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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings Spectra_1.17.1.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Spectra.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Spectra/DESCRIPTION’ ... OK
* this is package ‘Spectra’ version ‘1.17.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Spectra’ 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("_H5Dclose", ..., PACKAGE = "rhdf5")
  .Call("_H5Dopen", ..., PACKAGE = "rhdf5")
  .Call("_H5Dread", ..., PACKAGE = "rhdf5")
  .Call("_H5Fclose", ..., PACKAGE = "rhdf5")
  .Call("_H5Fopen", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MsBackend.Rd: bpparam, closest, SnowParam, NumericList
  MsBackendCached.Rd: NumericList
  Spectra.Rd: ProcessingStep-class, bpparam
  addProcessing.Rd: bpparam, nentropy, common
  combineSpectra.Rd: bpparam
  compareSpectra.Rd: ndotproduct
  estimatePrecursorIntensity.Rd: bpparam
  estimatePrecursorMz.Rd: SerialParam
  filterMsLevel.Rd: isotopologues, isotopicSubstitutionMatrix
  joinPeaks.Rd: gnps
  processingChunkSize.Rd: backendParallelFactor, bpparam
  spectra-plotting.Rd: common
  spectraData.Rd: bpparam, NumericList, SimpleList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 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
estimatePrecursorMz 47.034  0.838  47.774
addProcessing        8.303  0.879   9.051
plotMzDelta          7.464  1.295   7.866
combinePeaks         7.253  1.390   4.824
Spectra              3.769  1.808   3.906
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Spectra.Rcheck/00check.log’
for details.