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This page was generated on 2021-12-06 13:06:05 -0500 (Mon, 06 Dec 2021).

CHECK results for MSnID on machv2

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.

raw results

Package 1223/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.28.0  (landing page)
Vlad Petyuk
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/MSnID
git_branch: RELEASE_3_14
git_last_commit: 0e6de89
git_last_commit_date: 2021-10-26 12:16:01 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSnID
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSnID.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSnID_1.28.0.tar.gz
StartedAt: 2021-12-05 17:01:05 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 17:07:43 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 398.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MSnID.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSnID.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSnID_1.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MSnID.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.28.0’
* 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 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  19.082  1.220  22.606
remap_accessions-method  9.424  0.410  10.550
remap_fasta_entry_names  9.366  0.369  10.328
optimize_filter          2.686  0.162  16.324
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/MSnID.Rcheck/00check.log’
for details.



Installation output

MSnID.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSnID
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

MSnID.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 -- Sun Dec  5 17:07:23 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 
 58.184   1.515  73.682 

Example timings

MSnID.Rcheck/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class0.0000.0000.001
MSnIDFilter-class0.7390.0150.755
accessions0.0980.0080.105
add_mod_symbol0.9250.0220.948
apply_filter0.2530.0080.261
assess_missed_cleavages0.2010.0060.208
assess_termini0.2300.0020.232
correct_peak_selection0.1390.0050.145
data0.6250.0050.630
evaluate_filter0.2930.0090.301
fetch_conversion_table19.082 1.22022.606
id_quality0.1740.0050.178
infer_parsimonious_accessions1.4680.0471.515
map_mod_sites1.5520.0411.595
mass_measurement_error0.0770.0030.081
optimize_filter 2.686 0.16216.324
peptides0.1050.0020.108
psms0.1260.0080.135
read_mzIDs000
recalibrate0.1100.0050.115
remap_accessions-method 9.424 0.41010.550
remap_fasta_entry_names 9.366 0.36910.328
report_mods1.1860.0471.234