Back to Rapid builds (Linux only) of a subset of BioC 3.22 Report updated every 6 hours |
This page was generated on 2025-10-11 09:59 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 925 |
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 147/229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
MsBackendSql 1.9.2 (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: 1.9.2 |
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings MsBackendSql_1.9.2.tar.gz |
StartedAt: 2025-10-11 08:56:03 -0400 (Sat, 11 Oct 2025) |
EndedAt: 2025-10-11 09:00:00 -0400 (Sat, 11 Oct 2025) |
EllapsedTime: 236.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MsBackendSql.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:MsBackendSql.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings MsBackendSql_1.9.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/MsBackendSql.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘1.9.2’ * 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 * 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/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL MsBackendSql ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’ * installing *source* package ‘MsBackendSql’ ... ** this is package ‘MsBackendSql’ version ‘1.9.2’ ** 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 (2025-06-13) -- "Great Square Root" 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) > > 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 1 | SKIP 2 | PASS 574 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test_MsBackendSql-functions.R:426:1', 'test_MsBackendSql-functions.R:670:1' [ FAIL 0 | WARN 1 | SKIP 2 | PASS 574 ] > > 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 ⠦ | 37 | spectra_subsetting ⠼ | 85 | spectra_subsetting ⠇ | 139 | spectra_subsetting ⠹ | 193 | spectra_subsetting ⠋ | 241 | spectra_subsetting ⠼ | 295 | spectra_subsetting ⠇ | 349 | spectra_subsetting ⠸ | 384 | spectra_subsetting ⠦ | 437 | spectra_subsetting ⠋ | 491 | spectra_subsetting ⠇ | 539 | spectra_subsetting ⠙ | 592 | spectra_subsetting ⠋ | 601 | spectra_subsetting ⠸ | 604 | spectra_subsetting ⠦ | 607 | spectra_subsetting ⠏ | 610 | spectra_subsetting ⠹ | 613 | spectra_subsetting ⠴ | 616 | spectra_subsetting ⠇ | 619 | spectra_subsetting ⠙ | 622 | spectra_subsetting ⠼ | 625 | spectra_subsetting ⠧ | 628 | spectra_subsetting ⠋ | 631 | spectra_subsetting ⠸ | 634 | spectra_subsetting ⠦ | 637 | spectra_subsetting ⠏ | 640 | spectra_subsetting ⠹ | 643 | spectra_subsetting ⠴ | 646 | spectra_subsetting ⠇ | 649 | spectra_subsetting ⠙ | 652 | spectra_subsetting ⠼ | 655 | spectra_subsetting ⠧ | 658 | spectra_subsetting ⠋ | 661 | spectra_subsetting ⠸ | 664 | spectra_subsetting ⠦ | 667 | spectra_subsetting ⠏ | 670 | spectra_subsetting ⠹ | 673 | spectra_subsetting ⠴ | 676 | spectra_subsetting ⠇ | 679 | spectra_subsetting ⠙ | 682 | spectra_subsetting ⠼ | 685 | spectra_subsetting ⠧ | 688 | spectra_subsetting ⠋ | 691 | spectra_subsetting ⠸ | 694 | spectra_subsetting ⠦ | 697 | spectra_subsetting ⠏ | 700 | spectra_subsetting ⠹ | 703 | spectra_subsetting ⠴ | 706 | spectra_subsetting ⠧ | 708 | spectra_subsetting ⠋ | 711 | spectra_subsetting ⠸ | 714 | spectra_subsetting ⠦ | 717 | spectra_subsetting ⠏ | 720 | spectra_subsetting ⠹ | 723 | spectra_subsetting ⠴ | 726 | spectra_subsetting ⠇ | 729 | spectra_subsetting ⠙ | 732 | spectra_subsetting ⠼ | 735 | spectra_subsetting ⠧ | 738 | spectra_subsetting ⠋ | 741 | spectra_subsetting ⠸ | 744 | spectra_subsetting ⠦ | 747 | spectra_subsetting ⠏ | 750 | spectra_subsetting ⠹ | 753 | spectra_subsetting ⠴ | 756 | spectra_subsetting ⠇ | 759 | spectra_subsetting ⠙ | 762 | spectra_subsetting ⠼ | 765 | spectra_subsetting ⠧ | 768 | spectra_subsetting ⠋ | 771 | spectra_subsetting ⠸ | 774 | spectra_subsetting ⠦ | 777 | spectra_subsetting ⠏ | 780 | spectra_subsetting ⠹ | 783 | spectra_subsetting ⠴ | 786 | spectra_subsetting ⠇ | 789 | spectra_subsetting ⠙ | 792 | spectra_subsetting ⠼ | 795 | spectra_subsetting ⠏ | 800 | spectra_subsetting ⠼ | 815 | spectra_subsetting ⠏ | 830 | spectra_subsetting ✔ | 838 | spectra_subsetting [10.4s] ⠏ | 0 | spectra_variables ⠸ | 14 | spectra_variables ⠦ | 37 | spectra_variables ⠇ | 59 | spectra_variables ✔ | 64 | spectra_variables ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 10.8 s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 906 ] 🌈 Your tests are over the rainbow 🌈 Warning message: call dbDisconnect() when finished working with a connection > > 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 [2.2s] ⠏ | 0 | spectra_subsetting ⠋ | 31 | spectra_subsetting ⠼ | 85 | spectra_subsetting ⠹ | 123 | spectra_subsetting ⠴ | 176 | spectra_subsetting ⠇ | 229 | spectra_subsetting ⠴ | 276 | spectra_subsetting ⠧ | 328 | spectra_subsetting ⠙ | 382 | spectra_subsetting ⠏ | 430 | spectra_subsetting ⠹ | 483 | spectra_subsetting ⠼ | 535 | spectra_subsetting ⠹ | 583 | spectra_subsetting ⠼ | 635 | spectra_subsetting ⠧ | 688 | spectra_subsetting ⠴ | 736 | spectra_subsetting ⠧ | 788 | spectra_subsetting ⠋ | 841 | spectra_subsetting ⠇ | 889 | spectra_subsetting ⠴ | 906 | spectra_subsetting ⠧ | 908 | spectra_subsetting ⠋ | 911 | spectra_subsetting ⠙ | 912 | spectra_subsetting ⠼ | 915 | spectra_subsetting ⠧ | 918 | spectra_subsetting ⠏ | 920 | spectra_subsetting ⠙ | 922 | spectra_subsetting ⠼ | 925 | spectra_subsetting ⠧ | 928 | spectra_subsetting ⠋ | 931 | spectra_subsetting ⠸ | 934 | spectra_subsetting ⠦ | 937 | spectra_subsetting ⠏ | 940 | spectra_subsetting ⠙ | 942 | spectra_subsetting ⠹ | 943 | spectra_subsetting ⠼ | 945 | spectra_subsetting ⠧ | 948 | spectra_subsetting ⠋ | 951 | spectra_subsetting ⠸ | 954 | spectra_subsetting ⠦ | 957 | spectra_subsetting ⠏ | 960 | spectra_subsetting ⠹ | 963 | spectra_subsetting ⠼ | 965 | spectra_subsetting ⠧ | 968 | 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 ⠋ | 1001 | spectra_subsetting ⠸ | 1004 | spectra_subsetting ⠦ | 1007 | spectra_subsetting ⠏ | 1010 | spectra_subsetting ⠹ | 1013 | spectra_subsetting ⠴ | 1016 | spectra_subsetting ⠇ | 1019 | 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 ⠙ | 1052 | spectra_subsetting ⠸ | 1054 | spectra_subsetting ⠦ | 1057 | spectra_subsetting ⠏ | 1060 | spectra_subsetting ⠹ | 1063 | spectra_subsetting ⠴ | 1066 | 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 ⠴ | 1106 | 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 ⠹ | 1143 | spectra_subsetting ⠴ | 1146 | spectra_subsetting ⠇ | 1149 | spectra_subsetting ⠙ | 1152 | spectra_subsetting ⠼ | 1155 | spectra_subsetting ⠧ | 1158 | spectra_subsetting ⠋ | 1161 | spectra_subsetting ⠸ | 1164 | spectra_subsetting ⠦ | 1167 | spectra_subsetting ⠏ | 1170 | spectra_subsetting ⠹ | 1173 | spectra_subsetting ⠸ | 1174 | spectra_subsetting ⠦ | 1177 | spectra_subsetting ⠏ | 1180 | spectra_subsetting ⠹ | 1183 | spectra_subsetting ⠴ | 1186 | spectra_subsetting ⠇ | 1189 | spectra_subsetting ⠙ | 1192 | spectra_subsetting ⠸ | 1194 | spectra_subsetting ⠦ | 1197 | spectra_subsetting ⠏ | 1200 | spectra_subsetting ⠹ | 1203 | spectra_subsetting ⠧ | 1208 | spectra_subsetting ⠦ | 1217 | spectra_subsetting ⠹ | 1223 | spectra_subsetting ⠧ | 1238 | spectra_subsetting ✔ | 1246 | spectra_subsetting [25.5s] ⠏ | 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 [8.9s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 36.5 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 135.186 14.175 145.712
MsBackendSql.Rcheck/MsBackendSql-Ex.timings
name | user | system | elapsed | |
MsBackendSql | 2.185 | 0.342 | 2.501 | |