Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1320/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSnID 1.39.0 (landing page) Vlad Petyuk
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the MSnID package: - 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 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: MSnID |
Version: 1.39.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MSnID_1.39.0.tar.gz |
StartedAt: 2024-07-16 02:03:45 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 02:10:19 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 394.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSnID.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MSnID_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MSnID.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MSnID/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MSnID' version '1.39.0' * 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 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 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 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fetch_conversion_table 11.19 1.67 13.35 remap_accessions-method 6.36 0.75 7.43 remap_fasta_entry_names 5.64 0.65 6.73 optimize_filter 3.85 0.28 17.57 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MSnID.Rcheck/00check.log' for details.
MSnID.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MSnID ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 -- Tue Jul 16 02:10:09 2024 *********************************************** 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 36.45 3.25 57.20
MSnID.Rcheck/MSnID-Ex.timings
name | user | system | elapsed | |
MSnID-class | 0 | 0 | 0 | |
MSnIDFilter-class | 0.11 | 0.01 | 0.13 | |
accessions | 0.14 | 0.00 | 0.14 | |
add_mod_symbol | 1.25 | 0.03 | 1.52 | |
apply_filter | 0.14 | 0.06 | 0.20 | |
assess_missed_cleavages | 1.10 | 0.02 | 1.11 | |
assess_termini | 0.11 | 0.01 | 0.13 | |
correct_peak_selection | 0.06 | 0.00 | 0.06 | |
data | 0.03 | 0.02 | 0.06 | |
evaluate_filter | 0.11 | 0.05 | 0.16 | |
fetch_conversion_table | 11.19 | 1.67 | 13.35 | |
id_quality | 0.06 | 0.00 | 0.08 | |
infer_parsimonious_accessions | 0.74 | 0.14 | 1.05 | |
map_mod_sites | 1.81 | 0.11 | 1.92 | |
mass_measurement_error | 0.06 | 0.00 | 0.06 | |
optimize_filter | 3.85 | 0.28 | 17.57 | |
peptides | 0.04 | 0.00 | 0.04 | |
psms | 0.04 | 0.04 | 0.07 | |
read_mzIDs | 0 | 0 | 0 | |
recalibrate | 0.07 | 0.00 | 0.07 | |
remap_accessions-method | 6.36 | 0.75 | 7.43 | |
remap_fasta_entry_names | 5.64 | 0.65 | 6.73 | |
report_mods | 1.46 | 0.19 | 1.61 | |