| Back to Rapid builds (Linux only) of a subset of BioC 3.23 Report updated every 6 hours |
This page was generated on 2025-11-14 10:17 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" | 917 |
| 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 148/230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| MsBackendSql 1.11.1 (landing page) Johannes Rainer
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||
|
To the developers/maintainers of the MsBackendSql package: - 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: 1.11.1 |
| Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings MsBackendSql_1.11.1.tar.gz |
| StartedAt: 2025-11-14 09:07:12 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 09:11:37 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 264.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendSql.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings MsBackendSql_1.11.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MsBackendSql.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 ‘1.11.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Johannes Rainer <Johannes.Rainer@eurac.edu>’
Unknown, possibly misspelled, fields in DESCRIPTION:
‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’
Uses the non-portable package: ‘mzR’
The Title field should be in title case. Current version is:
‘SQL-based Mass Spectrometry Data Backend’
In title case that is:
‘SQL-Based Mass Spectrometry Data Backend’
* 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 use of S3 registration ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MsBackendSql.Rcheck/00check.log’
for details.
MsBackendSql.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL MsBackendSql ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’ * installing *source* package ‘MsBackendSql’ ... ** this is package ‘MsBackendSql’ version ‘1.11.1’ ** 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 (MsBackendSql)
MsBackendSql.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-28 r88973) -- "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(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)
>
> ################################################################################
> ##
> ## 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 40s
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 <- 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
⠼ | 35 | spectra_subsetting
⠼ | 85 | spectra_subsetting
⠋ | 131 | spectra_subsetting
⠙ | 182 | spectra_subsetting
⠙ | 232 | spectra_subsetting
⠦ | 277 | spectra_subsetting
⠧ | 328 | spectra_subsetting
⠦ | 377 | spectra_subsetting
⠦ | 427 | spectra_subsetting
⠙ | 472 | spectra_subsetting
⠋ | 521 | spectra_subsetting
⠋ | 571 | spectra_subsetting
⠇ | 599 | spectra_subsetting
⠙ | 602 | spectra_subsetting
⠼ | 605 | spectra_subsetting
⠧ | 608 | spectra_subsetting
⠋ | 611 | spectra_subsetting
⠸ | 614 | spectra_subsetting
⠦ | 617 | spectra_subsetting
⠏ | 620 | spectra_subsetting
⠹ | 623 | spectra_subsetting
⠴ | 626 | spectra_subsetting
⠇ | 629 | spectra_subsetting
⠙ | 632 | spectra_subsetting
⠼ | 635 | spectra_subsetting
⠧ | 638 | spectra_subsetting
⠋ | 641 | spectra_subsetting
⠸ | 644 | spectra_subsetting
⠦ | 647 | spectra_subsetting
⠏ | 650 | spectra_subsetting
⠹ | 653 | spectra_subsetting
⠸ | 654 | spectra_subsetting
⠦ | 657 | spectra_subsetting
⠏ | 660 | spectra_subsetting
⠹ | 663 | spectra_subsetting
⠴ | 666 | spectra_subsetting
⠇ | 669 | spectra_subsetting
⠙ | 672 | spectra_subsetting
⠼ | 675 | spectra_subsetting
⠧ | 678 | spectra_subsetting
⠋ | 681 | spectra_subsetting
⠸ | 684 | spectra_subsetting
⠦ | 687 | spectra_subsetting
⠏ | 690 | spectra_subsetting
⠹ | 693 | spectra_subsetting
⠴ | 696 | spectra_subsetting
⠇ | 699 | spectra_subsetting
⠙ | 702 | spectra_subsetting
⠸ | 704 | spectra_subsetting
⠴ | 706 | spectra_subsetting
⠇ | 709 | spectra_subsetting
⠋ | 711 | spectra_subsetting
⠸ | 714 | spectra_subsetting
⠴ | 716 | spectra_subsetting
⠇ | 719 | spectra_subsetting
⠙ | 722 | spectra_subsetting
⠼ | 725 | spectra_subsetting
⠦ | 727 | spectra_subsetting
⠏ | 730 | spectra_subsetting
⠹ | 733 | spectra_subsetting
⠴ | 736 | spectra_subsetting
⠧ | 738 | spectra_subsetting
⠏ | 740 | spectra_subsetting
⠹ | 743 | spectra_subsetting
⠼ | 745 | spectra_subsetting
⠧ | 748 | spectra_subsetting
⠏ | 750 | spectra_subsetting
⠹ | 753 | spectra_subsetting
⠴ | 756 | spectra_subsetting
⠇ | 759 | spectra_subsetting
⠋ | 761 | spectra_subsetting
⠸ | 764 | spectra_subsetting
⠦ | 767 | spectra_subsetting
⠏ | 770 | spectra_subsetting
⠙ | 772 | spectra_subsetting
⠼ | 775 | spectra_subsetting
⠧ | 778 | spectra_subsetting
⠋ | 781 | spectra_subsetting
⠸ | 784 | spectra_subsetting
⠦ | 787 | spectra_subsetting
⠇ | 789 | spectra_subsetting
⠙ | 792 | spectra_subsetting
⠼ | 795 | spectra_subsetting
⠏ | 800 | spectra_subsetting
⠸ | 814 | spectra_subsetting
⠹ | 823 | spectra_subsetting
⠏ | 830 | spectra_subsetting
✔ | 838 | spectra_subsetting [11.6s]
⠏ | 0 | spectra_variables
⠸ | 14 | spectra_variables
⠦ | 37 | spectra_variables
⠸ | 54 | spectra_variables
✔ | 64 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 12.0 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 [2.7s]
⠏ | 0 | spectra_subsetting
⠧ | 28 | spectra_subsetting
⠦ | 77 | spectra_subsetting
⠙ | 122 | spectra_subsetting
⠙ | 172 | spectra_subsetting
⠙ | 222 | spectra_subsetting
⠙ | 272 | spectra_subsetting
⠦ | 317 | spectra_subsetting
⠦ | 367 | spectra_subsetting
⠧ | 418 | spectra_subsetting
⠙ | 432 | spectra_subsetting
⠙ | 482 | spectra_subsetting
⠙ | 532 | spectra_subsetting
⠋ | 581 | spectra_subsetting
⠦ | 627 | spectra_subsetting
⠦ | 677 | spectra_subsetting
⠧ | 728 | spectra_subsetting
⠼ | 775 | spectra_subsetting
⠴ | 826 | spectra_subsetting
⠴ | 876 | spectra_subsetting
⠼ | 905 | spectra_subsetting
⠦ | 907 | spectra_subsetting
⠇ | 909 | spectra_subsetting
⠋ | 911 | spectra_subsetting
⠙ | 912 | spectra_subsetting
⠼ | 915 | spectra_subsetting
⠦ | 917 | spectra_subsetting
⠏ | 920 | spectra_subsetting
⠙ | 922 | spectra_subsetting
⠼ | 925 | spectra_subsetting
⠦ | 927 | spectra_subsetting
⠏ | 930 | spectra_subsetting
⠹ | 933 | spectra_subsetting
⠸ | 934 | spectra_subsetting
⠦ | 937 | spectra_subsetting
⠇ | 939 | spectra_subsetting
⠋ | 941 | spectra_subsetting
⠹ | 943 | spectra_subsetting
⠼ | 945 | spectra_subsetting
⠧ | 948 | spectra_subsetting
⠋ | 951 | spectra_subsetting
⠸ | 954 | spectra_subsetting
⠦ | 957 | spectra_subsetting
⠏ | 960 | spectra_subsetting
⠙ | 962 | spectra_subsetting
⠼ | 965 | spectra_subsetting
⠦ | 967 | spectra_subsetting
⠏ | 970 | spectra_subsetting
⠙ | 972 | spectra_subsetting
⠸ | 974 | spectra_subsetting
⠦ | 977 | spectra_subsetting
⠏ | 980 | spectra_subsetting
⠋ | 981 | spectra_subsetting
⠹ | 983 | spectra_subsetting
⠴ | 986 | spectra_subsetting
⠧ | 988 | spectra_subsetting
⠋ | 991 | spectra_subsetting
⠹ | 993 | spectra_subsetting
⠴ | 996 | spectra_subsetting
⠧ | 998 | spectra_subsetting
⠏ | 1000 | spectra_subsetting
⠙ | 1002 | spectra_subsetting
⠼ | 1005 | spectra_subsetting
⠧ | 1008 | spectra_subsetting
⠋ | 1011 | spectra_subsetting
⠸ | 1014 | spectra_subsetting
⠦ | 1017 | spectra_subsetting
⠏ | 1020 | spectra_subsetting
⠙ | 1022 | spectra_subsetting
⠼ | 1025 | spectra_subsetting
⠧ | 1028 | spectra_subsetting
⠋ | 1031 | spectra_subsetting
⠹ | 1033 | spectra_subsetting
⠼ | 1035 | spectra_subsetting
⠧ | 1038 | spectra_subsetting
⠋ | 1041 | spectra_subsetting
⠹ | 1043 | spectra_subsetting
⠼ | 1045 | spectra_subsetting
⠧ | 1048 | spectra_subsetting
⠇ | 1049 | spectra_subsetting
⠋ | 1051 | spectra_subsetting
⠹ | 1053 | spectra_subsetting
⠼ | 1055 | spectra_subsetting
⠴ | 1056 | spectra_subsetting
⠇ | 1059 | spectra_subsetting
⠙ | 1062 | spectra_subsetting
⠼ | 1065 | spectra_subsetting
⠧ | 1068 | spectra_subsetting
⠋ | 1071 | spectra_subsetting
⠸ | 1074 | spectra_subsetting
⠴ | 1076 | spectra_subsetting
⠇ | 1079 | spectra_subsetting
⠋ | 1081 | spectra_subsetting
⠸ | 1084 | spectra_subsetting
⠴ | 1086 | spectra_subsetting
⠦ | 1087 | spectra_subsetting
⠏ | 1090 | spectra_subsetting
⠹ | 1093 | spectra_subsetting
⠴ | 1096 | spectra_subsetting
⠇ | 1099 | spectra_subsetting
⠋ | 1101 | spectra_subsetting
⠹ | 1103 | spectra_subsetting
⠸ | 1104 | spectra_subsetting
⠦ | 1107 | spectra_subsetting
⠇ | 1109 | spectra_subsetting
⠋ | 1111 | spectra_subsetting
⠸ | 1114 | spectra_subsetting
⠦ | 1117 | spectra_subsetting
⠏ | 1120 | spectra_subsetting
⠹ | 1123 | spectra_subsetting
⠴ | 1126 | spectra_subsetting
⠇ | 1129 | spectra_subsetting
⠙ | 1132 | spectra_subsetting
⠸ | 1134 | spectra_subsetting
⠦ | 1137 | spectra_subsetting
⠏ | 1140 | spectra_subsetting
⠙ | 1142 | spectra_subsetting
⠼ | 1145 | spectra_subsetting
⠦ | 1147 | spectra_subsetting
⠇ | 1149 | spectra_subsetting
⠙ | 1152 | spectra_subsetting
⠼ | 1155 | spectra_subsetting
⠦ | 1157 | spectra_subsetting
⠏ | 1160 | spectra_subsetting
⠹ | 1163 | spectra_subsetting
⠴ | 1166 | spectra_subsetting
⠇ | 1169 | spectra_subsetting
⠙ | 1172 | spectra_subsetting
⠸ | 1174 | spectra_subsetting
⠦ | 1177 | spectra_subsetting
⠏ | 1180 | spectra_subsetting
⠹ | 1183 | spectra_subsetting
⠴ | 1186 | spectra_subsetting
⠇ | 1189 | spectra_subsetting
⠋ | 1191 | spectra_subsetting
⠸ | 1194 | spectra_subsetting
⠦ | 1197 | spectra_subsetting
⠏ | 1200 | spectra_subsetting
⠙ | 1202 | spectra_subsetting
⠦ | 1207 | spectra_subsetting
⠦ | 1217 | spectra_subsetting
⠹ | 1223 | spectra_subsetting
⠧ | 1238 | spectra_subsetting
⠴ | 1246 | spectra_subsetting
✔ | 1246 | spectra_subsetting [27.6s]
⠏ | 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 [9.2s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 39.5 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
150.290 16.655 162.646
MsBackendSql.Rcheck/MsBackendSql-Ex.timings
| name | user | system | elapsed | |
| MsBackendSql | 2.768 | 0.403 | 3.191 | |