##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RMassBank.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RMassBank_3.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RMassBank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RMassBank’ version ‘3.14.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RMassBank’ 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ChemmineOB’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘MSnbase:::writeMgfContent’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analyzeMsMs.formula.optimized: no visible binding for global variable
  ‘occurrenceMatrix’
msmsRead.ticms2: no visible global function definition for
  ‘c.msmsWSspecs’
reanalyzeFailpeak: no visible binding for global variable ‘mass.calc’
updateObject,RmbSpectraSet: no visible global function definition for
  ‘updateObjectFromSlots’
Undefined global functions or variables:
  c.msmsWSspecs mass.calc occurrenceMatrix updateObjectFromSlots
* checking Rd files ... NOTE
checkRd: (-1) RmbSettings.Rd:11-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:17-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:21-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:28-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:36-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:63-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:68-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:73-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:79-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:82-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:87-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:90-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:100-134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:135-149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkIsotopes.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) filterPeaksMultiplicity.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findMsMsHR.Rd:49: Lost braces
    49 | to use for formula lookup. Note: In \\code{findMsMsHR.mass}, this is entirely optional and
       |                                           ^
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/00check.log’
for details.