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This page was generated on 2026-04-02 11:35 -0400 (Thu, 02 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.6.0 alpha (2026-03-30 r89742) 4885
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-03-28 r89739) 4619
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 1389/2374HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendSql 1.11.3  (landing page)
Johannes Rainer
Snapshot Date: 2026-04-01 13:40 -0400 (Wed, 01 Apr 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 -0400 (Thu, 05 Feb 2026)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
See other builds for MsBackendSql in R Universe.


CHECK results for MsBackendSql on kjohnson3

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.

raw results


Summary

Package: MsBackendSql
Version: 1.11.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendSql_1.11.3.tar.gz
StartedAt: 2026-04-01 20:52:23 -0400 (Wed, 01 Apr 2026)
EndedAt: 2026-04-01 20:56:22 -0400 (Wed, 01 Apr 2026)
EllapsedTime: 238.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendSql.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendSql_1.11.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MsBackendSql.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-02 00:52:23 UTC
* using option ‘--no-vignettes’
* 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 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

MsBackendSql.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendSql
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/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)

Tests output

MsBackendSql.Rcheck/tests/testthat.Rout


R version 4.6.0 alpha (2026-03-28 r89739)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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  1s
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  2s
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 24s
Creating indices .... Done
[1] TRUE
> tmt_be <- backendInitialize(MsBackendSql(), tmt_db)
> 
> test_check("MsBackendSql")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 640 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 640 ]
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

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✔ |          4 | peaks_variables

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══ Results ═════════════════════════════════════════════════════════════════════
Duration: 25.9 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                                                
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✔ |          4 | peaks_variables [1.1s]

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⠋ |        941 | spectra_subsetting                                             
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⠋ |        951 | spectra_subsetting                                             
⠴ |        956 | spectra_subsetting                                             
⠏ |        960 | spectra_subsetting                                             
⠹ |        963 | spectra_subsetting                                             
⠼ |        965 | spectra_subsetting                                             
⠏ |        970 | spectra_subsetting                                             
⠼ |        975 | spectra_subsetting                                             
⠦ |        977 | spectra_subsetting                                             
⠙ |        982 | spectra_subsetting                                             
⠸ |        984 | spectra_subsetting                                             
⠧ |        988 | spectra_subsetting                                             
⠋ |        991 | spectra_subsetting                                             
⠴ |        996 | spectra_subsetting                                             
⠧ |        998 | spectra_subsetting                                             
⠋ |        1001 | spectra_subsetting                                            
⠴ |        1006 | spectra_subsetting                                            
⠋ |        1011 | spectra_subsetting                                            
⠴ |        1016 | spectra_subsetting                                            
⠏ |        1020 | spectra_subsetting                                            
⠼ |        1025 | spectra_subsetting                                            
⠏ |        1030 | spectra_subsetting                                            
⠸ |        1034 | spectra_subsetting                                            
⠇ |        1039 | spectra_subsetting                                            
⠹ |        1043 | spectra_subsetting                                            
⠧ |        1048 | spectra_subsetting                                            
⠋ |        1051 | spectra_subsetting                                            
⠼ |        1055 | spectra_subsetting                                            
⠏ |        1060 | spectra_subsetting                                            
⠙ |        1062 | spectra_subsetting                                            
⠸ |        1064 | spectra_subsetting                                            
⠇ |        1069 | spectra_subsetting                                            
⠸ |        1074 | spectra_subsetting                                            
⠇ |        1079 | spectra_subsetting                                            
⠙ |        1082 | spectra_subsetting                                            
⠼ |        1085 | spectra_subsetting                                            
⠇ |        1089 | spectra_subsetting                                            
⠸ |        1094 | spectra_subsetting                                            
⠇ |        1099 | spectra_subsetting                                            
⠸ |        1104 | spectra_subsetting                                            
⠇ |        1109 | spectra_subsetting                                            
⠹ |        1113 | spectra_subsetting                                            
⠧ |        1118 | spectra_subsetting                                            
⠹ |        1123 | spectra_subsetting                                            
⠦ |        1127 | spectra_subsetting                                            
⠙ |        1132 | spectra_subsetting                                            
⠼ |        1135 | spectra_subsetting                                            
⠧ |        1138 | spectra_subsetting                                            
⠋ |        1141 | spectra_subsetting                                            
⠼ |        1145 | spectra_subsetting                                            
⠧ |        1148 | spectra_subsetting                                            
⠙ |        1152 | spectra_subsetting                                            
⠦ |        1157 | spectra_subsetting                                            
⠙ |        1162 | spectra_subsetting                                            
⠸ |        1164 | spectra_subsetting                                            
⠇ |        1169 | spectra_subsetting                                            
⠹ |        1173 | spectra_subsetting                                            
⠴ |        1176 | spectra_subsetting                                            
⠏ |        1180 | spectra_subsetting                                            
⠼ |        1185 | spectra_subsetting                                            
⠏ |        1190 | spectra_subsetting                                            
⠙ |        1192 | spectra_subsetting                                            
⠦ |        1197 | spectra_subsetting                                            
⠙ |        1202 | spectra_subsetting                                            
⠼ |        1215 | spectra_subsetting                                            
⠦ |        1217 | spectra_subsetting                                            
⠹ |        1223 | spectra_subsetting                                            
⠧ |        1238 | spectra_subsetting                                            
✔ |        1246 | spectra_subsetting [13.5s]

⠏ |          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 [4.1s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 18.7 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 
180.188  20.588 200.119 

Example timings

MsBackendSql.Rcheck/MsBackendSql-Ex.timings

nameusersystemelapsed
MsBackendSql3.5350.3974.299