##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:MsExperiment.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings MsExperiment_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsExperiment.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 ‘MsExperiment/DESCRIPTION’ ... OK
* this is package ‘MsExperiment’ version ‘1.9.1’
* 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 ‘MsExperiment’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘IRanges:::.showAtomicList’
  See the note in ?`:::` about the use of this operator.
* 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 ... ERROR
Running examples in ‘MsExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbWriteSampleData
> ### Title: Write sample annotations to a MsBackendSql SQL database
> ### Aliases: dbWriteSampleData
> 
> ### ** Examples
> 
> 
> library(MsExperiment)
> 
> ## Create a MsBackendSql database from two mzML files.
> ## Connect first to an empty SQLite database (for the example we create
> ## a database in a temporary file).
> library(RSQLite)
> sqlite_db <- tempfile()
> con <- dbConnect(SQLite(), sqlite_db)
> 
> ## Define the files from which we import the data
> fls <- dir(system.file("sciex", package = "msdata"), pattern = "mzML",
+     full.names = TRUE)
> 
> ## Create a MsBackendSql database containing the full MS data
> 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
> createMsBackendSqlDatabase(con, fls)
Importing data ... 
Error: database or disk is full
Error: no such savepoint: dbAppendTable_1686619_loatcfjjfo
Error: no such savepoint: dbWriteTable_1686619_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:
   16.                     ├─DBI::dbSendQuery(conn, statement, ...)
   17.                     └─RSQLite::dbSendQuery(conn, statement, ...)
   18.                       └─RSQLite (local) .local(conn, statement, ...)
   19.                         ├─methods::new(...)
   20.                         │ ├─methods::initialize(value, ...)
   21.                         │ └─methods::initialize(value, ...)
   22.                         └─RSQLite:::result_create(conn@ptr, statement)
  ── Failure ('test_MsExperiment.R:189:5'): show,MsExperiment works ──────────────
  `show(MsExperiment())` produced no output
  ── Failure ('test_MsExperiment.R:191:5'): show,MsExperiment works ──────────────
  `show(mse)` produced no output
  
  [ FAIL 8 | WARN 18 | SKIP 0 | PASS 228 ]
  Error: Test failures
  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 ‘MsExperiment.Rmd’ using rmarkdown
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsExperiment.Rcheck/vign_test/MsExperiment/vignettes/MsExperiment_files/figure-html/plot_sp-1.png" but not available.

Quitting from MsExperiment.Rmd:599-610 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     ▆
  1. └─MsBackendSql::createMsBackendSqlDatabase(dbcon = con, fls)
  2.   └─MsBackendSql:::.insert_data(...)
  3.     └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
  4.       ├─DBI::dbWriteTable(...)
  5.       └─RSQLite::dbWriteTable(...)
  6.         └─RSQLite (local) .local(conn, name, value, ...)
  7.           ├─DBI::dbCommit(conn, name = savepoint_id)
  8.           └─RSQLite::dbCommit(conn, name = savepoint_id)
  9.             └─RSQLite (local) .local(conn, ...)
 10.               ├─DBI::dbExecute(...)
 11.               └─DBI::dbExecute(...)
 12.                 ├─DBI::dbSendStatement(conn, statement, ...)
 13.                 └─DBI::dbSendStatement(conn, statement, ...)
 14.                   ├─DBI::dbSendQuery(conn, statement, ...)
 15.                   └─RSQLite::dbSendQuery(conn, statement, ...)
 16.                     └─RSQLite (local) .local(conn, statement, ...)
 17.                       ├─methods::new(...)
 18.                       │ ├─methods::initialize(value, ...)
 19.                       │ └─methods::initialize(value, ...)
 20.                       └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsExperiment.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL MsExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘MsExperiment’ ...
** this is package ‘MsExperiment’ version ‘1.9.1’
** 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 (MsExperiment)

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("MsExperiment")
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

> library("msdata")
> library("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

> library("Spectra")
Loading required package: BiocParallel
> 
> fls <- dir(system.file("sciex", package = "msdata"), pattern = "mzML",
+            full.names = TRUE)
> 
> mse <- MsExperiment()
> df <- data.frame(sample = c("QC1", "QC2"),
+                  time = c(1, 2),
+                  mzML_file = basename(fls))
> sampleData(mse) <- DataFrame(df)
> experimentFiles(mse) <- MsExperimentFiles(mzML_file = fls,
+                                           other_file = "other_file.txt")
> spectra(mse) <- Spectra(fls)
> 
> test_check("MsExperiment")
[ FAIL 8 | WARN 18 | SKIP 0 | PASS 228 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_MsExperiment-db.R:6:1'): (code run outside of `test_that()`) ───
Error: database or disk is full
Backtrace:
     ▆
  1. ├─ProtGenerics::setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con) at test_MsExperiment-db.R:6:1
  2. └─MsBackendSql (local) setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con)
  3.   └─MsBackendSql (local) .local(object, backend, ...)
  4.     └─MsBackendSql:::.set_backend_insert_data(...)
  5.       └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
  6.         ├─DBI::dbWriteTable(...)
  7.         └─RSQLite::dbWriteTable(...)
  8.           └─RSQLite (local) .local(conn, name, value, ...)
  9.             ├─DBI::dbAppendTable(conn = conn, name = name, value = value)
 10.             └─RSQLite::dbAppendTable(conn = conn, name = name, value = value)
 11.               ├─methods::callNextMethod()
 12.               └─DBI (local) .nextMethod(conn = conn, name = name, value = value)
 13.                 ├─DBI::dbExecute(conn, query, params = unname(as.list(value)))
 14.                 └─DBI::dbExecute(conn, query, params = unname(as.list(value)))
 15.                   ├─DBI::dbSendStatement(conn, statement, ...)
 16.                   └─DBI::dbSendStatement(conn, statement, ...)
 17.                     ├─DBI::dbSendQuery(conn, statement, ...)
 18.                     └─RSQLite::dbSendQuery(conn, statement, ...)
 19.                       └─RSQLite (local) .local(conn, statement, ...)
 20.                         ├─DBI::dbBind(rs, params)
 21.                         └─RSQLite::dbBind(rs, params)
 22.                           └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
 23.                             └─RSQLite:::result_bind(res@ptr, params)
── Error ('test_MsExperiment-db.R:6:1'): (code run outside of `test_that()`) ───
Error: no such savepoint: dbAppendTable_1688820_tzpxpbfseh
Backtrace:
     ▆
  1. ├─ProtGenerics::setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con) at test_MsExperiment-db.R:6:1
  2. └─MsBackendSql (local) setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con)
  3.   └─MsBackendSql (local) .local(object, backend, ...)
  4.     └─MsBackendSql:::.set_backend_insert_data(...)
  5.       └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
  6.         ├─DBI::dbWriteTable(...)
  7.         └─RSQLite::dbWriteTable(...)
  8.           └─RSQLite (local) .local(conn, name, value, ...)
  9.             ├─DBI::dbAppendTable(conn = conn, name = name, value = value)
 10.             └─RSQLite::dbAppendTable(conn = conn, name = name, value = value)
 11.               ├─DBI::dbRollback(conn, name = savepoint_id)
 12.               └─RSQLite::dbRollback(conn, name = savepoint_id)
 13.                 └─RSQLite (local) .local(conn, ...)
 14.                   ├─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
 15.                   └─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
 16.                     ├─DBI::dbSendStatement(conn, statement, ...)
 17.                     └─DBI::dbSendStatement(conn, statement, ...)
 18.                       ├─DBI::dbSendQuery(conn, statement, ...)
 19.                       └─RSQLite::dbSendQuery(conn, statement, ...)
 20.                         └─RSQLite (local) .local(conn, statement, ...)
 21.                           ├─methods::new(...)
 22.                           │ ├─methods::initialize(value, ...)
 23.                           │ └─methods::initialize(value, ...)
 24.                           └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsExperiment-db.R:6:1'): (code run outside of `test_that()`) ───
Error: no such savepoint: dbWriteTable_1688820_rgrscsmlbe
Backtrace:
     ▆
  1. ├─ProtGenerics::setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con) at test_MsExperiment-db.R:6:1
  2. └─MsBackendSql (local) setBackend(spectra(mse_db), MsBackendSql(), dbcon = ref_con)
  3.   └─MsBackendSql (local) .local(object, backend, ...)
  4.     └─MsBackendSql:::.set_backend_insert_data(...)
  5.       └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
  6.         ├─DBI::dbWriteTable(...)
  7.         └─RSQLite::dbWriteTable(...)
  8.           └─RSQLite (local) .local(conn, name, value, ...)
  9.             ├─DBI::dbRollback(conn, name = savepoint_id)
 10.             └─RSQLite::dbRollback(conn, name = savepoint_id)
 11.               └─RSQLite (local) .local(conn, ...)
 12.                 ├─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
 13.                 └─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
 14.                   ├─DBI::dbSendStatement(conn, statement, ...)
 15.                   └─DBI::dbSendStatement(conn, statement, ...)
 16.                     ├─DBI::dbSendQuery(conn, statement, ...)
 17.                     └─RSQLite::dbSendQuery(conn, statement, ...)
 18.                       └─RSQLite (local) .local(conn, statement, ...)
 19.                         ├─methods::new(...)
 20.                         │ ├─methods::initialize(value, ...)
 21.                         │ └─methods::initialize(value, ...)
 22.                         └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsExperiment.R:160:5'): MsExperiment works ─────────────────────
Error: database or disk is full
Backtrace:
     ▆
  1. ├─ProtGenerics::setBackend(...) at test_MsExperiment.R:160:5
  2. └─MsBackendSql (local) setBackend(...)
  3.   └─MsBackendSql (local) .local(object, backend, ...)
  4.     └─MsBackendSql:::.set_backend_insert_data(...)
  5.       └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
  6.         ├─DBI::dbWriteTable(...)
  7.         └─RSQLite::dbWriteTable(...)
  8.           └─RSQLite (local) .local(conn, name, value, ...)
  9.             ├─DBI::dbAppendTable(conn = conn, name = name, value = value)
 10.             └─RSQLite::dbAppendTable(conn = conn, name = name, value = value)
 11.               ├─methods::callNextMethod()
 12.               └─DBI (local) .nextMethod(conn = conn, name = name, value = value)
 13.                 ├─DBI::dbExecute(conn, query, params = unname(as.list(value)))
 14.                 └─DBI::dbExecute(conn, query, params = unname(as.list(value)))
 15.                   ├─DBI::dbSendStatement(conn, statement, ...)
 16.                   └─DBI::dbSendStatement(conn, statement, ...)
 17.                     ├─DBI::dbSendQuery(conn, statement, ...)
 18.                     └─RSQLite::dbSendQuery(conn, statement, ...)
 19.                       └─RSQLite (local) .local(conn, statement, ...)
 20.                         ├─DBI::dbBind(rs, params)
 21.                         └─RSQLite::dbBind(rs, params)
 22.                           └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
 23.                             └─RSQLite:::result_bind(res@ptr, params)
── Error ('test_MsExperiment.R:160:5'): MsExperiment works ─────────────────────
Error: no such savepoint: dbAppendTable_1688820_wwysesmjuz
Backtrace:
     ▆
  1. ├─ProtGenerics::setBackend(...) at test_MsExperiment.R:160:5
  2. └─MsBackendSql (local) setBackend(...)
  3.   └─MsBackendSql (local) .local(object, backend, ...)
  4.     └─MsBackendSql:::.set_backend_insert_data(...)
  5.       └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
  6.         ├─DBI::dbWriteTable(...)
  7.         └─RSQLite::dbWriteTable(...)
  8.           └─RSQLite (local) .local(conn, name, value, ...)
  9.             ├─DBI::dbAppendTable(conn = conn, name = name, value = value)
 10.             └─RSQLite::dbAppendTable(conn = conn, name = name, value = value)
 11.               ├─DBI::dbRollback(conn, name = savepoint_id)
 12.               └─RSQLite::dbRollback(conn, name = savepoint_id)
 13.                 └─RSQLite (local) .local(conn, ...)
 14.                   ├─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
 15.                   └─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
 16.                     ├─DBI::dbSendStatement(conn, statement, ...)
 17.                     └─DBI::dbSendStatement(conn, statement, ...)
 18.                       ├─DBI::dbSendQuery(conn, statement, ...)
 19.                       └─RSQLite::dbSendQuery(conn, statement, ...)
 20.                         └─RSQLite (local) .local(conn, statement, ...)
 21.                           ├─methods::new(...)
 22.                           │ ├─methods::initialize(value, ...)
 23.                           │ └─methods::initialize(value, ...)
 24.                           └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsExperiment.R:160:5'): MsExperiment works ─────────────────────
Error: no such savepoint: dbWriteTable_1688820_hyaghcqetq
Backtrace:
     ▆
  1. ├─ProtGenerics::setBackend(...) at test_MsExperiment.R:160:5
  2. └─MsBackendSql (local) setBackend(...)
  3.   └─MsBackendSql (local) .local(object, backend, ...)
  4.     └─MsBackendSql:::.set_backend_insert_data(...)
  5.       └─MsBackendSql:::.insert_backend_blob2(con, s, index = index)
  6.         ├─DBI::dbWriteTable(...)
  7.         └─RSQLite::dbWriteTable(...)
  8.           └─RSQLite (local) .local(conn, name, value, ...)
  9.             ├─DBI::dbRollback(conn, name = savepoint_id)
 10.             └─RSQLite::dbRollback(conn, name = savepoint_id)
 11.               └─RSQLite (local) .local(conn, ...)
 12.                 ├─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
 13.                 └─DBI::dbExecute(conn, paste0("ROLLBACK TO ", name_quoted))
 14.                   ├─DBI::dbSendStatement(conn, statement, ...)
 15.                   └─DBI::dbSendStatement(conn, statement, ...)
 16.                     ├─DBI::dbSendQuery(conn, statement, ...)
 17.                     └─RSQLite::dbSendQuery(conn, statement, ...)
 18.                       └─RSQLite (local) .local(conn, statement, ...)
 19.                         ├─methods::new(...)
 20.                         │ ├─methods::initialize(value, ...)
 21.                         │ └─methods::initialize(value, ...)
 22.                         └─RSQLite:::result_create(conn@ptr, statement)
── Failure ('test_MsExperiment.R:189:5'): show,MsExperiment works ──────────────
`show(MsExperiment())` produced no output
── Failure ('test_MsExperiment.R:191:5'): show,MsExperiment works ──────────────
`show(mse)` produced no output

[ FAIL 8 | WARN 18 | SKIP 0 | PASS 228 ]
Error: Test failures
Execution halted