Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1666/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rawrr 1.14.0 (landing page) Christian Panse
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the rawrr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rawrr.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: rawrr |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rawrr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rawrr_1.14.0.tar.gz |
StartedAt: 2024-12-20 08:12:34 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:15:06 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 151.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rawrr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rawrr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rawrr_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rawrr.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rawrr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rawrr’ version ‘1.14.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘rawrr’ 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed readChromatogram 24.989 4.917 27.167 readSpectrum 21.322 3.351 22.136 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
rawrr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rawrr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘rawrr’ ... ** 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 (rawrr)
rawrr.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > #R > > library(testthat) > > suppressPackageStartupMessages(library(rawrr)) > > test_check("rawrr") Total Ion Current: 78725448 Scan Low Mass: 350 Scan High Mass: 1800 Scan Start Time (min): 0.001619751 Scan Number: 1 Base Peak Intensity: 5979308 Base Peak Mass: 445.1181 Scan Mode: FTMS + c NSI Full ms [350.0000-1800.0000] ======= Instrument data ===== : NULL Multiple Injection: ii Multi Inject Info: IT=28;28 AGC: On Micro Scan Count: 1 Scan Segment: 1 Scan Event: 1 Master Index: 0 Charge State: 0 Monoisotopic M/Z: 0.0000 Ion Injection Time (ms): 55.000 Max. Ion Time (ms): 55.00 FT Resolution: 120000 MS2 Isolation Width: 1450.00 MS2 Isolation Offset: 0.00 AGC Target: 3000000 HCD Energy: Analyzer Temperature: 27.06 === Mass Calibration: NULL Conversion Parameter B: 211820589.2896 Conversion Parameter C: -41163067.8349 Temperature Comp. (ppm): -2.35 RF Comp. (ppm): -0.09 Space Charge Comp. (ppm): -2.30 Resolution Comp. (ppm): 0.57 Number of Lock Masses: 0 Lock Mass #1 (m/z): 0.0000 Lock Mass #2 (m/z): 0.0000 Lock Mass #3 (m/z): 0.0000 LM Search Window (ppm): 0.0 LM Search Window (mmu): 0.0 Number of LM Found: 0 Last Locking (sec): 0.0 LM m/z-Correction (ppm): 0.00 === Ion Optics Settings: NULL S-Lens RF Level: 40.00 S-Lens Voltage (V): 21.00 Skimmer Voltage (V): 15.00 Inject Flatapole Offset (V): 5.00 Bent Flatapole DC (V): 2.00 MP2 and MP3 RF (V): 900.00 Gate Lens Voltage (V): 2.25 C-Trap RF (V): 2400.0 ==== Diagnostic Data: NULL Dynamic RT Shift (min): 0.00 Intens Comp Factor: 1.4281 Res. Dep. Intens: 0.981 CTCD NumF: 0 CTCD Comp: 1.009 CTCD ScScr: 0.844 RawOvFtT: 2378645.5 LC FWHM parameter: 15.0 Rod: 0 PS Inj. Time (ms): 0.640 AGC PS Mode: 1 AGC PS Diag: 3501800 HCD Energy eV: 0.000 AGC Fill: 0.76 Injection t0: -0.071 t0 FLP: 355.07 Access Id: 0 Analog Input 1 (V): 0.000 Analog Input 2 (V): 0.000 Total Ion Current: 78725448 Scan Low Mass: 350 Scan High Mass: 1800 Scan Start Time (min): 0.001619751 Scan Number: 1 Base Peak Intensity: 5979308 Base Peak Mass: 445.1181 Scan Mode: FTMS + c NSI Full ms [350.0000-1800.0000] XIC generated from sample.raw consisting of 27 data points. Filter : ms m/z : 445.1181 Tolerance : 10 ppm RT : 0.001619751 - 0.7801059 min [ FAIL 0 | WARN 4 | SKIP 0 | PASS 179 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 179 ] > > proc.time() user system elapsed 29.903 6.952 42.170
rawrr.Rcheck/rawrr-Ex.timings
name | user | system | elapsed | |
basePeak | 0.575 | 0.249 | 0.985 | |
dependentScan | 0.620 | 0.170 | 0.757 | |
faimsVoltageOn | 0.552 | 0.170 | 0.704 | |
installRawFileReaderDLLs | 0.000 | 0.000 | 0.001 | |
is.rawrrChromatogram | 0.587 | 0.201 | 0.751 | |
is.rawrrSpectrum | 0.547 | 0.150 | 0.784 | |
is.rawrrSpectrumSet | 0.537 | 0.147 | 0.726 | |
makeAccessor | 0.536 | 0.145 | 0.690 | |
massRange | 0.537 | 0.167 | 0.693 | |
masterScan | 0.620 | 0.182 | 0.752 | |
plot.rawrrChromatogram | 0.597 | 0.223 | 0.759 | |
rawrrAssemblyPath | 0.000 | 0.000 | 0.001 | |
rawrrSpectrum | 0.040 | 0.002 | 0.043 | |
readChromatogram | 24.989 | 4.917 | 27.167 | |
readFileHeader | 0.483 | 0.148 | 0.665 | |
readIndex | 0.644 | 0.156 | 0.798 | |
readSpectrum | 21.322 | 3.351 | 22.136 | |
readTrailer | 0.912 | 0.351 | 1.202 | |
sampleFilePath | 0.002 | 0.001 | 0.002 | |
scanNumber | 0.556 | 0.172 | 0.778 | |
summary.rawrrChromatogram | 0.599 | 0.201 | 0.756 | |
tic | 0.534 | 0.171 | 0.713 | |
validate_rawrrIndex | 0.691 | 0.272 | 0.970 | |
validate_rawrrSpectrum | 0.544 | 0.166 | 0.717 | |