Multiple platform build/check report for BioC 3.19 - BUILD results for MSnID on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4760
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4494
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4508
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4466
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*

BUILD results for MSnID on merida1

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.

raw results

Summary

Package: MSnID

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MSnID

StartedAt: 2024-06-23 21:04:32 -0400 (Sun, 23 Jun 2024)

EndedAt: 2024-06-23 21:09:31 -0400 (Sun, 23 Jun 2024)

EllapsedTime: 299.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MSnID
###
##############################################################################
##############################################################################


* checking for file ‘MSnID/DESCRIPTION’ ... OK
* preparing ‘MSnID’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘handling_mods.Rnw’ using Sweave
Loading required package: Rcpp

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:dplyr’:

    combine, intersect, setdiff, union

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:dplyr’:

    first, rename

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: ‘IRanges’

The following objects are masked from ‘package:dplyr’:

    collapse, desc, slice

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...

Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Detected extra chararacters in the peptide sequences!

Peptides with no modifications in question were detected. 
The correspoding identifications will be removed.

loading from cache
Warning: Couldn't set cache size: file is not a database
Use `cache_size` = NULL to turn off this warning.
Warning: Couldn't set synchronous mode: file is not a database
Use `synchronous` = NULL to turn off this warning.

Error: processing vignette 'handling_mods.Rnw' failed with diagnostics:
 chunk 13 
Error : failed to load resource
  name: AH116710
  title: org.Hs.eg.db.sqlite
  reason: file is not a database

--- failed re-building ‘handling_mods.Rnw’

--- re-building ‘msnid_vignette.Rnw’ using Sweave
Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...

Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning in type.convert.default(...) :
  'as.is' should be specified by the caller; using TRUE
Warning: call dbDisconnect() when finished working with a connection
Warning: The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0.
ℹ Please use `after_stat(count)` instead.
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:MSnID’:

    peptides

The following object is masked from ‘package:stats’:

    smooth


This is MSnbase version 2.30.1 
  Visit https://lgatto.github.io/MSnbase/ to get started.
 Consider switching to the 'R for Mass Spectrometry'
 packages - see https://RforMassSpectrometry.org for details.


Attaching package: ‘MSnbase’

The following object is masked _by_ ‘.GlobalEnv’:

    msnset

The following object is masked from ‘package:base’:

    trimws

Warning in .combineFeatures(object, groupBy, method, fcol, redundancy.handler,  :
  Parameter 'fun' is deprecated. Please use 'method' instead
--- finished re-building ‘msnid_vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘handling_mods.Rnw’

Error: Vignette re-building failed.
Execution halted