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This page was generated on 2022-02-17 08:36:53 -0500 (Thu, 17 Feb 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 1362
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 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 283/406HostnameOS / ArchINSTALLBUILDCHECK
pRolocdata 1.33.1  (landing page)
Laurent Gatto
Snapshot Date: 2022-02-17 04:00:02 -0500 (Thu, 17 Feb 2022)
git_url: https://git.bioconductor.org/packages/pRolocdata
git_branch: master
git_last_commit: 16e1ab5
git_last_commit_date: 2021-12-01 16:17:49 -0500 (Wed, 01 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pRolocdata
Version: 1.33.1
Command: /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.15-data-experiment/R/library --no-vignettes --timings pRolocdata_1.33.1.tar.gz
StartedAt: 2022-02-17 07:46:52 -0500 (Thu, 17 Feb 2022)
EndedAt: 2022-02-17 07:54:07 -0500 (Thu, 17 Feb 2022)
EllapsedTime: 435.3 seconds
RetCode: 0
Status:   OK  
CheckDir: pRolocdata.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.15-data-experiment/R/library --no-vignettes --timings pRolocdata_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/pRolocdata.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.33.1’
* 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 587.1Mb
  sub-directories of 1Mb or more:
    data     180.9Mb
    extdata  405.6Mb
* 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   13.665  0.208  13.874
krahmer2018pcp 11.109  0.300  11.409
Shin2020        7.947  0.473   8.546
hyperLOPIT2015  5.252  0.141   5.393
* 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

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


* installing to library ‘/home/biocbuild/bbs-3.15-data-experiment/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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 2.21.5 
  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 1.33.1.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 140 ]
> 
> proc.time()
   user  system elapsed 
 47.955   2.020  49.961 

Example timings

pRolocdata.Rcheck/pRolocdata-Ex.timings

nameusersystemelapsed
E14TG2a0.0450.0040.049
Shin20207.9470.4738.546
ToxoLopit0.7210.0120.732
andreyev20101.4280.0561.484
andy20110.0580.0040.062
at_chloro0.0900.0040.095
baers20180.4460.0160.462
beltran20160.7950.0160.810
courtland20200.6990.0240.723
davies20180.3970.0040.401
dunkley20060.0120.0000.012
fabre20150.3410.0040.345
foster20060.0330.0000.032
groen20141.0170.1001.117
hall20090.2220.0000.222
havugimana20120.1830.0120.195
hirst20181.6230.1241.746
hyperLOPIT20155.2520.1415.393
hyperLOPITU2OS20172.5110.0362.547
itzhak20160.9130.0160.929
itzhak20171.9740.0392.016
itzhak2017dynamic1.3710.0401.411
kirkwood20130.0410.0050.045
kozik20200.2550.0030.259
krahmer2018pcp11.109 0.30011.409
kristensen20120.0260.0000.026
lopimsSyn20.8410.0080.849
mulvey20154.3030.2244.527
nikolovski20120.370.000.37
nikolovski20140.4330.0120.445
orre20190.5160.0200.535
pRolocdata0.0240.0000.024
pRolocmetadata0.0180.0040.022
rodriguez2012r10.7920.0040.797
stekhoven20140.2930.0080.300
tan20090.0160.0000.017
thpLOPIT202113.665 0.20813.874
thpTimecourse20210.1400.0040.144
trotter20100.4090.0040.413
yeast0.4200.0080.428