##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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 \"2bf7cc74a359fe_2bf7cc74a359fe\" 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('/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpwy1RMc/Rinst233435392ebc20/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 "2bf7cc74a359fe_2bf7cc74a359fe" 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 \"2bf7cc74a359fe_2bf7cc74a359fe\" 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 \"2bf7cc74a359fe_2bf7cc74a359fe\" 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.