Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:46 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the MSnID package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSnID.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1204/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSnID 1.26.0 (landing page) Vlad Petyuk
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MSnID |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MSnID_1.26.0.tar.gz |
StartedAt: 2021-10-14 10:43:26 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:47:26 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 239.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSnID.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MSnID_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MSnID.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSnID/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSnID’ version ‘1.26.0’ * 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 ‘MSnID’ 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 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 ... NOTE Namespaces in Imports field not imported from: ‘BiocGenerics’ ‘BiocStyle’ ‘RUnit’ ‘ggplot2’ ‘msmsTests’ ‘xtable’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘peptideRef’ Undefined global functions or variables: peptideRef * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fetch_conversion_table 12.605 0.460 14.179 remap_accessions-method 5.854 0.440 6.749 remap_fasta_entry_names 5.445 0.369 6.247 optimize_filter 2.528 0.305 11.333 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/MSnID.Rcheck/00check.log’ for details.
MSnID.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MSnID ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘MSnID’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** demo ** 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 (MSnID)
MSnID.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > BiocGenerics:::testPackage("MSnID") Note, the anticipated/suggested columns in the peptide-to-spectrum matching results are: ----------------------------------------------- accession calculatedMassToCharge chargeState experimentalMassToCharge isDecoy peptide spectrumFile spectrumID Reading from mzIdentMLs ... reading c_elegans.mzid.gz... DONE! Reading from mzIdentMLs ... RUNIT TEST PROTOCOL -- Thu Oct 14 10:47:22 2021 *********************************************** Number of test functions: 19 Number of errors: 0 Number of failures: 0 1 Test Suite : MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures Number of test functions: 19 Number of errors: 0 Number of failures: 0 There were 12 warnings (use warnings() to see them) > > proc.time() user system elapsed 35.542 1.338 43.403
MSnID.Rcheck/MSnID-Ex.timings
name | user | system | elapsed | |
MSnID-class | 0.000 | 0.000 | 0.001 | |
MSnIDFilter-class | 1.083 | 0.024 | 1.081 | |
accessions | 0.090 | 0.012 | 0.102 | |
add_mod_symbol | 1.064 | 0.016 | 1.081 | |
apply_filter | 0.227 | 0.016 | 0.206 | |
assess_missed_cleavages | 0.157 | 0.004 | 0.155 | |
assess_termini | 0.160 | 0.000 | 0.161 | |
correct_peak_selection | 0.101 | 0.000 | 0.101 | |
data | 0.751 | 0.048 | 0.788 | |
evaluate_filter | 0.202 | 0.004 | 0.172 | |
fetch_conversion_table | 12.605 | 0.460 | 14.179 | |
id_quality | 0.083 | 0.003 | 0.084 | |
infer_parsimonious_accessions | 1.759 | 0.001 | 1.007 | |
map_mod_sites | 1.114 | 0.051 | 1.162 | |
mass_measurement_error | 0.066 | 0.017 | 0.081 | |
optimize_filter | 2.528 | 0.305 | 11.333 | |
peptides | 0.066 | 0.008 | 0.070 | |
psms | 0.086 | 0.004 | 0.090 | |
read_mzIDs | 0.001 | 0.000 | 0.000 | |
recalibrate | 0.087 | 0.004 | 0.091 | |
remap_accessions-method | 5.854 | 0.440 | 6.749 | |
remap_fasta_entry_names | 5.445 | 0.369 | 6.247 | |
report_mods | 1.052 | 0.115 | 1.168 | |