Johannes Rainer
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/MsBackendSql |
| git_branch: devel |
| git_last_commit: d3bb395 |
| git_last_commit_date: 2025-10-20 02:19:09 -0400 (Mon, 20 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:06 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1379/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendSql 1.9.4 (landing page) Johannes Rainer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 1.9.4 |
| 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_1.9.4.tar.gz |
| StartedAt: 2025-10-24 20:54:39 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 20:56:50 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 131.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendSql.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.9.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MsBackendSql.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendSql/DESCRIPTION’ ... OK
* this is package ‘MsBackendSql’ version ‘1.9.4’
* 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
MsBackendSql.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendSql ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘MsBackendSql’ ... ** this is package ‘MsBackendSql’ version ‘1.9.4’ ** 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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 0s
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 0s
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 0s
Creating indices .... Done
[1] TRUE
> mm8_be_blob2 <- backendInitialize(MsBackendSql(), mm8_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)
> ##
> ################################################################################
>
> 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 27s
Creating indices .... Done
[1] TRUE
> tmt_be <- backendInitialize(MsBackendSql(), tmt_db)
>
> test_check("MsBackendSql")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 607 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_MsBackendSql-functions.R:426:1'
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 607 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> test_suite <- system.file("test_backends", "test_MsBackend",
+ package = "Spectra")
>
> be <- mm8_be_blob
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠇ | 89 | spectra_subsetting
⠼ | 185 | spectra_subsetting
⠦ | 277 | spectra_subsetting
⠇ | 379 | spectra_subsetting
⠼ | 475 | spectra_subsetting
⠧ | 568 | spectra_subsetting
⠙ | 602 | spectra_subsetting
⠦ | 607 | spectra_subsetting
⠙ | 612 | spectra_subsetting
⠦ | 617 | spectra_subsetting
⠙ | 622 | spectra_subsetting
⠦ | 627 | spectra_subsetting
⠙ | 632 | spectra_subsetting
⠦ | 637 | spectra_subsetting
⠙ | 642 | spectra_subsetting
⠦ | 647 | spectra_subsetting
⠙ | 652 | spectra_subsetting
⠦ | 657 | spectra_subsetting
⠙ | 662 | spectra_subsetting
⠦ | 667 | spectra_subsetting
⠙ | 672 | spectra_subsetting
⠦ | 677 | spectra_subsetting
⠙ | 682 | spectra_subsetting
⠦ | 687 | spectra_subsetting
⠙ | 692 | spectra_subsetting
⠦ | 697 | spectra_subsetting
⠹ | 703 | spectra_subsetting
⠧ | 708 | spectra_subsetting
⠹ | 713 | spectra_subsetting
⠇ | 719 | spectra_subsetting
⠸ | 724 | spectra_subsetting
⠇ | 729 | spectra_subsetting
⠼ | 735 | spectra_subsetting
⠏ | 740 | spectra_subsetting
⠼ | 745 | spectra_subsetting
⠏ | 750 | spectra_subsetting
⠴ | 756 | spectra_subsetting
⠋ | 761 | spectra_subsetting
⠴ | 766 | spectra_subsetting
⠙ | 772 | spectra_subsetting
⠦ | 777 | spectra_subsetting
⠙ | 782 | spectra_subsetting
⠦ | 787 | spectra_subsetting
⠙ | 792 | spectra_subsetting
⠇ | 799 | spectra_subsetting
⠹ | 823 | spectra_subsetting
⠧ | 838 | spectra_subsetting
✔ | 838 | spectra_subsetting [5.0s]
⠏ | 0 | spectra_variables
⠋ | 31 | spectra_variables
✔ | 64 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 5.2 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 906 ]
🌈 Your tests are over the rainbow 🌈
>
> 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 [1.6s]
⠏ | 0 | spectra_subsetting
⠴ | 76 | spectra_subsetting
⠙ | 172 | spectra_subsetting
⠼ | 265 | spectra_subsetting
⠇ | 359 | spectra_subsetting
⠏ | 460 | spectra_subsetting
⠸ | 554 | spectra_subsetting
⠴ | 646 | spectra_subsetting
⠦ | 747 | spectra_subsetting
⠸ | 844 | spectra_subsetting
⠴ | 906 | spectra_subsetting
⠧ | 908 | spectra_subsetting
⠙ | 912 | spectra_subsetting
⠦ | 917 | spectra_subsetting
⠏ | 920 | spectra_subsetting
⠹ | 923 | spectra_subsetting
⠧ | 928 | spectra_subsetting
⠹ | 933 | spectra_subsetting
⠴ | 936 | spectra_subsetting
⠋ | 941 | spectra_subsetting
⠹ | 943 | spectra_subsetting
⠼ | 945 | spectra_subsetting
⠏ | 950 | spectra_subsetting
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⠹ | 963 | spectra_subsetting
⠴ | 966 | spectra_subsetting
⠏ | 970 | spectra_subsetting
⠹ | 973 | spectra_subsetting
⠧ | 978 | spectra_subsetting
⠋ | 981 | spectra_subsetting
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⠙ | 1002 | spectra_subsetting
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⠙ | 1012 | spectra_subsetting
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⠙ | 1022 | spectra_subsetting
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⠏ | 1030 | spectra_subsetting
⠹ | 1033 | spectra_subsetting
⠦ | 1037 | spectra_subsetting
⠋ | 1041 | spectra_subsetting
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⠇ | 1049 | spectra_subsetting
⠹ | 1053 | spectra_subsetting
⠴ | 1056 | spectra_subsetting
⠙ | 1062 | spectra_subsetting
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⠋ | 1071 | spectra_subsetting
⠴ | 1076 | spectra_subsetting
⠏ | 1080 | spectra_subsetting
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⠙ | 1092 | spectra_subsetting
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⠋ | 1101 | spectra_subsetting
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⠇ | 1109 | spectra_subsetting
⠋ | 1111 | spectra_subsetting
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⠋ | 1121 | spectra_subsetting
⠸ | 1124 | spectra_subsetting
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⠇ | 1139 | spectra_subsetting
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⠹ | 1153 | spectra_subsetting
⠧ | 1158 | spectra_subsetting
⠹ | 1163 | spectra_subsetting
⠧ | 1168 | spectra_subsetting
⠙ | 1172 | spectra_subsetting
⠼ | 1175 | spectra_subsetting
⠏ | 1180 | spectra_subsetting
⠹ | 1183 | spectra_subsetting
⠧ | 1188 | spectra_subsetting
⠹ | 1193 | spectra_subsetting
⠴ | 1196 | spectra_subsetting
⠏ | 1200 | spectra_subsetting
⠦ | 1207 | spectra_subsetting
⠦ | 1217 | spectra_subsetting
⠹ | 1223 | spectra_subsetting
⠧ | 1238 | spectra_subsetting
✔ | 1246 | spectra_subsetting [14.6s]
⠏ | 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 [6.0s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 22.3 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1314 ]
>
> dbDisconnect(mm8_db_long)
> dbDisconnect(mm8_db_blob)
> dbDisconnect(mm8_db_blob2)
> dbDisconnect(mm_db)
> dbDisconnect(tmt_db)
>
> proc.time()
user system elapsed
88.731 9.892 98.264
MsBackendSql.Rcheck/MsBackendSql-Ex.timings
| name | user | system | elapsed | |
| MsBackendSql | 1.238 | 0.179 | 1.416 | |