Johannes Rainer
| Snapshot Date: 2026-02-16 13:40 -0500 (Mon, 16 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/MsBackendSql |
| git_branch: devel |
| git_last_commit: 9b5f2fe |
| git_last_commit_date: 2026-02-05 04:55:08 -0500 (Thu, 05 Feb 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-17 11:32 -0500 (Tue, 17 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4865 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1378/2352 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendSql 1.11.3 (landing page) Johannes Rainer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for MsBackendSql in R Universe. | ||||||||||||||
|
To the developers/maintainers of the MsBackendSql package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendSql.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MsBackendSql |
| Version: 1.11.3 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MsBackendSql_1.11.3.tar.gz |
| StartedAt: 2026-02-17 01:57:42 -0500 (Tue, 17 Feb 2026) |
| EndedAt: 2026-02-17 02:08:01 -0500 (Tue, 17 Feb 2026) |
| EllapsedTime: 619.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendSql.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MsBackendSql_1.11.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MsBackendSql.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendSql/DESCRIPTION’ ... OK
* this is package ‘MsBackendSql’ version ‘1.11.3’
* 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MsBackendSql 9.305 1.023 10.529
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
MsBackendSql.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MsBackendSql ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘MsBackendSql’ ... ** this is package ‘MsBackendSql’ version ‘1.11.3’ ** 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)
MsBackendSql.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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(MsDataHub)
>
> setClass("DummySQL",
+ contains = "SQLiteConnection")
>
> setMethod("dbExecute", c("DummySQL", "character"),
+ function(conn, statement, ...) {
+ TRUE
+ })
>
> a_file <- MsDataHub::X20171016_POOL_POS_1_105.134.mzML()
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> a_sps <- Spectra(a_file)
> a_db_long <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(a_db_long, a_file, blob = FALSE,
+ peaksStorageMode = "long")
Importing data ...
[==========================================================] 1/1 (100%) in 3s
Creating indices .... Done
[1] TRUE
> a_be_long <- backendInitialize(MsBackendSql(), a_db_long)
>
> a_db_blob <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(a_db_blob, a_file, blob = TRUE,
+ peaksStorageMode = "blob")
Importing data ...
[==========================================================] 1/1 (100%) in 1s
Creating indices .... Done
[1] TRUE
> a_be_blob <- backendInitialize(MsBackendSql(), a_db_blob)
>
> a_db_blob2 <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(a_db_blob2, a_file, blob = TRUE,
+ peaksStorageMode = "blob2")
Importing data ...
[==========================================================] 1/1 (100%) in 1s
Creating indices .... Done
[1] TRUE
> a_be_blob2 <- backendInitialize(MsBackendSql(), a_db_blob2)
>
> ################################################################################
> ##
> ## OPTIONAL TESTS WITH duckdb
> ## library(duckdb)
> ## mm8_db_long <- dbConnect(duckdb(), tempfile())
> ## createMsBackendSqlDatabase(mm8_db_long, mm8_file, blob = FALSE,
> ## peaksStorageMode = "long")
> ## mm8_be_long <- backendInitialize(MsBackendSql(), mm8_db_long)
>
> ## mm8_db_blob <- dbConnect(duckdb(), tempfile())
> ## createMsBackendSqlDatabase(mm8_db_blob, mm8_file, blob = TRUE,
> ## peaksStorageMode = "blob")
> ## mm8_be_blob <- backendInitialize(MsBackendSql(), mm8_db_blob)
>
> ## mm8_db_blob2 <- dbConnect(duckdb(), tempfile())
> ## createMsBackendSqlDatabase(mm8_db_blob2, mm8_file, blob = TRUE,
> ## peaksStorageMode = "blob2")
> ## mm8_be_blob2 <- backendInitialize(MsBackendSql(), mm8_db_blob2)
> ##
> ################################################################################
>
> b_file <- MsDataHub::X20171016_POOL_POS_3_105.134.mzML()
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> mm_db <- dbConnect(SQLite(), tempfile())
> createMsBackendSqlDatabase(mm_db, c(a_file, b_file), blob = FALSE)
Importing data ...
[==========================================================] 1/1 (100%) in 5s
Creating indices .... Done
[1] TRUE
> mm_be <- backendInitialize(MsBackendSql(), mm_db)
>
> tmt_file <- MsDataHub::TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz()
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> 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")
[ FAIL 0 | WARN 3 | SKIP 1 | PASS 628 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_MsBackendSql-functions.R:764:1'
[ FAIL 0 | WARN 3 | SKIP 1 | PASS 628 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> test_suite <- system.file("test_backends", "test_MsBackend",
+ package = "Spectra")
>
> be <- a_be_blob
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
⠙ | 2 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
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⠴ | 3756 | spectra_subsetting
⠙ | 3762 | spectra_subsetting
⠦ | 3767 | spectra_subsetting
✔ | 3770 | spectra_subsetting [82.7s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠹ | 23 | spectra_variables
⠋ | 31 | spectra_variables
⠹ | 43 | spectra_variables
⠸ | 54 | spectra_variables
✔ | 64 | spectra_variables [1.1s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 84.1 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3838 ]
>
> be <- tmt_be[sample(seq_along(tmt_be), 300)]
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
⠙ | 2 | peaks_variables
⠸ | 4 | peaks_variables
✔ | 4 | peaks_variables [2.5s]
⠏ | 0 | spectra_subsetting
⠙ | 12 | spectra_subsetting
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⠏ | 1150 | spectra_subsetting
⠙ | 1152 | spectra_subsetting
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⠏ | 1160 | spectra_subsetting
⠙ | 1162 | spectra_subsetting
⠹ | 1163 | spectra_subsetting
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⠹ | 1173 | spectra_subsetting
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⠇ | 1179 | spectra_subsetting
⠏ | 1180 | spectra_subsetting
⠙ | 1182 | spectra_subsetting
⠸ | 1184 | spectra_subsetting
⠴ | 1186 | spectra_subsetting
⠧ | 1188 | spectra_subsetting
⠏ | 1190 | spectra_subsetting
⠋ | 1191 | spectra_subsetting
⠙ | 1192 | spectra_subsetting
⠸ | 1194 | spectra_subsetting
⠴ | 1196 | spectra_subsetting
⠧ | 1198 | spectra_subsetting
⠏ | 1200 | spectra_subsetting
⠙ | 1202 | spectra_subsetting
⠸ | 1204 | spectra_subsetting
⠧ | 1208 | spectra_subsetting
⠦ | 1217 | spectra_subsetting
⠹ | 1223 | spectra_subsetting
⠋ | 1231 | spectra_subsetting
⠧ | 1238 | spectra_subsetting
⠹ | 1243 | spectra_subsetting
✔ | 1246 | spectra_subsetting [36.4s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠴ | 16 | spectra_variables
⠦ | 27 | spectra_variables
⠇ | 29 | spectra_variables
⠋ | 31 | spectra_variables
⠹ | 43 | spectra_variables
⠸ | 54 | spectra_variables
✔ | 64 | spectra_variables [9.3s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 48.2 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1314 ]
>
> dbDisconnect(a_db_long)
> dbDisconnect(a_db_blob)
> dbDisconnect(a_db_blob2)
> dbDisconnect(mm_db)
> dbDisconnect(tmt_db)
>
> proc.time()
user system elapsed
453.434 38.203 482.979
MsBackendSql.Rcheck/MsBackendSql-Ex.timings
| name | user | system | elapsed | |
| MsBackendSql | 9.305 | 1.023 | 10.529 | |