Multiple platform build/check report for BioC 3.7 experimental data

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pRolocdata_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/pRolocdata.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 ‘pRolocdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRolocdata’ version ‘1.18.0’
* 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 134.1Mb
  sub-directories of 1Mb or more:
    data     42.4Mb
    extdata  91.3Mb
* 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 ... 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 examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
andreyev2010 4.492  0.136   8.787
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-data-experiment/meat/pRolocdata.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL pRolocdata
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘pRolocdata’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pRolocdata)

Tests output


R version 3.5.1 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.

> # 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, 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

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 2.6.4 
  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 1.18.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 75 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 10.616   0.272  11.529

Example timings

name	user	system	elapsed
E14TG2a	0.036	0.000	0.036
andreyev2010	4.492	0.136	8.787
andy2011	0.076	0.016	0.089
at_chloro	0.592	0.004	0.596
beltran2016	0.312	0.000	0.311
dunkley2006	0.012	0.000	0.011
fabre2015	0.188	0.016	0.207
foster2006	0.028	0.004	0.030
groen2014	2.164	0.032	2.199
hall2009	0.132	0.000	0.130
havugimana2012	0.092	0.016	0.111
hirst2018	0.396	0.016	0.409
hyperLOPIT2015	4.268	0.012	4.288
hyperLOPITU2OS2017	0.968	0.004	1.004
itzhak2016	0.360	0.004	0.363
itzhak2017	1.008	0.000	1.009
kirkwood2013	0.056	0.000	0.052
kristensen2012	0.024	0.000	0.023
lopimsSyn2	0.280	0.004	0.286
mulvey2015	2.868	0.016	2.889
nikolovski2012	0.284	0.008	0.289
nikolovski2014	0.268	0.000	0.268
pRolocdata	0.008	0.032	0.143
pRolocmetadata	0.016	0.000	0.016
rodriguez2012r1	0.392	0.052	0.454
stekhoven2014	0.200	0.012	0.213
tan2009	0.016	0.000	0.016
trotter2010	0.28	0.02	0.30

CHECK report for pRolocdata on malbec2

Summary

Command output

Installation output

Tests output

Example timings