Package: sangerseqR

Version: 1.16.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:sangerseqR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings sangerseqR_1.16.0.tar.gz

StartedAt: 2018-10-16 03:33:05 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 03:34:34 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 88.7 seconds

RetCode: 0

Status:  OK

CheckDir: sangerseqR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:sangerseqR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings sangerseqR_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/sangerseqR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sangerseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sangerseqR’ version ‘1.16.0’
* 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 ‘sangerseqR’ 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
chromatogram,sangerseq: no visible global function definition for ‘par’
chromatogram,sangerseq: no visible global function definition for
  ‘quantile’
chromatogram,sangerseq: no visible global function definition for ‘IQR’
chromatogram,sangerseq: no visible global function definition for ‘pdf’
chromatogram,sangerseq: no visible global function definition for
  ‘plot’
chromatogram,sangerseq: no visible global function definition for
  ‘rect’
chromatogram,sangerseq: no visible global function definition for
  ‘lines’
chromatogram,sangerseq: no visible global function definition for
  ‘mtext’
chromatogram,sangerseq: no visible global function definition for
  ‘axis’
chromatogram,sangerseq: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  IQR axis dev.off lines mtext par pdf plot quantile rect
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot", "rect")
  importFrom("stats", "IQR", "quantile")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setAllelePhase 9.320  0.024   9.356
makeBaseCalls  9.324  0.012   9.355
chromatogram   9.180  0.024   9.214
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/sangerseqR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL sangerseqR
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘sangerseqR’ ...
** 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 (sangerseqR)

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

> BiocGenerics:::testPackage("sangerseqR")

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


Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Tue Oct 16 03:34:32 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sangerseqR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  2.728   0.096   2.984 

name	user	system	elapsed
PolyPeakParser	0.000	0.000	0.001
abif-class	0.108	0.016	0.138
chromatogram	9.180	0.024	9.214
makeBaseCalls	9.324	0.012	9.355
read.abif	0.1	0.0	0.1
read.scf	0.056	0.000	0.072
readsangerseq	0.112	0.000	0.110
sangerseq-class	0.112	0.000	0.110
sangerseqAccessors	0.048	0.000	0.049
scf-class	0.056	0.000	0.054
setAllelePhase	9.320	0.024	9.356