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This page was generated on 2025-04-02 19:31 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1665/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rawDiag 1.2.0  (landing page)
Christian Panse
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/rawDiag
git_branch: RELEASE_3_20
git_last_commit: 93447f9
git_last_commit_date: 2024-10-29 11:28:03 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped

BUILD results for rawDiag on palomino8

To the developers/maintainers of the rawDiag package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rawDiag.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: rawDiag
Version: 1.2.0
Command: chmod a+r rawDiag -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data rawDiag
StartedAt: 2025-03-31 21:17:53 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 21:18:33 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 40.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r rawDiag -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data rawDiag
###
##############################################################################
##############################################################################


* checking for file 'rawDiag/DESCRIPTION' ... OK
* preparing 'rawDiag':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'rawDiag.Rmd' using rmarkdown
trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.BackgroundSubtraction.dll'
Content type 'application/octet-stream' length 44544 bytes (43 KB)
==================================================
downloaded 43 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.Data.dll'
Content type 'application/octet-stream' length 406016 bytes (396 KB)
==================================================
downloaded 396 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.MassPrecisionEstimator.dll'
Content type 'application/octet-stream' length 11264 bytes (11 KB)
==================================================
downloaded 11 KB

trying URL 'https://github.com/thermofisherlsms/RawFileReader/raw/main/Libs/Net471//ThermoFisher.CommonCore.RawFileReader.dll'
Content type 'application/octet-stream' length 654336 bytes (639 KB)
==================================================
downloaded 639 KB

trying URL 'https://github.com/fgcz/rawrr/releases/download/1.9.2/rawrr.1.9.2.exe'
Content type 'application/octet-stream' length 28672 bytes (28 KB)
==================================================
downloaded 28 KB


Unhandled Exception: System.IO.FileLoadException: Could not load file or assembly 'ThermoFisher.CommonCore.Data, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953' or one of its dependencies. The process cannot access the file because it is being used by another process. (Exception from HRESULT: 0x80070020)
   at FGCZ_Raw.Program.Main(String[] args)

Quitting from rawDiag.Rmd:265-270 [readEH4547OrbitrapTrailerTable]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'Reduce': replacement has 0 rows, data has 8742
---
Backtrace:
    ▆
 1. ├─BiocGenerics::Reduce(...)
 2. ├─BiocGenerics::lapply(rawfile, FUN = rawDiag::readRaw)
 3. ├─base::lapply(rawfile, FUN = rawDiag::readRaw)
 4. │ └─rawDiag (local) FUN(X[[i]], ...)
 5. │   ├─base::`$<-`(`*tmp*`, "IonInjectionTime", value = `<dbl>`)
 6. │   └─base::`$<-.data.frame`(`*tmp*`, "IonInjectionTime", value = `<dbl>`)
 7. │     └─base::stop(...)
 8. └─base::.handleSimpleError(...)
 9.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'rawDiag.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'Reduce': replacement has 0 rows, data has 8742
--- failed re-building 'rawDiag.Rmd'

SUMMARY: processing the following file failed:
  'rawDiag.Rmd'

Error: Vignette re-building failed.
Execution halted