Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-11-26 11:05:52 -0500 (Sat, 26 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4201
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
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 nebbiolo1


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? 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 1263/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.33.0  (landing page)
Vlad Petyuk
Snapshot Date: 2022-11-25 14:00:12 -0500 (Fri, 25 Nov 2022)
git_url: https://git.bioconductor.org/packages/MSnID
git_branch: master
git_last_commit: 981bf32
git_last_commit_date: 2022-11-01 11:10:19 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'MSnbase' which is not available

Summary

Package: MSnID
Version: 1.33.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MSnID_1.33.0.tar.gz
StartedAt: 2022-11-25 21:55:22 -0500 (Fri, 25 Nov 2022)
EndedAt: 2022-11-25 22:01:31 -0500 (Fri, 25 Nov 2022)
EllapsedTime: 369.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MSnID.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MSnID_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MSnID.Rcheck’
* using R Under development (unstable) (2022-10-25 r83175)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘MSnID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSnID’ version ‘1.33.0’
* 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  9.335  1.164  11.378
remap_accessions-method 4.693  0.588   5.657
optimize_filter         2.848  0.232  12.567
* 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-3.17-bioc/meat/MSnID.Rcheck/00check.log’
for details.



Installation output

MSnID.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MSnID
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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)

Tests output

MSnID.Rcheck/tests/runTests.Rout


R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences"
Copyright (C) 2022 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 -- Fri Nov 25 21:59:26 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 
 35.783   1.520  44.747 

Example timings

MSnID.Rcheck/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.1660.0280.177
accessions0.6080.0080.617
add_mod_symbol0.7670.0660.834
apply_filter0.2070.0080.180
assess_missed_cleavages0.1430.0120.150
assess_termini0.1370.0000.138
correct_peak_selection0.0950.0000.096
data0.0900.0080.089
evaluate_filter0.2070.0080.184
fetch_conversion_table 9.335 1.16411.378
id_quality0.0850.0000.080
infer_parsimonious_accessions1.6460.0080.899
map_mod_sites1.1420.0721.207
mass_measurement_error0.0700.0030.073
optimize_filter 2.848 0.23212.567
peptides0.0740.0080.077
psms0.0750.0040.079
read_mzIDs000
recalibrate0.0880.0200.108
remap_accessions-method4.6930.5885.657
remap_fasta_entry_names3.9560.5724.805
report_mods0.8580.1360.993