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This page was generated on 2024-02-28 11:37:28 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 442/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cosmiq 1.37.0  (landing page)
David Fischer
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/cosmiq
git_branch: devel
git_last_commit: 2d606b7
git_last_commit_date: 2023-10-24 09:59:19 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

BUILD results for cosmiq on palomino3


To the developers/maintainers of the cosmiq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cosmiq.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: cosmiq
Version: 1.37.0
Command: chmod a+r cosmiq -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data cosmiq
StartedAt: 2024-02-26 19:58:14 -0500 (Mon, 26 Feb 2024)
EndedAt: 2024-02-26 20:00:49 -0500 (Mon, 26 Feb 2024)
EllapsedTime: 155.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r cosmiq -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data cosmiq
###
##############################################################################
##############################################################################


* checking for file 'cosmiq/DESCRIPTION' ... OK
* preparing 'cosmiq':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'cosmiq.Rnw' using Sweave
Loading required package: Rcpp
Create profile matrix with method 'bin' and step 1 ... OK
Combining spectra ...
1 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
2 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
3 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
4 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
5 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
6 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
7 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
8 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
9 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
10 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
11 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
12 of 12 done.
Detecting mz peaks on master spectrum ...
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Creating EIC matrix ...
Create profile matrix with method 'bin' and step 1 ... OK
1 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
2 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
3 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
4 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
5 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
6 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
7 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
8 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
9 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
10 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
11 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
12 of 12 done.
Detecting chromatographic peaks from EIC matrix ...
Detecting mz peaks on master spectrum ...
1 of  8 Peaknum =  4
Detecting mz peaks on master spectrum ...
2 of  8 Peaknum =  7
Detecting mz peaks on master spectrum ...
3 of  8 Peaknum =  8
Detecting mz peaks on master spectrum ...
4 of  8 Peaknum =  11
Detecting mz peaks on master spectrum ...
5 of  8 Peaknum =  15
Detecting mz peaks on master spectrum ...
6 of  8 Peaknum =  17
Detecting mz peaks on master spectrum ...
7 of  8 Peaknum =  21
Detecting mz peaks on master spectrum ...
8 of  8 Peaknum =  26
Quantifying mz/RT features ...
Create profile matrix with method 'bin' and step 1 ... OK
1 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
2 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
3 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
4 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
5 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
6 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
7 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
8 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
9 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
10 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
11 of 12 done.
Create profile matrix with method 'bin' and step 1 ... OK
12 of 12 done.
Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "cosmiq.tex" ' had status 1033
Error: processing vignette 'cosmiq.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'cosmiq.pdf' for vignette with name 'cosmiq' and engine 'utils::Sweave'. The following files exist in working directory 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsVmYvN\Rbuildf44a473d18\cosmiq\vignettes': 'cosmiq-007.pdf' (12120 bytes), 'cosmiq-008.pdf' (7763 bytes), 'cosmiq-010.pdf' (36448 bytes), 'cosmiq.Rnw' (9929 bytes), 'cosmiq.bib' (2275 bytes), 'cosmiq.tex' (16856 bytes), 'poster' (14419 bytes)
--- failed re-building 'cosmiq.Rnw'

SUMMARY: processing the following file failed:
  'cosmiq.Rnw'

Error: Vignette re-building failed.
Execution halted