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This page was generated on 2024-03-28 14:52:06 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
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 297/429 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
pRolocdata 1.40.0 (landing page) Laurent Gatto
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
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. |
Package: pRolocdata |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings pRolocdata_1.40.0.tar.gz |
StartedAt: 2024-03-28 11:58:05 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 12:04:18 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 372.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pRolocdata.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings pRolocdata_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/pRolocdata.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘1.40.0’ * 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 607.5Mb sub-directories of 1Mb or more: data 190.4Mb extdata 416.6Mb * 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 loading without being on the library search path ... OK * checking 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 ... 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 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 13.598 0.303 13.903 krahmer2018pcp 10.180 0.388 10.568 Shin2020 8.860 0.528 9.400 * 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-3.18-data-experiment/meat/pRolocdata.Rcheck/00check.log’ for details.
pRolocdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL pRolocdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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)
pRolocdata.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 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, 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, 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 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 2.28.1 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 1.40.0. Use 'pRolocdata()' to list available data sets. > > test_check("pRolocdata") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ] > > proc.time() user system elapsed 41.928 1.574 43.491
pRolocdata.Rcheck/pRolocdata-Ex.timings
name | user | system | elapsed | |
E14TG2a | 0.028 | 0.012 | 0.041 | |
Shin2020 | 8.860 | 0.528 | 9.400 | |
ToxoLopit | 0.593 | 0.020 | 0.614 | |
andreyev2010 | 0.590 | 0.016 | 0.606 | |
andy2011 | 0.058 | 0.000 | 0.059 | |
at_chloro | 0.823 | 0.092 | 0.915 | |
baers2018 | 0.357 | 0.008 | 0.365 | |
beltran2016 | 0.567 | 0.004 | 0.571 | |
courtland2020 | 0.598 | 0.016 | 0.614 | |
davies2018 | 0.332 | 0.013 | 0.345 | |
dunkley2006 | 0.012 | 0.000 | 0.012 | |
fabre2015 | 0.273 | 0.012 | 0.285 | |
foster2006 | 0.032 | 0.000 | 0.031 | |
groen2014 | 0.969 | 0.016 | 0.984 | |
hall2009 | 0.148 | 0.008 | 0.156 | |
havugimana2012 | 0.110 | 0.016 | 0.126 | |
hirst2018 | 0.474 | 0.028 | 0.503 | |
hyperLOPIT2015 | 3.449 | 0.064 | 3.513 | |
hyperLOPITU2OS2017 | 1.373 | 0.032 | 1.405 | |
itzhak2016stcSILAC | 0.632 | 0.012 | 0.643 | |
itzhak2017 | 1.734 | 0.068 | 1.802 | |
itzhak2017dynamic | 1.290 | 0.016 | 1.313 | |
kirkwood2013 | 0.041 | 0.000 | 0.041 | |
kozik2020 | 0.211 | 0.000 | 0.211 | |
krahmer2018pcp | 10.180 | 0.388 | 10.568 | |
kristensen2012 | 0.023 | 0.000 | 0.023 | |
lopimsSyn2 | 0.649 | 0.012 | 0.662 | |
moloney2023 | 0.770 | 0.023 | 0.795 | |
mulvey2015 | 2.315 | 0.104 | 2.420 | |
nikolovski2012 | 0.293 | 0.008 | 0.301 | |
nikolovski2014 | 0.359 | 0.011 | 0.371 | |
orre2019 | 0.411 | 0.008 | 0.419 | |
pRolocdata | 0.013 | 0.002 | 0.015 | |
pRolocmetadata | 0.010 | 0.004 | 0.014 | |
rodriguez2012r1 | 0.643 | 0.004 | 0.647 | |
stekhoven2014 | 0.207 | 0.000 | 0.207 | |
tan2009 | 0.016 | 0.000 | 0.015 | |
thpLOPIT2021 | 13.598 | 0.303 | 13.903 | |
thpTimecourse2021 | 0.141 | 0.004 | 0.145 | |
trotter2010 | 0.374 | 0.000 | 0.373 | |
yeast | 0.366 | 0.008 | 0.373 | |