##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MsBackendSql_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MsBackendSql.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendSql/DESCRIPTION’ ... OK
* this is package ‘MsBackendSql’ version ‘1.9.0’
* 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 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MsBackendSql
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘MsBackendSql’ ...
** this is package ‘MsBackendSql’ version ‘1.9.0’
** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices .... Done
[1] TRUE
> mm8_be_long <- backendInitialize(MsBackendSql(), mm8_db_long)
> 
> mm8_db_blob <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm8_db_blob, mm8_file, blob = TRUE,
+                            peaksStorageMode = "blob")
Importing data ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices .... Done
[1] TRUE
> mm8_be_blob <- backendInitialize(MsBackendSql(), mm8_db_blob)
> 
> mm8_db_blob2 <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm8_db_blob2, mm8_file, blob = TRUE,
+                            peaksStorageMode = "blob2")
Importing data ... 

[==========================================================] 1/1 (100%) in  1s
Creating indices .... Done
[1] TRUE
> mm8_be_blob2 <- backendInitialize(MsBackendSql(), mm8_db_blob2)
> 
> 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 .... 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 ... 

[==========================================================] 1/1 (100%) in  1m
Creating indices .... Done
[1] TRUE
> tmt_be <- backendInitialize(MsBackendSql(), tmt_db)
> 
> test_check("MsBackendSql")