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This page was generated on 2022-01-25 11:07:47 -0500 (Tue, 25 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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

CHECK results for MSnID on riesling1


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 1218/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.29.0  (landing page)
Vlad Petyuk
Snapshot Date: 2022-01-24 13:55:18 -0500 (Mon, 24 Jan 2022)
git_url: https://git.bioconductor.org/packages/MSnID
git_branch: master
git_last_commit: 421aa9e
git_last_commit_date: 2021-10-26 12:16:01 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'MSnbase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSnID
Version: 1.29.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSnID.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSnID_1.29.0.tar.gz
StartedAt: 2022-01-24 19:28:13 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 19:31:59 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 225.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MSnID.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSnID.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSnID_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MSnID.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSnID/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSnID' version '1.29.0'
* 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 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  8.67   1.18   11.78
remap_accessions-method 3.71   0.60    5.03
optimize_filter         1.77   0.13   10.09
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/MSnID.Rcheck/00check.log'
for details.



Installation output

MSnID.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MSnID
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'MSnID'
    finding HTML links ... done
    MSnID-class                             html  
    finding level-2 HTML links ... done

    MSnID-package                           html  
    MSnIDFilter-class                       html  
    accessions                              html  
    add_mod_symbol                          html  
    apply_filter                            html  
    assess_missed_cleavages                 html  
    assess_termini                          html  
    correct_peak_selection                  html  
    data                                    html  
    evaluate_filter                         html  
    fetch_conversion_table                  html  
    id_quality                              html  
    infer_parsimonious_accessions           html  
    map_mod_sites                           html  
    mass_measurement_error                  html  
    optimize_filter                         html  
    peptides                                html  
    psms                                    html  
    read_mzIDs                              html  
    recalibrate                             html  
    remap_accessions-method                 html  
    remap_fasta_entry_names                 html  
    report_mods                             html  
** 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)
Making 'packages.html' ... done

Tests output

MSnID.Rcheck/tests/runTests.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Mon Jan 24 19:31:46 2022 
*********************************************** 
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 
  28.04    1.51   37.56 

Example timings

MSnID.Rcheck/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.610.010.61
accessions0.080.000.08
add_mod_symbol0.890.020.90
apply_filter0.180.060.25
assess_missed_cleavages0.180.030.20
assess_termini0.170.050.22
correct_peak_selection0.060.030.10
data0.090.020.11
evaluate_filter0.190.040.23
fetch_conversion_table 8.67 1.1811.78
id_quality0.110.000.11
infer_parsimonious_accessions0.750.040.81
map_mod_sites0.840.030.87
mass_measurement_error0.050.020.07
optimize_filter 1.77 0.1310.09
peptides0.090.010.11
psms0.090.000.09
read_mzIDs000
recalibrate0.030.060.10
remap_accessions-method3.710.605.03
remap_fasta_entry_names3.180.484.34
report_mods0.60.00.6