Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:58 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 1337/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.36.0  (landing page)
Vlad Petyuk
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/MSnID
git_branch: RELEASE_3_18
git_last_commit: 605438e
git_last_commit_date: 2023-10-24 10:38:36 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for MSnID on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MSnID
Version: 1.36.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings MSnID_1.36.0.tar.gz
StartedAt: 2023-11-02 12:28:37 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 12:34:36 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 359.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MSnID.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings MSnID_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSnID.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSnID’ version ‘1.36.0’
* 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  15.223  0.719  22.882
remap_accessions-method  8.124  0.475  12.772
remap_fasta_entry_names  8.160  0.307  11.789
optimize_filter          2.828  0.047  13.517
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  MSnID RUnit Tests - 19 test functions, 0 errors, 1 failure
  FAILURE in test_data_load: Error in checkIdentical(psms(msnidObj), psms(msnid2)) : FALSE 
   
  
  Test files with failing tests
  
     test_data_load.R 
       test_data_load 
  
  
  Error in BiocGenerics:::testPackage("MSnID") : 
    unit tests failed for package MSnID
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MSnID.Rcheck/00check.log’
for details.


Installation output

MSnID.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL MSnID
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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)

Tests output

MSnID.Rcheck/tests/runTests.Rout.fail


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 ...

Timing stopped at: 0.125 0 0.124
Error in checkIdentical(psms(msnidObj), psms(msnid2)) : FALSE 
 
In addition: There were 12 warnings (use warnings() to see them)


RUNIT TEST PROTOCOL -- Thu Nov  2 12:34:33 2023 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
MSnID RUnit Tests - 19 test functions, 0 errors, 1 failure
FAILURE in test_data_load: Error in checkIdentical(psms(msnidObj), psms(msnid2)) : FALSE 
 

Test files with failing tests

   test_data_load.R 
     test_data_load 


Error in BiocGenerics:::testPackage("MSnID") : 
  unit tests failed for package MSnID
Execution halted

Example timings

MSnID.Rcheck/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.1960.0230.205
accessions0.6990.0000.702
add_mod_symbol1.0060.0121.023
apply_filter0.2340.0120.224
assess_missed_cleavages0.1660.0150.182
assess_termini0.1620.0040.166
correct_peak_selection0.1200.0160.136
data0.1150.0000.105
evaluate_filter0.2280.0040.216
fetch_conversion_table15.223 0.71922.882
id_quality0.1120.0000.106
infer_parsimonious_accessions1.5190.0481.373
map_mod_sites1.4470.0711.528
mass_measurement_error0.0900.0080.099
optimize_filter 2.828 0.04713.517
peptides0.0890.0000.090
psms0.1240.0040.128
read_mzIDs0.0000.0000.001
recalibrate0.1060.0000.108
remap_accessions-method 8.124 0.47512.772
remap_fasta_entry_names 8.160 0.30711.789
report_mods1.2690.0401.313