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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 Oct 2021).

CHECK results for pRolocdata on nebbiolo2

To the developers/maintainers of the pRolocdata package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 281/404HostnameOS / ArchINSTALLBUILDCHECK
pRolocdata 1.31.0  (landing page)
Laurent Gatto
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/pRolocdata
git_branch: master
git_last_commit: 0c25706
git_last_commit_date: 2021-05-19 11:38:43 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pRolocdata
Version: 1.31.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings pRolocdata_1.31.0.tar.gz
StartedAt: 2021-10-16 12:28:46 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 12:31:50 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 183.7 seconds
RetCode: 0
Status:   OK  
CheckDir: pRolocdata.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings pRolocdata_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/pRolocdata.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.31.0’
* 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 8.234    0.2   8.434
* 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-3.14-data-experiment/meat/pRolocdata.Rcheck/00check.log’
for details.



Installation output

pRolocdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL pRolocdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.1 (2021-08-10) -- "Kick Things"
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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.19.2 
  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 1.31.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ]
> 
> proc.time()
   user  system elapsed 
 13.853   0.777  14.611 

Example timings

pRolocdata.Rcheck/pRolocdata-Ex.timings

nameusersystemelapsed
E14TG2a0.0330.0000.034
Shin20204.6330.2484.978
ToxoLopit0.4700.0080.478
andreyev20101.2420.2641.506
andy20110.0350.0160.051
at_chloro0.0810.0080.090
baers20180.3130.0080.321
beltran20160.4670.0120.479
davies20180.2110.0440.255
dunkley20060.0080.0040.013
fabre20150.2190.0560.276
foster20060.0230.0040.026
groen20140.7920.1360.928
hall20090.1500.0040.154
havugimana20120.0870.0120.099
hirst20180.3760.0160.391
hyperLOPIT20153.0920.1763.268
hyperLOPITU2OS20171.0720.0161.089
itzhak20161.0560.0041.061
itzhak20171.3080.0201.329
itzhak2017dynamic1.0390.0201.059
kirkwood20130.0380.0040.042
kozik20200.1680.0000.167
krahmer2018pcp8.2340.2008.434
kristensen20120.0190.0000.019
lopimsSyn20.5120.0080.520
mulvey20151.7510.0161.767
nikolovski20120.2490.0000.249
nikolovski20140.2910.0040.295
orre20190.3420.0040.346
pRolocdata0.0100.0050.016
pRolocmetadata0.0140.0000.014
rodriguez2012r10.5410.0000.542
stekhoven20140.1720.0040.176
tan20090.0130.0000.013
trotter20100.2380.0080.246
yeast0.2990.0040.303