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This page was generated on 2022-10-18 14:50:13 -0400 (Tue, 18 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for pRolocdata on nebbiolo1


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 284/410HostnameOS / ArchINSTALLBUILDCHECK
pRolocdata 1.34.0  (landing page)
Laurent Gatto
Snapshot Date: 2022-10-18 07:30:03 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/pRolocdata
git_branch: RELEASE_3_15
git_last_commit: 4973339
git_last_commit_date: 2022-04-26 13:07:08 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pRolocdata
Version: 1.34.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings pRolocdata_1.34.0.tar.gz
StartedAt: 2022-10-18 11:36:50 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 11:41:45 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 295.5 seconds
RetCode: 0
Status:   OK  
CheckDir: pRolocdata.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings pRolocdata_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/pRolocdata.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.34.0’
* 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 534.2Mb
  sub-directories of 1Mb or more:
    data     181.9Mb
    extdata  351.9Mb
* 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 ... NOTE
  Note: found 22 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
thpLOPIT2021   10.369  0.185  10.557
krahmer2018pcp  8.968  0.404   9.372
Shin2020        4.979  0.310   5.381
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-data-experiment/meat/pRolocdata.Rcheck/00check.log’
for details.



Installation output

pRolocdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL pRolocdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 2.22.0 
  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 1.34.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 140 ]
> 
> proc.time()
   user  system elapsed 
 32.844   1.309  34.142 

Example timings

pRolocdata.Rcheck/pRolocdata-Ex.timings

nameusersystemelapsed
E14TG2a0.0390.0000.039
Shin20204.9790.3105.381
ToxoLopit0.4620.0360.498
andreyev20100.5230.0280.551
andy20110.0650.0050.070
at_chloro0.0630.0180.081
baers20180.8720.0520.924
beltran20160.4720.0200.492
courtland20200.4950.0160.510
davies20180.2800.0040.284
dunkley20060.0100.0000.011
fabre20150.2280.0080.235
foster20060.0240.0020.025
groen20140.7740.0840.857
hall20090.1370.0040.141
havugimana20120.1110.0240.135
hirst20180.9540.0721.026
hyperLOPIT20153.8710.1804.052
hyperLOPITU2OS20171.8930.1212.014
itzhak20160.4760.0250.502
itzhak20171.4050.0481.453
itzhak2017dynamic1.0540.0281.082
kirkwood20130.0320.0040.036
kozik20200.1910.0040.195
krahmer2018pcp8.9680.4049.372
kristensen20120.0210.0000.021
lopimsSyn20.5470.0160.562
mulvey20151.8830.0481.930
nikolovski20120.2600.0160.276
nikolovski20140.3210.0080.329
orre20190.3640.0120.376
pRolocdata0.0030.0160.018
pRolocmetadata0.0150.0000.015
rodriguez2012r10.5680.0440.612
stekhoven20140.1780.0080.185
tan20090.0120.0020.014
thpLOPIT202110.369 0.18510.557
thpTimecourse20210.1230.0010.124
trotter20100.3610.0180.379
yeast0.3230.0200.347