Multiple platform build/check report for BioC 3.6 experimental data

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings pRolocdata_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/pRolocdata.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 ‘pRolocdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRolocdata’ 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 ‘pRolocdata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 121.7Mb
  sub-directories of 1Mb or more:
    data     39.3Mb
    extdata  82.1Mb
* checking package 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘hyperLOPITU2OS2017’ ‘hyperLOPITU2OS2017b’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
andreyev2010 5.052  0.148   7.091
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-data-experiment/meat/pRolocdata.Rcheck/00check.log’
for details.

Installation output

* installing *source* package ‘pRolocdata’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pRolocdata)

Tests output


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.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(MSnbase)
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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 2.4.2 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws

> library(pRolocdata)

This is pRolocdata version 1.16.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 62 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.164   0.228  12.820

Example timings

name	user	system	elapsed
E14TG2a	0.076	0.000	0.075
andreyev2010	5.052	0.148	7.091
andy2011	0.076	0.000	0.074
at_chloro	0.548	0.000	0.548
dunkley2006	0.028	0.000	0.025
fabre2015	0.348	0.004	0.353
foster2006	0.028	0.000	0.031
groen2014	2.392	0.004	2.399
hall2009	0.22	0.00	0.22
havugimana2012	0.524	0.000	0.524
hyperLOPIT2015	4.924	0.028	4.960
itzhak2016	0.528	0.000	0.528
kirkwood2013	0.04	0.00	0.04
kristensen2012	0.020	0.004	0.023
lopimsSyn2	0.328	0.000	0.330
mulvey2015	3.308	0.028	3.356
nikolovski2012	0.352	0.000	0.353
nikolovski2014	0.272	0.012	0.286
pRolocdata	0.008	0.024	0.065
pRolocmetadata	0.012	0.004	0.016
rodriguez2012r1	0.368	0.016	0.384
stekhoven2014	0.288	0.012	0.299
tan2009	0.016	0.000	0.016
trotter2010	0.300	0.012	0.311

CHECK report for pRolocdata on malbec1

Summary

Command output

Installation output

Tests output

Example timings