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This page was generated on 2025-09-20 12:05 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1790/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 3.19.0  (landing page)
RMassBank at Eawag
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/RMassBank
git_branch: devel
git_last_commit: 8175a30
git_last_commit_date: 2025-04-15 10:14:52 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RMassBank on lconway

To the developers/maintainers of the RMassBank package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RMassBank.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: RMassBank
Version: 3.19.0
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_3.19.0.tar.gz
StartedAt: 2025-09-19 23:32:14 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 23:38:34 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 380.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RMassBank.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_3.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RMassBank.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RMassBank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RMassBank’ version ‘3.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RmbSpectrum2-class.Rd: generate.formula
  buildRecord.Rd: normalize
  getMolecule.Rd: parse.smiles
  to.limits.rcdk.Rd: generate.formula
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 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/RMassBank.Rcheck/00check.log’
for details.


Installation output

RMassBank.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RMassBank
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘RMassBank’ ...
** this is package ‘RMassBank’ version ‘3.19.0’
** using staged installation
** R
** 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 (RMassBank)

Tests output

RMassBank.Rcheck/tests/doRUnit.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> #### doRUnit.R --- Run RUnit tests
> ####------------------------------------------------------------------------
> 
> ### Structure borrowed from rcppgls:
> ### https://github.com/eddelbuettel/rcppgsl/blob/master/tests/doRUnit.R
> 
> if(require("RUnit", quietly = TRUE)) {
+ 	if(require("RMassBankData", quietly = TRUE) && !(compareVersion(installed.packages()["RMassBankData","Version"],"1.99.0") == -1)) {
+ 		pkg <- "RMassBank"
+ 		print("Starting tests")
+ 		require(pkg, character.only=TRUE)
+ 
+ 		path <- system.file("unitTests", package = pkg)
+ 
+ 		stopifnot(file.exists(path), file.info(path.expand(path))$isdir)
+ 
+ 		source(file.path(path, "runTests.R"), echo = TRUE)
+ 	} else {
+ 		## Taking this message out until the new RMassBankData is on bioc, just to avoid confusion.
+         # message("Package RMassBankData with version > 1.99 not available, cannot run unit tests")
+ 	}
+ } else {
+ 	message("Package RUnit not available, cannot run unit tests")
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  1.834   1.059   2.964 

Example timings

RMassBank.Rcheck/RMassBank-Ex.timings

nameusersystemelapsed
CAS2SMILES0.0490.0101.109
CTS.externalIdSubset0.0000.0010.000
CTS.externalIdTypes000
RmbDefaultSettings0.0050.0020.008
add.formula0.0040.0000.005
addMB000
addPeaks0.0000.0000.001
addPeaksManually000
aggregateSpectra0.0000.0010.000
analyzeMsMs0.0000.0000.001
annotator.default000
archiveResults0.0110.0010.012
cleanElnoise000
combineMultiplicities000
compoundlist2SDF000
createCompoundlist0.0000.0010.000
createMolfile000
dbe0.0000.0010.001
deprofile0.0010.0000.001
dot-parseTitleString000
filterCompoundlist000
filterLowaccResults0.0000.0000.001
filterMultiplicity000
filterPeakSatellites0.0000.0000.001
filterPeaksMultiplicity0.0000.0010.000
findMass0.6010.0590.217
findMsMsHR0.0010.0010.000
findMsMsHRperxcms0.0010.0000.000
findMz0.0010.0010.000
findMz.formula0.3950.0370.219
findProgress0.0000.0000.001
flatten0.0000.0010.000
formulastring.to.list0.0010.0000.001
gatherCCTE000
gatherData0.0000.0000.001
gatherDataBabel0.0000.0000.001
gatherDataUnknown000
gatherPubChem000
getCASRN000
getCSID000
getCactus0.0210.0011.202
getCtsKey0.0110.0021.065
getCtsRecord0.0070.0010.277
getDTXCID000
getDTXSID000
getDTXSMILES000
getField000
getMolecule0.0380.0070.026
getPcId0.0140.0020.579
getPrefName0.0010.0000.001
is.valid.formula0.0010.0000.001
loadInfolists0.0000.0010.000
loadList0.0000.0000.001
makeRecalibration0.0000.0000.001
mbWorkflow0.0000.0000.001
mergePeaks000
order.formula0.0030.0010.002
parseMassBank000
parseMbRecord000
plotMbWorkspaces000
ppm0.0000.0000.001
problematicPeaks0.1040.0020.107
reanalyzeFailpeaks000
recalibrate000
recalibrate.addMS1data0.0000.0010.000
smiles2mass000
to.limits.rcdk0.0020.0010.002
toMassbank000
toRMB000
updateHeader0.0000.0000.001
updateSettings000
validate000