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### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings MsBackendSql_1.7.4.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsBackendSql.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendSql/DESCRIPTION’ ... OK
* this is package ‘MsBackendSql’ version ‘1.7.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MsBackendSql’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
filterRt,MsBackendSql: no visible global function definition for
  ‘msLevel’
filterRt,MsBackendSql: no visible global function definition for
  ‘rtime’
Undefined global functions or variables:
  msLevel rtime
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MsBackendSql-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MsBackendSql
> ### Title: 'Spectra' MS backend storing data in a SQL database
> ### Aliases: MsBackendSql createMsBackendSqlDatabase MsBackendSql-class
> ###   backendMerge,MsBackendOfflineSql-method
> ###   dataStorage,MsBackendOfflineSql-method
> ###   dbconn,MsBackendOfflineSql-method
> ###   filterDataOrigin,MsBackendOfflineSql-method
> ###   filterMsLevel,MsBackendOfflineSql-method
> ###   filterPrecursorMzRange,MsBackendOfflineSql-method
> ###   filterPrecursorMzValues,MsBackendOfflineSql-method
> ###   filterRt,MsBackendOfflineSql-method
> ###   peaksData,MsBackendOfflineSql-method
> ###   peaksVariables,MsBackendOfflineSql-method
> ###   reset,MsBackendOfflineSql-method show,MsBackendOfflineSql-method
> ###   spectraData,MsBackendOfflineSql-method
> ###   supportsSetBackend,MsBackendOfflineSql-method
> ###   tic,MsBackendOfflineSql-method
> ###   uniqueMsLevels,MsBackendOfflineSql-method
> ###   intensity,MsBackendOfflineSql-method mz,MsBackendOfflineSql-method
> ###   show,MsBackendSql-method backendInitialize,MsBackendSql-method
> ###   dataStorage,MsBackendSql-method [,MsBackendSql-method
> ###   extractByIndex,MsBackendSql,ANY-method peaksData,MsBackendSql-method
> ###   peaksVariables,MsBackendSql-method intensity,MsBackendSql-method
> ###   intensity<-,MsBackendSql-method mz,MsBackendSql-method
> ###   mz<-,MsBackendSql-method $<-,MsBackendSql-method
> ###   spectraData,MsBackendSql-method reset,MsBackendSql-method
> ###   spectraNames,MsBackendSql-method spectraNames<-,MsBackendSql-method
> ###   filterMsLevel,MsBackendSql-method filterRt,MsBackendSql-method
> ###   filterDataOrigin,MsBackendSql-method
> ###   filterPrecursorMzRange,MsBackendSql-method
> ###   filterPrecursorMzValues,MsBackendSql-method
> ###   uniqueMsLevels,MsBackendSql-method backendMerge,MsBackendSql-method
> ###   precScanNum,MsBackendSql-method centroided,MsBackendSql-method
> ###   smoothed,MsBackendSql-method tic,MsBackendSql-method
> ###   supportsSetBackend,MsBackendSql-method
> ###   backendBpparam,MsBackendSql-method dbconn,MsBackendSql-method
> 
> ### ** Examples
> 
> 
> ####
> ## Create a new MsBackendSql database
> 
> ## Define a file from which to import the data
> data_file <- system.file("microtofq", "MM8.mzML", package = "msdata")
> 
> ## Create a database/connection to a database
> library(RSQLite)
> db_file <- tempfile()
> dbc <- dbConnect(SQLite(), db_file)
> 
> ## Import the data from the file into the database
> createMsBackendSqlDatabase(dbc, data_file)
Importing data ... 
Error: database or disk is full
Error: no such savepoint: dbAppendTable_991976_loatcfjjfo
Error: no such savepoint: dbWriteTable_991976_ueiyneebjy
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > setMethod("dbExecute", c("DummySQL", "character"),
  +           function(conn, statement, ...) {
  +               TRUE
  +           })
  > 
  > mm8_file <- system.file("microtofq", "MM8.mzML", package = "msdata")
  > mm8_sps <- Spectra(mm8_file)
  > mm8_db_long <- dbConnect(SQLite(), tempfile())
  > createMsBackendSqlDatabase(mm8_db_long, mm8_file, blob = FALSE,
  +                            peaksStorageMode = "long")
  Importing data ... 
  Error: database or disk is full
  Error: no such savepoint: dbAppendTable_992042_vsxhinptsz
  Error: no such savepoint: dbWriteTable_992042_mezwuenvuh
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MsBackendSql.Rmd’ using rmarkdown

Quitting from MsBackendSql.Rmd:66-77 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     ▆
  1. └─MsBackendSql::createMsBackendSqlDatabase(con, fls)
  2.   └─MsBackendSql:::.insert_data(...)
  3.     └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
  4.       └─MsBackendSql:::.insert_spectra_variables(con, spd)
  5.         ├─DBI::dbWriteTable(...)
  6.         └─RSQLite::dbWriteTable(...)
  7.           └─RSQLite (local) .local(conn, name, value, ...)
  8.             ├─DBI::dbCommit(conn, name = savepoint_id)
  9.             └─RSQLite::dbCommit(conn, name = savepoint_id)
 10.               └─RSQLite (local) .local(conn, ...)
 11.                 ├─DBI::dbExecute(...)
 12.                 └─DBI::dbExecute(...)
 13.                   ├─DBI::dbSendStatement(conn, statement, ...)
 14.                   └─DBI::dbSendStatement(conn, statement, ...)
 15.                     ├─DBI::dbSendQuery(conn, statement, ...)
 16.                     └─RSQLite::dbSendQuery(conn, statement, ...)
 17.                       └─RSQLite (local) .local(conn, statement, ...)
 18.                         ├─methods::new(...)
 19.                         │ ├─methods::initialize(value, ...)
 20.                         │ └─methods::initialize(value, ...)
 21.                         └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MsBackendSql.Rmd' failed with diagnostics:
database or disk is full
--- failed re-building ‘MsBackendSql.Rmd’

SUMMARY: processing the following file failed:
  ‘MsBackendSql.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without index ... ERROR
* DONE

Status: 4 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsBackendSql.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL MsBackendSql
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘MsBackendSql’ ...
** this is package ‘MsBackendSql’ version ‘1.7.4’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MsBackendSql)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MsBackendSql)
Loading required package: Spectra
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: BiocParallel
> library(Spectra)
> library(RSQLite)
> library(msdata)
> 
> setClass("DummySQL",
+          contains = "SQLiteConnection")
> 
> setMethod("dbExecute", c("DummySQL", "character"),
+           function(conn, statement, ...) {
+               TRUE
+           })
> 
> mm8_file <- system.file("microtofq", "MM8.mzML", package = "msdata")
> mm8_sps <- Spectra(mm8_file)
> mm8_db_long <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm8_db_long, mm8_file, blob = FALSE,
+                            peaksStorageMode = "long")
Importing data ... 
Error: database or disk is full
Error: no such savepoint: dbAppendTable_992042_vsxhinptsz
Error: no such savepoint: dbWriteTable_992042_mezwuenvuh
Execution halted