| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-01 11:36:39 -0400 (Wed, 01 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| 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 1784/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RMassBank 3.14.0 (landing page) RMassBank at Eawag
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: RMassBank |
| Version: 3.14.0 |
| 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_3.14.0.tar.gz |
| StartedAt: 2024-05-01 06:03:26 -0400 (Wed, 01 May 2024) |
| EndedAt: 2024-05-01 06:09:31 -0400 (Wed, 01 May 2024) |
| EllapsedTime: 365.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RMassBank.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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 beta (2024-04-14 r86421)
* 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) 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
| ^
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 ?
* 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.
RMassBank.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RMassBank ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)
RMassBank.Rcheck/tests/doRUnit.Rout
R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 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
1.780 0.938 2.725
RMassBank.Rcheck/RMassBank-Ex.timings
| name | user | system | elapsed | |
| CAS2SMILES | 0.055 | 0.015 | 2.483 | |
| CTS.externalIdSubset | 0.000 | 0.001 | 0.000 | |
| CTS.externalIdTypes | 0.000 | 0.000 | 0.001 | |
| RmbDefaultSettings | 0.006 | 0.002 | 0.008 | |
| add.formula | 0.005 | 0.001 | 0.006 | |
| addMB | 0 | 0 | 0 | |
| addPeaks | 0.000 | 0.000 | 0.001 | |
| addPeaksManually | 0 | 0 | 0 | |
| aggregateSpectra | 0.000 | 0.001 | 0.000 | |
| analyzeMsMs | 0 | 0 | 0 | |
| annotator.default | 0 | 0 | 0 | |
| archiveResults | 0.011 | 0.001 | 0.012 | |
| cleanElnoise | 0.000 | 0.001 | 0.000 | |
| combineMultiplicities | 0 | 0 | 0 | |
| compoundlist2SDF | 0 | 0 | 0 | |
| createCompoundlist | 0.000 | 0.001 | 0.000 | |
| createMolfile | 0.000 | 0.000 | 0.001 | |
| dbe | 0.000 | 0.000 | 0.001 | |
| deprofile | 0.000 | 0.000 | 0.001 | |
| dot-parseTitleString | 0 | 0 | 0 | |
| filterCompoundlist | 0 | 0 | 0 | |
| filterLowaccResults | 0.000 | 0.000 | 0.001 | |
| filterMultiplicity | 0.001 | 0.000 | 0.000 | |
| filterPeakSatellites | 0.000 | 0.000 | 0.001 | |
| filterPeaksMultiplicity | 0.000 | 0.000 | 0.001 | |
| findMass | 0.627 | 0.067 | 0.234 | |
| findMsMsHR | 0.003 | 0.000 | 0.001 | |
| findMsMsHRperxcms | 0.001 | 0.000 | 0.000 | |
| findMz | 0.001 | 0.000 | 0.000 | |
| findMz.formula | 0.403 | 0.036 | 0.263 | |
| findProgress | 0 | 0 | 0 | |
| flatten | 0 | 0 | 0 | |
| formulastring.to.list | 0.000 | 0.001 | 0.001 | |
| gatherData | 0 | 0 | 0 | |
| gatherDataBabel | 0 | 0 | 0 | |
| gatherDataUnknown | 0 | 0 | 0 | |
| gatherPubChem | 0.001 | 0.000 | 0.000 | |
| getCSID | 0.000 | 0.000 | 0.001 | |
| getCactus | 0.025 | 0.002 | 0.496 | |
| getCtsKey | 0.007 | 0.003 | 0.808 | |
| getCtsRecord | 0.006 | 0.002 | 0.244 | |
| getField | 0 | 0 | 0 | |
| getMolecule | 0.046 | 0.008 | 0.033 | |
| getPcId | 0.020 | 0.003 | 0.511 | |
| is.valid.formula | 0.001 | 0.000 | 0.001 | |
| loadInfolists | 0.000 | 0.000 | 0.001 | |
| loadList | 0 | 0 | 0 | |
| makeRecalibration | 0.000 | 0.001 | 0.001 | |
| mbWorkflow | 0.001 | 0.000 | 0.000 | |
| mergePeaks | 0 | 0 | 0 | |
| order.formula | 0.002 | 0.001 | 0.003 | |
| parseMassBank | 0 | 0 | 0 | |
| parseMbRecord | 0 | 0 | 0 | |
| plotMbWorkspaces | 0 | 0 | 0 | |
| ppm | 0 | 0 | 0 | |
| problematicPeaks | 0.131 | 0.002 | 0.134 | |
| reanalyzeFailpeaks | 0.000 | 0.001 | 0.000 | |
| recalibrate | 0.000 | 0.000 | 0.001 | |
| recalibrate.addMS1data | 0 | 0 | 0 | |
| smiles2mass | 0 | 0 | 0 | |
| to.limits.rcdk | 0.001 | 0.000 | 0.001 | |
| toMassbank | 0.000 | 0.000 | 0.001 | |
| toRMB | 0 | 0 | 0 | |
| updateHeader | 0 | 0 | 0 | |
| updateSettings | 0.000 | 0.001 | 0.000 | |
| validate | 0.000 | 0.000 | 0.001 | |