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This page was generated on 2024-07-16 11:39 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (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 56/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaMissenseR 1.1.5  (landing page)
Martin Morgan
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/AlphaMissenseR
git_branch: devel
git_last_commit: 1214ac9
git_last_commit_date: 2024-06-26 14:02:32 -0400 (Wed, 26 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped


BUILD results for AlphaMissenseR on palomino6

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.