##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r MSnID -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe 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

The following object is masked from 'package:grDevices':

    windows

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.


Error: processing vignette 'handling_mods.Rnw' failed with diagnostics:
 chunk 13 
Error : Corrupt Cache: index file
  See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
  cache: F:\biocbuild\AnnotationHub_cache
  filename: annotationhub.index.rds

--- 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: 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