Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-12 17:39 -0400 (Fri, 12 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
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: /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: 2024-07-11 02:55:32 -0400 (Thu, 11 Jul 2024) |
EndedAt: 2024-07-11 03:09:22 -0400 (Thu, 11 Jul 2024) |
EllapsedTime: 829.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: RMassBank.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ... ERROR Running examples in ‘RMassBank-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CAS2SMILES > ### Title: Convert CAS to SMILES > ### Aliases: CAS2SMILES > > ### ** Examples > > SMILES_ethanol <- CAS2SMILES("64-17-5", "Ethanol") Request failed [503]. Retrying in 1 seconds... Request failed [503]. Retrying in 1.5 seconds... Service not available. Returning NA. Error in cir_query(CAS_number, from = "cas", to = "smiles") : Calls: CAS2SMILES -> cir_query Execution halted * 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 ... ERROR Error(s) in re-building vignettes: --- re-building ‘RMassBank.Rmd’ using rmarkdown INFO [2024-07-11 03:02:32] Loaded compoundlist successfully INFO [2024-07-11 03:02:32] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-07-11 03:02:38] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:02:57] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-07-11 03:02:57] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-07-11 03:02:58] msmsWorkflow: Done. The magick package is required to crop "/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/vign_test/RMassBank/vignettes/RMassBank_files/figure-html/unnamed-chunk-10-1.png" but not available. INFO [2024-07-11 03:04:01] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-07-11 03:04:06] msmsWorkflow: Done. INFO [2024-07-11 03:04:06] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-07-11 03:04:07] msmsWorkflow: Done. The magick package is required to crop "/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/vign_test/RMassBank/vignettes/RMassBank_files/figure-html/unnamed-chunk-16-1.png" but not available. INFO [2024-07-11 03:04:07] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:04:25] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-07-11 03:04:25] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:06:07] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-07-11 03:06:08] msmsWorkflow: Done. INFO [2024-07-11 03:06:08] mbWorkflow: Step 1. Gather info from several databases Quitting from lines 433-434 [unnamed-chunk-22] (RMassBank.Rmd) Error: processing vignette 'RMassBank.Rmd' failed with diagnostics: non-character argument --- failed re-building ‘RMassBank.Rmd’ --- re-building ‘RMassBankNonstandard.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/vign_test/RMassBank/vignettes/RMassBankNonstandard_files/figure-html/unnamed-chunk-6-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/vign_test/RMassBank/vignettes/RMassBankNonstandard_files/figure-html/unnamed-chunk-6-2.png" but not available. INFO [2024-07-11 03:08:30] All compounds are unknown, the workflow will be adjusted accordingly INFO [2024-07-11 03:08:33] Loaded compoundlist successfully INFO [2024-07-11 03:08:33] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-07-11 03:08:38] msmsWorkflow: Done. INFO [2024-07-11 03:08:38] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:08:40] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-07-11 03:08:40] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-07-11 03:08:41] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:08:43] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-07-11 03:08:43] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:08:53] msmsWorkflow: Done. The magick package is required to crop "/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/vign_test/RMassBank/vignettes/RMassBankNonstandard_files/figure-html/unnamed-chunk-11-1.png" but not available. INFO [2024-07-11 03:08:54] msmsWorkflow: Step 1. Acquire all MSMS spectra from files | | | 0% | |================================ | 50% | |================================================================| 100%INFO [2024-07-11 03:09:00] msmsWorkflow: Done. INFO [2024-07-11 03:09:00] msmsWorkflow: Step 2. First analysis pre recalibration | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:09:02] msmsWorkflow: Step 3. Aggregate all spectra INFO [2024-07-11 03:09:02] msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra INFO [2024-07-11 03:09:02] msmsWorkflow: Step 5. Reanalyze recalibrated spectra | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:09:04] msmsWorkflow: Step 6. Aggregate recalibrated results INFO [2024-07-11 03:09:04] msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O | | | 0% | |================================ | 50% | |================================================================| 100% INFO [2024-07-11 03:09:14] msmsWorkflow: Done. The magick package is required to crop "/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/vign_test/RMassBank/vignettes/RMassBankNonstandard_files/figure-html/unnamed-chunk-12-1.png" but not available. INFO [2024-07-11 03:09:15] msmsWorkflow: Step 8. Peak multiplicity filtering INFO [2024-07-11 03:09:15] msmsWorkflow: Done. --- finished re-building ‘RMassBankNonstandard.Rmd’ SUMMARY: processing the following file failed: ‘RMassBank.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/00check.log’ for details.
RMassBank.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
RMassBank.Rcheck/tests/doRUnit.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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 0.198 0.076 0.265
RMassBank.Rcheck/RMassBank-Ex.timings
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