Peter Blattmann
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/SWATH2stats |
| git_branch: RELEASE_3_20 |
| git_last_commit: 0378c99 |
| git_last_commit_date: 2024-10-29 10:04:27 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| 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 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 2098/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SWATH2stats 1.36.0 (landing page) Peter Blattmann
| 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 | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the SWATH2stats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SWATH2stats.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SWATH2stats |
| Version: 1.36.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data SWATH2stats |
| StartedAt: 2025-01-08 23:02:23 -0000 (Wed, 08 Jan 2025) |
| EndedAt: 2025-01-08 23:02:55 -0000 (Wed, 08 Jan 2025) |
| EllapsedTime: 32.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data SWATH2stats
###
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* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* preparing ‘SWATH2stats’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SWATH2stats_example_script.Rmd’ using rmarkdown
Error: processing vignette 'SWATH2stats_example_script.Rmd' failed with diagnostics:
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- failed re-building ‘SWATH2stats_example_script.Rmd’
--- re-building ‘SWATH2stats_vignette.Rnw’ using Sweave
Warning: Use of `data.plot$value` is discouraged.
ℹ Use `value` instead.
Warning: Use of `data.plot$value` is discouraged.
ℹ Use `value` instead.
Number of non-decoy identifiers: 262
Number of decoy identifiers: 11
Decoy rate: 0.0420
assess_fdr_overall_testrun.pdf written to working folder
assess_fdr_overall_testruntable.csv written to working folder
The average FDR by run on assay level is 0.003
The average FDR by run on peptide level is 0.004
The average FDR by run on protein level is 0.078
Individual run FDR qualities can be retrieved from assess_fdr_byrun_testrun .csv
assess_fdr_byrun_testrun.csv reports written to working folder
assess_fdr_byrun_testrun.pdf report plots written to working folder
assess_fdr_byrun_testrun.pdf report plots written to working folder
The average FDR by run on assay level is 0.003
The average FDR by run on peptide level is 0.004
The average FDR by run on protein level is 0.078
Target assay FDR: 0.01
Required overall m-score cutoff:0.01
achieving assay FDR =0.0066
Target peptide FDR:0.02
Required overall m-score cutoff:0.01
achieving peptide FDR =0.00905
Target protein FDR:0.02
Required overall m-score cutoff:0.00017783
achieving protein FDR =0
Dimension difference: 915, 0
Treshold, peptides need to have been quantified in more conditions than: 4.8
Fraction of peptides selected: 0.39
Dimension difference: 1361, 0
Target protein FDR:0.03
Required overall m-score cutoff:0.00017783
achieving protein FDR =0
filter_mscore_fdr is filtering the data...
-----------------------------------------------------------
finding m-score cutoff to achieve desired protein FDR in protein master list..
finding m-score cutoff to achieve desired global peptide FDR..
Target peptide FDR:0.05
Required overall m-score cutoff:0.01
achieving peptide FDR =0.00905
-------------------------------------------------------------
Proteins selected:
Total proteins selected: 9
Thereof target proteins: 9
Thereof decoy proteins: 0
Peptides mapping to these protein entries selected:
Total mapping peptides: 232
Thereof target peptides: 232
Thereof decoy peptides: 0
Total peptides selected from:
Total peptides: 235
Thereof target peptides: 235
Thereof decoy peptides: 0
-------------------------------------------------------------
Individual run FDR quality of the peptides was not calculated
as not every run contains a decoy.
The decoys have been removed from the returned data
Number of proteins detected: 10
Protein identifiers: Protein6, Protein1, Protein7, Protein8, Protein2, Protein4
Number of proteins detected that are supported by a proteotypic peptide: 8
Number of proteotypic peptides detected: 121
Number of proteins detected: 10
Protein identifiers: Protein6, Protein1, Protein7, Protein8, Protein2, Protein4
Before filtering:
Number of proteins: 9
Number of peptides: 123
Percentage of peptides removed: 70.73%
After filtering:
Number of proteins: 9
Number of peptides: 36
Before filtering:
Number of proteins: 9
Number of peptides: 36
Percentage of peptides removed: 2.78%
After filtering:
Number of proteins: 8
Number of peptides: 35
The library contains 6 transitions per precursor.
The data table was transformed into a table containing one row per transition.
--- finished re-building ‘SWATH2stats_vignette.Rnw’
SUMMARY: processing the following file failed:
‘SWATH2stats_example_script.Rmd’
Error: Vignette re-building failed.
Execution halted