Back to Build/check report for BioC 3.19 experimental data |
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This page was generated on 2024-10-17 14:51 -0400 (Thu, 17 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
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 298/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
pRolocdata 1.42.0 (landing page) Laurent Gatto
| nebbiolo1 | 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: 1.42.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings pRolocdata_1.42.0.tar.gz |
StartedAt: 2024-10-17 11:54:22 -0400 (Thu, 17 Oct 2024) |
EndedAt: 2024-10-17 12:02:33 -0400 (Thu, 17 Oct 2024) |
EllapsedTime: 491.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pRolocdata.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:pRolocdata.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings pRolocdata_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/pRolocdata.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘pRolocdata/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pRolocdata’ version ‘1.42.0’ * 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 554.7Mb sub-directories of 1Mb or more: data 191.4Mb extdata 362.9Mb * 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 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 12.910 0.480 13.389 krahmer2018pcp 10.522 0.672 11.194 Shin2020 4.703 0.331 5.043 * 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-3.19-data-experiment/meat/pRolocdata.Rcheck/00check.log’ for details.
pRolocdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL pRolocdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life" 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 2.30.1 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 1.42.0. Use 'pRolocdata()' to list available data sets. > > test_check("pRolocdata") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ] > > proc.time() user system elapsed 43.869 1.868 45.728
pRolocdata.Rcheck/pRolocdata-Ex.timings
name | user | system | elapsed | |
E14TG2a | 0.032 | 0.000 | 0.032 | |
Shin2020 | 4.703 | 0.331 | 5.043 | |
ToxoLopit | 0.553 | 0.028 | 0.582 | |
andreyev2010 | 0.619 | 0.020 | 0.639 | |
andy2011 | 0.059 | 0.004 | 0.063 | |
at_chloro | 0.127 | 0.004 | 0.132 | |
baers2018 | 0.364 | 0.016 | 0.380 | |
beltran2016 | 0.578 | 0.020 | 0.599 | |
courtland2020 | 0.601 | 0.040 | 0.641 | |
davies2018 | 0.358 | 0.008 | 0.366 | |
dunkley2006 | 0.005 | 0.008 | 0.013 | |
fabre2015 | 0.267 | 0.016 | 0.283 | |
foster2006 | 0.028 | 0.004 | 0.032 | |
groen2014 | 1.067 | 0.203 | 1.271 | |
hall2009 | 0.164 | 0.012 | 0.176 | |
havugimana2012 | 0.124 | 0.006 | 0.130 | |
hirst2018 | 0.500 | 0.014 | 0.515 | |
hyperLOPIT2015 | 4.209 | 0.384 | 4.593 | |
hyperLOPITU2OS2017 | 1.443 | 0.036 | 1.479 | |
itzhak2016stcSILAC | 0.644 | 0.016 | 0.660 | |
itzhak2017 | 1.790 | 0.096 | 1.886 | |
itzhak2017dynamic | 1.295 | 0.020 | 1.315 | |
kirkwood2013 | 0.058 | 0.008 | 0.066 | |
kozik2020 | 0.203 | 0.016 | 0.219 | |
krahmer2018pcp | 10.522 | 0.672 | 11.194 | |
kristensen2012 | 0.025 | 0.000 | 0.025 | |
lopimsSyn2 | 0.646 | 0.012 | 0.658 | |
moloney2023 | 0.768 | 0.032 | 0.799 | |
mulvey2015 | 2.298 | 0.101 | 2.399 | |
nikolovski2012 | 0.310 | 0.008 | 0.318 | |
nikolovski2014 | 0.357 | 0.012 | 0.369 | |
orre2019 | 0.425 | 0.008 | 0.433 | |
pRolocdata | 0.015 | 0.000 | 0.016 | |
pRolocmetadata | 0.014 | 0.000 | 0.015 | |
rodriguez2012r1 | 0.643 | 0.008 | 0.651 | |
stekhoven2014 | 0.209 | 0.016 | 0.225 | |
tan2009 | 0.018 | 0.000 | 0.018 | |
thpLOPIT2021 | 12.910 | 0.480 | 13.389 | |
thpTimecourse2021 | 0.150 | 0.000 | 0.151 | |
trotter2010 | 0.362 | 0.000 | 0.362 | |
yeast | 0.358 | 0.020 | 0.378 | |