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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MsBackendSql_0.99.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MsBackendSql.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendSql/DESCRIPTION’ ... OK
* this is package ‘MsBackendSql’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 R 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 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 ... OK
* 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 ... OK
* 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:
  > mm_db <- dbConnect(SQLite(), tempfile())
  > createMsBackendSqlDatabase(mm_db, c(mm8_file, mm14_file), blob = FALSE)
  Importing data ... 
  
  [==========================================================] 1/1 (100%) in  1s
  Creating indices (this can take, depending on the database's size, very long) .. Done
  [1] TRUE
  > mm_be <- backendInitialize(MsBackendSql(), mm_db)
  > 
  > tmt_file <- proteomics(full.names = TRUE)[4L]
  > tmt_mzr <- backendInitialize(MsBackendMzR(), tmt_file)
  > tmt_db <- dbConnect(SQLite(), tempfile())
  > createMsBackendSqlDatabase(tmt_db, tmt_file, blob = FALSE)
  Importing data ... 
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MsBackendSql.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MsBackendSql.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MsBackendSql
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘MsBackendSql’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

> library(Spectra)
> library(RSQLite)
> library(msdata)
> 
> mm8_file <- system.file("microtofq", "MM8.mzML", package = "msdata")
> mm8_sps <- Spectra(mm8_file)
> mm8_db <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm8_db, mm8_file, blob = FALSE)
Importing data ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices (this can take, depending on the database's size, very long) .. Done
[1] TRUE
> mm8_be <- backendInitialize(MsBackendSql(), mm8_db)
> 
> mm8_db_blob <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm8_db_blob, mm8_file, blob = TRUE)
Importing data ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices (this can take, depending on the database's size, very long) .. Done
[1] TRUE
> mm8_be_blob <- backendInitialize(MsBackendSql(), mm8_db_blob)
> 
> mm14_file <- system.file("microtofq", "MM14.mzML", package = "msdata")
> mm_db <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm_db, c(mm8_file, mm14_file), blob = FALSE)
Importing data ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices (this can take, depending on the database's size, very long) .. Done
[1] TRUE
> mm_be <- backendInitialize(MsBackendSql(), mm_db)
> 
> tmt_file <- proteomics(full.names = TRUE)[4L]
> tmt_mzr <- backendInitialize(MsBackendMzR(), tmt_file)
> tmt_db <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(tmt_db, tmt_file, blob = FALSE)
Importing data ... 
Killed