Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:39 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 56/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlphaMissenseR 1.1.5 (landing page) Martin Morgan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the AlphaMissenseR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AlphaMissenseR.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: AlphaMissenseR |
Version: 1.1.5 |
Command: chmod a+r AlphaMissenseR -R && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data AlphaMissenseR |
StartedAt: 2024-07-15 16:29:13 -0400 (Mon, 15 Jul 2024) |
EndedAt: 2024-07-15 16:29:33 -0400 (Mon, 15 Jul 2024) |
EllapsedTime: 19.8 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r AlphaMissenseR -R && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data AlphaMissenseR ### ############################################################################## ############################################################################## * checking for file 'AlphaMissenseR/DESCRIPTION' ... OK * preparing 'AlphaMissenseR': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'alphafold.Rmd' using rmarkdown Quitting from lines 58-60 [am_data] (alphafold.Rmd) Error: processing vignette 'alphafold.Rmd' failed with diagnostics: {"exception_type":"Invalid Input","exception_message":"Attempting to execute an unsuccessful or closed pending query result\nError: Invalid Input Error: Cannot execute statement of type \"CREATE\" on database \"3dd032a5e22_3dd032a5e22\" which is attached in read-only mode!"} --- failed re-building 'alphafold.Rmd' --- re-building 'clinvar.Rmd' using rmarkdown Quitting from lines 44-45 [download_cv] (clinvar.Rmd) Error: processing vignette 'clinvar.Rmd' failed with diagnostics: rapi_prepare: Failed to execute statement -- import csv from file at 'file_path' to data table 'db_tbl_name' -- create the clinvar table, but with label as TEXT CREATE TABLE clinvar AS SELECT * EXCLUDE(label), CASE WHEN label = 0 THEN 'benign' WHEN label = 1 THEN 'pathogenic' END AS label FROM read_csv_auto('C:/Users/biocbuild/bbs-3.20-bioc/tmpdir/RtmpI5Zhqc/Rinst150c4383b3e6a/AlphaMissenseR/extdata/science.adg7492_data_s5.csv.gz', delim = ',', compression = 'gzip'); -- create levels for the label column CREATE TYPE label_level AS ENUM ('benign', 'pathogenic'); -- coerce label to factor ALTER TABLE clinvar ALTER label TYPE label_level; Error: Invalid Input Error: Cannot execute statement of type "CREATE" on database "3dd032a5e22_3dd032a5e22" which is attached in read-only mode! --- failed re-building 'clinvar.Rmd' --- re-building 'introduction.Rmd' using rmarkdown Quitting from lines 100-102 [am_data] (introduction.Rmd) Error: processing vignette 'introduction.Rmd' failed with diagnostics: {"exception_type":"Invalid Input","exception_message":"Attempting to execute an unsuccessful or closed pending query result\nError: Invalid Input Error: Cannot execute statement of type \"CREATE\" on database \"3dd032a5e22_3dd032a5e22\" which is attached in read-only mode!"} --- failed re-building 'introduction.Rmd' --- re-building 'issues.Rmd' using rmarkdown Quitting from lines 74-75 [unnamed-chunk-4] (issues.Rmd) Error: processing vignette 'issues.Rmd' failed with diagnostics: {"exception_type":"Invalid Input","exception_message":"Attempting to execute an unsuccessful or closed pending query result\nError: Invalid Input Error: Cannot execute statement of type \"CREATE\" on database \"3dd032a5e22_3dd032a5e22\" which is attached in read-only mode!"} --- failed re-building 'issues.Rmd' SUMMARY: processing the following files failed: 'alphafold.Rmd' 'clinvar.Rmd' 'introduction.Rmd' 'issues.Rmd' Error: Vignette re-building failed. Execution halted Warning messages: 1: Connection is garbage-collected, use dbDisconnect() to avoid this. 2: Connection is garbage-collected, use dbDisconnect() to avoid this. 3: Connection is garbage-collected, use dbDisconnect() to avoid this. 4: Connection is garbage-collected, use dbDisconnect() to avoid this. 5: Connection is garbage-collected, use dbDisconnect() to avoid this.