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CHECK report for pRolocdata on malbec1

This page was generated on 2021-05-06 14:10:12 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the pRolocdata package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 282/398HostnameOS / ArchINSTALLBUILDCHECK
pRolocdata 1.28.0  (landing page)
Laurent Gatto
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/pRolocdata
Branch: RELEASE_3_12
Last Commit: 1764dcb
Last Changed Date: 2020-10-27 10:00:16 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: pRolocdata
Version: 1.28.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings pRolocdata_1.28.0.tar.gz
StartedAt: 2021-05-06 12:32:32 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 12:36:28 -0400 (Thu, 06 May 2021)
EllapsedTime: 236.9 seconds
RetCode: 0
Status:   OK  
CheckDir: pRolocdata.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings pRolocdata_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/pRolocdata.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.28.0’
* package encoding: UTF-8
* 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 304.2Mb
  sub-directories of 1Mb or more:
    data      70.3Mb
    extdata  233.4Mb
* 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 (user + system) or elapsed time > 5s
                user system elapsed
krahmer2018pcp 9.356  0.136   9.505
Shin2020       4.864  0.220   9.045
* 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-3.12-data-experiment/meat/pRolocdata.Rcheck/00check.log’
for details.



Installation output

pRolocdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL pRolocdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘pRolocdata’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pRolocdata)

Tests output

pRolocdata.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    trimws

> library(pRolocdata)

This is pRolocdata version 1.28.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ]
> 
> proc.time()
   user  system elapsed 
 17.252   0.476  17.935 

Example timings

pRolocdata.Rcheck/pRolocdata-Ex.timings

nameusersystemelapsed
E14TG2a0.0320.0120.043
Shin20204.8640.2209.045
ToxoLopit0.5720.0160.589
andreyev20101.1400.0361.201
andy20110.0520.0040.058
at_chloro0.0840.0080.092
baers20180.3760.0080.385
beltran20160.5640.0040.567
davies20180.2920.0040.297
dunkley20060.0120.0000.012
fabre20150.2840.0000.287
foster20060.0320.0000.032
groen20142.1000.0042.106
hall20090.1840.0000.183
havugimana20120.1280.0160.148
hirst20180.5200.0080.532
hyperLOPIT20154.4960.0964.596
hyperLOPITU2OS20171.3480.0161.389
itzhak20160.6720.0040.674
itzhak20171.7560.0121.767
itzhak2017dynamic1.3040.0161.322
kirkwood20130.0440.0000.041
kozik20200.2440.0000.246
krahmer2018pcp9.3560.1369.505
kristensen20120.0240.0000.023
lopimsSyn20.6480.0040.652
mulvey20153.0680.0563.126
nikolovski20120.3160.0040.319
nikolovski20140.3920.0120.405
orre20190.4400.0080.449
pRolocdata0.0240.0240.360
pRolocmetadata0.0120.0040.016
rodriguez2012r10.7160.0200.785
stekhoven20140.2520.0040.255
tan20090.0200.0000.017
trotter20100.3240.0200.344
yeast0.4160.0320.449