Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:36:09 -0400 (Fri, 29 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 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 1337/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSnID 1.36.0 (landing page) Vlad Petyuk
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.36.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSnID_1.36.0.tar.gz |
StartedAt: 2024-03-28 00:32:33 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 00:38:49 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 376.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSnID.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSnID_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSnID.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 ‘MSnID/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSnID’ version ‘1.36.0’ * 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 loading without being on the library search path ... 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 11.640 0.899 13.289 remap_accessions-method 5.895 0.772 6.946 remap_fasta_entry_names 5.919 0.611 6.799 optimize_filter 2.961 0.657 11.924 * 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 ... ‘handling_mods.Rnw’... OK ‘msnid_vignette.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/MSnID.Rcheck/00check.log’ for details.
MSnID.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MSnID ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (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. > 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 Mar 28 00:36:46 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 32.192 1.021 39.344
MSnID.Rcheck/MSnID-Ex.timings
name | user | system | elapsed | |
MSnID-class | 0.000 | 0.000 | 0.001 | |
MSnIDFilter-class | 0.163 | 0.024 | 0.167 | |
accessions | 0.561 | 0.056 | 0.616 | |
add_mod_symbol | 0.774 | 0.000 | 0.774 | |
apply_filter | 0.213 | 0.008 | 0.189 | |
assess_missed_cleavages | 0.143 | 0.008 | 0.142 | |
assess_termini | 0.139 | 0.000 | 0.139 | |
correct_peak_selection | 0.092 | 0.000 | 0.092 | |
data | 0.089 | 0.000 | 0.078 | |
evaluate_filter | 0.189 | 0.000 | 0.167 | |
fetch_conversion_table | 11.640 | 0.899 | 13.289 | |
id_quality | 0.095 | 0.004 | 0.094 | |
infer_parsimonious_accessions | 1.563 | 0.020 | 0.899 | |
map_mod_sites | 1.153 | 0.108 | 1.255 | |
mass_measurement_error | 0.079 | 0.000 | 0.080 | |
optimize_filter | 2.961 | 0.657 | 11.924 | |
peptides | 0.074 | 0.004 | 0.070 | |
psms | 0.099 | 0.000 | 0.099 | |
read_mzIDs | 0 | 0 | 0 | |
recalibrate | 0.074 | 0.007 | 0.081 | |
remap_accessions-method | 5.895 | 0.772 | 6.946 | |
remap_fasta_entry_names | 5.919 | 0.611 | 6.799 | |
report_mods | 0.901 | 0.128 | 1.030 | |