273
frameShift	2.759	0.091	2.907
lengthDist	1.631	0.063	1.711
plotCDS	2.760	0.105	2.887
plotTranscript	2.686	0.099	2.813
readRibodata	1.643	0.065	1.768
rnaCounts	2.607	0.096	2.743
sliceCounts	2.209	0.084	2.310