Back to Build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-07 15:40 -0400 (Sat, 07 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
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 2071/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SWATH2stats 1.35.0 (landing page) Peter Blattmann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
To the developers/maintainers of the SWATH2stats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SWATH2stats.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: SWATH2stats |
Version: 1.35.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SWATH2stats_1.35.0.tar.gz |
StartedAt: 2024-09-07 01:41:26 -0400 (Sat, 07 Sep 2024) |
EndedAt: 2024-09-07 01:44:10 -0400 (Sat, 07 Sep 2024) |
EllapsedTime: 164.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SWATH2stats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SWATH2stats_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SWATH2stats.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 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘SWATH2stats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SWATH2stats’ version ‘1.35.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘aLFQ’ * 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 ‘SWATH2stats’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/SWATH2stats.Rcheck/00check.log’ for details.
SWATH2stats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SWATH2stats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘SWATH2stats’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (SWATH2stats)
SWATH2stats.Rcheck/tests/test-all.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. > library(testthat) > test_check("SWATH2stats") Loading required package: SWATH2stats [1] "peterb_J131223_054" [1] "peterb_L150425_011_SW" [1] "peterb_L150514_002_SW" [ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ] [ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ] > > proc.time() user system elapsed 12.158 0.797 15.360
SWATH2stats.Rcheck/SWATH2stats-Ex.timings
name | user | system | elapsed | |
JPP_update | 0.097 | 0.004 | 0.101 | |
add_genesymbol | 0.007 | 0.000 | 0.006 | |
assess_decoy_rate | 0.093 | 0.004 | 0.097 | |
assess_fdr_byrun | 0.164 | 0.000 | 0.165 | |
assess_fdr_overall | 0.122 | 0.008 | 0.130 | |
convert4MSstats | 0.580 | 0.053 | 0.632 | |
convert4PECA | 0.129 | 0.003 | 0.133 | |
convert4aLFQ | 0.577 | 0.008 | 0.585 | |
convert4mapDIA | 0.320 | 0.016 | 0.337 | |
convert4pythonscript | 0.118 | 0.000 | 0.119 | |
convert_protein_ids | 0 | 0 | 0 | |
count_analytes | 0.119 | 0.003 | 0.122 | |
disaggregate | 0.186 | 0.008 | 0.194 | |
filter_all_peptides | 0.124 | 0.000 | 0.125 | |
filter_mscore | 0.162 | 0.001 | 0.149 | |
filter_mscore_condition | 0.162 | 0.000 | 0.149 | |
filter_mscore_fdr | 0.295 | 0.000 | 0.295 | |
filter_mscore_freqobs | 0.146 | 0.003 | 0.138 | |
filter_on_max_peptides | 0.148 | 0.001 | 0.134 | |
filter_on_min_peptides | 0.138 | 0.000 | 0.124 | |
filter_proteotypic_peptides | 0.106 | 0.004 | 0.110 | |
import_data | 0.413 | 0.031 | 0.445 | |
load_mart | 1.175 | 0.141 | 4.034 | |
mscore4assayfdr | 0.289 | 0.008 | 0.297 | |
mscore4pepfdr | 0.219 | 0.000 | 0.219 | |
mscore4protfdr | 0.183 | 0.000 | 0.183 | |
plot.fdr_cube | 0.136 | 0.004 | 0.140 | |
plot.fdr_table | 0.148 | 0.000 | 0.148 | |
plot_correlation_between_samples | 0.414 | 0.024 | 0.438 | |
plot_variation | 0.384 | 0.012 | 0.396 | |
plot_variation_vs_total | 0.308 | 0.016 | 0.324 | |
reduce_OpenSWATH_output | 0.118 | 0.000 | 0.118 | |
removeDecoyProteins | 0.108 | 0.000 | 0.108 | |
sample_annotation | 0.133 | 0.000 | 0.133 | |
transform_MSstats_OpenSWATH | 0.002 | 0.000 | 0.002 | |
unifyProteinGroupLabels | 0.121 | 0.000 | 0.121 | |
validate_columns | 0.000 | 0.000 | 0.001 | |
write_matrix_peptides | 0.113 | 0.000 | 0.113 | |
write_matrix_proteins | 0.104 | 0.008 | 0.112 | |