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This page was generated on 2025-08-28 15:41 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
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

Package 301/431HostnameOS / ArchINSTALLBUILDCHECK
pRolocdata 1.47.0  (landing page)
Lisa Breckels
Snapshot Date: 2025-08-28 07:30 -0400 (Thu, 28 Aug 2025)
git_url: https://git.bioconductor.org/packages/pRolocdata
git_branch: devel
git_last_commit: 40b364e
git_last_commit_date: 2025-04-15 09:21:13 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for pRolocdata on nebbiolo2

To the developers/maintainers of the pRolocdata package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: pRolocdata
Version: 1.47.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings pRolocdata_1.47.0.tar.gz
StartedAt: 2025-08-28 13:30:19 -0400 (Thu, 28 Aug 2025)
EndedAt: 2025-08-28 13:38:34 -0400 (Thu, 28 Aug 2025)
EllapsedTime: 495.0 seconds
RetCode: 0
Status:   OK  
CheckDir: pRolocdata.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings pRolocdata_1.47.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/pRolocdata.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘pRolocdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRolocdata’ version ‘1.47.0’
* 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 ... INFO
  installed size is 192.1Mb
  sub-directories of 1Mb or more:
    data     190.3Mb
    extdata    1.1Mb
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) thpLOPIT2021.Rd:82: Lost braces
    82 |   PSM-level csv files are available in the code{extdata} directory
       |                                                ^
checkRd: (-1) thpTimecourse2021.Rd:52: Lost braces
    52 |   code{extdata} directory and have been imported as 
       |       ^
* 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
thpLOPIT2021   10.614  0.146  10.759
krahmer2018pcp 10.019  0.300  10.319
Shin2020        4.909  0.281   5.202
* 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-3.22-data-experiment/meat/pRolocdata.Rcheck/00check.log’
for details.


Installation output

pRolocdata.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL pRolocdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘pRolocdata’ ...
** this is package ‘pRolocdata’ version ‘1.47.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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:utils':

    findMatches

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 2.35.2 
  Visit https://lgatto.github.io/MSnbase/ to get started.
 Consider switching to the 'R for Mass Spectrometry'
 packages - see https://RforMassSpectrometry.org for details.


Attaching package: 'MSnbase'

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

    trimws

> library(pRolocdata)

This is pRolocdata version 1.47.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ]
> 
> proc.time()
   user  system elapsed 
 44.916   1.898  46.807 

Example timings

pRolocdata.Rcheck/pRolocdata-Ex.timings

nameusersystemelapsed
E14TG2a0.0290.0010.030
Shin20204.9090.2815.202
ToxoLopit1.3660.0161.382
andreyev20100.6230.0210.644
andy20110.0550.0070.062
at_chloro0.1050.0060.111
baers20180.3920.0060.398
beltran20160.5930.0340.627
courtland20200.5890.0280.617
davies20180.3450.0040.349
dunkley20060.0110.0010.012
fabre20150.2820.0050.287
foster20060.0310.0000.031
groen20140.2280.0050.233
hall20090.1590.0030.162
havugimana20120.1310.0080.139
hirst20180.4900.0110.501
hyperLOPIT20154.1050.1394.244
hyperLOPITU2OS20171.3510.0261.377
itzhak2016stcSILAC0.6310.0110.643
itzhak20171.6550.0321.685
itzhak2017dynamic1.3150.0091.325
kirkwood20130.0750.0000.076
kozik20200.2130.0020.216
krahmer2018pcp10.019 0.30010.319
kristensen20120.0240.0000.024
lopimsSyn20.6770.0090.686
moloney20230.7840.0050.789
mulvey20152.3080.0382.346
nikolovski20120.2980.0060.304
nikolovski20140.3910.0030.394
orre20190.4240.0060.430
pRolocdata0.0110.0050.016
pRolocmetadata0.0120.0020.014
rodriguez2012r10.7090.0080.718
stekhoven20140.2140.0090.223
tan20090.0170.0000.017
thpLOPIT202110.614 0.14610.759
thpTimecourse20210.1470.0020.149
trotter20100.4110.0080.419
yeast0.3930.0030.396