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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 1784/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 3.14.0  (landing page)
RMassBank at Eawag
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/RMassBank
git_branch: RELEASE_3_19
git_last_commit: 8ec7b0f
git_last_commit_date: 2024-04-30 10:28:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for RMassBank on nebbiolo1

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: 3.14.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RMassBank.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RMassBank_3.14.0.tar.gz
StartedAt: 2024-06-13 02:54:55 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 03:06:32 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 696.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RMassBank.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RMassBank.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RMassBank_3.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
getCactus 0.064  0.004    8.42
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

RMassBank.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RMassBank
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘RMassBank’ ...
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.212   0.064   0.267 

Example timings

RMassBank.Rcheck/RMassBank-Ex.timings

nameusersystemelapsed
CAS2SMILES0.0990.0000.599
CTS.externalIdSubset0.0010.0000.000
CTS.externalIdTypes000
RmbDefaultSettings0.0060.0000.006
add.formula0.0040.0000.004
addMB000
addPeaks000
addPeaksManually000
aggregateSpectra0.0000.0010.001
analyzeMsMs0.0000.0010.000
annotator.default000
archiveResults0.0100.0020.012
cleanElnoise0.0000.0010.000
combineMultiplicities000
compoundlist2SDF000
createCompoundlist000
createMolfile0.0000.0000.001
dbe0.0000.0010.001
deprofile0.0000.0010.000
dot-parseTitleString0.0000.0000.001
filterCompoundlist000
filterLowaccResults000
filterMultiplicity0.0000.0010.000
filterPeakSatellites0.0000.0010.001
filterPeaksMultiplicity000
findMass0.7930.0120.194
findMsMsHR0.0000.0000.001
findMsMsHRperxcms000
findMz0.0010.0000.000
findMz.formula0.6590.0210.156
findProgress000
flatten0.0000.0000.001
formulastring.to.list0.0010.0000.001
gatherData0.0000.0000.001
gatherDataBabel000
gatherDataUnknown000
gatherPubChem000
getCSID000
getCactus0.0640.0048.420
getCtsKey0.0710.0000.602
getCtsRecord0.0890.0040.320
getField000
getMolecule0.0620.0120.042
getPcId0.0790.0010.405
is.valid.formula0.0010.0000.001
loadInfolists000
loadList000
makeRecalibration000
mbWorkflow000
mergePeaks000
order.formula0.0000.0020.002
parseMassBank000
parseMbRecord000
plotMbWorkspaces0.0000.0010.000
ppm000
problematicPeaks0.1050.0040.109
reanalyzeFailpeaks000
recalibrate000
recalibrate.addMS1data000
smiles2mass0.0010.0000.001
to.limits.rcdk0.0020.0000.002
toMassbank000
toRMB0.0000.0010.000
updateHeader000
updateSettings000
validate0.0000.0010.000