Back to Build/check report for BioC 3.20 experimental data
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2024-07-02 14:51 -0400 (Tue, 02 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
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 295/425HostnameOS / ArchINSTALLBUILDCHECK
pRolocdata 1.43.0  (landing page)
Laurent Gatto
Snapshot Date: 2024-07-02 07:30 -0400 (Tue, 02 Jul 2024)
git_url: https://git.bioconductor.org/packages/pRolocdata
git_branch: devel
git_last_commit: 6294f16
git_last_commit_date: 2024-04-30 10:38:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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: 1.43.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings pRolocdata_1.43.0.tar.gz
StartedAt: 2024-07-02 11:52:14 -0400 (Tue, 02 Jul 2024)
EndedAt: 2024-07-02 12:00:20 -0400 (Tue, 02 Jul 2024)
EllapsedTime: 486.3 seconds
RetCode: 0
Status:   OK  
CheckDir: pRolocdata.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings pRolocdata_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/pRolocdata.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘pRolocdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRolocdata’ version ‘1.43.0’
* 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 607.6Mb
  sub-directories of 1Mb or more:
    data     190.4Mb
    extdata  416.7Mb
* 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 ... NOTE
  Note: found 24 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   12.193  0.328  12.521
krahmer2018pcp  9.619  0.647  10.266
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/pRolocdata.Rcheck/00check.log’
for details.


Installation output

pRolocdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL pRolocdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, 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: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 2.31.1 
  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 1.43.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ]
> 
> proc.time()
   user  system elapsed 
 43.932   1.884  45.806 

Example timings

pRolocdata.Rcheck/pRolocdata-Ex.timings

nameusersystemelapsed
E14TG2a0.0240.0080.031
Shin20204.0340.2354.276
ToxoLopit0.5230.0120.535
andreyev20100.610.040.65
andy20110.0520.0040.056
at_chloro0.0940.0080.102
baers20180.3540.0240.377
beltran20160.5950.0400.635
courtland20200.5660.0280.593
davies20180.3450.0200.365
dunkley20060.0120.0000.011
fabre20150.2630.0080.270
foster20060.0310.0000.031
groen20141.0490.1561.206
hall20090.1610.0000.160
havugimana20120.1190.0080.127
hirst20180.4750.0210.496
hyperLOPIT20154.0900.3234.414
hyperLOPITU2OS20171.3440.0441.389
itzhak2016stcSILAC0.6070.0200.627
itzhak20171.6730.0501.722
itzhak2017dynamic1.2730.0271.301
kirkwood20130.0410.0000.040
kozik20200.2200.0120.232
krahmer2018pcp 9.619 0.64710.266
kristensen20120.0190.0040.024
lopimsSyn20.6390.0200.659
moloney20230.7630.0150.779
mulvey20153.0350.1433.178
nikolovski20120.2870.0130.300
nikolovski20140.3510.0070.359
orre20190.4230.0010.424
pRolocdata0.0160.0000.016
pRolocmetadata0.0140.0000.014
rodriguez2012r10.6310.0000.631
stekhoven20140.2050.0000.205
tan20090.0150.0000.015
thpLOPIT202112.193 0.32812.521
thpTimecourse20210.1370.0070.145
trotter20100.3370.0120.348
yeast0.3680.0040.373