Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 419/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CompoundDb 1.10.0 (landing page) Johannes Rainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the CompoundDb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CompoundDb.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: CompoundDb |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CompoundDb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CompoundDb_1.10.0.tar.gz |
StartedAt: 2024-12-19 21:53:00 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 21:59:11 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 371.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CompoundDb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CompoundDb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CompoundDb_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CompoundDb.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘CompoundDb/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CompoundDb’ version ‘1.10.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘CompoundDb’ 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
CompoundDb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CompoundDb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘CompoundDb’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘mass2mz’ in package ‘CompoundDb’ ** 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 (CompoundDb)
CompoundDb.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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("CompoundDb") Loading required package: AnnotationFilter Attaching package: 'AnnotationFilter' The following object is masked from 'package:testthat': not Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, 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 > library(RSQLite) > > hmdb <- system.file("sdf/HMDB_sub.sdf.gz", package = "CompoundDb") > cmps <- compound_tbl_sdf(hmdb) > metad <- data.frame(name = c("source", "url", "source_version", + "source_date", "organism"), + value = c("HMDB_test", "http://www.hmdb.ca", + "v4", "2017-08-27", "Hsapiens")) > db_file <- createCompDb(cmps, metadata = metad, path = tempdir()) > cmp_db <- CompDb(db_file) > > dr <- system.file("xml/", package = "CompoundDb") > msms_spctra <- msms_spectra_hmdb(dr) Going to process 4 xml files. Postprocessing data ... OK > ## spl_ <- as(msms_spctra, "Spectra") > > metad2 <- data.frame(name = c("source", "url", "source_version", + "source_date", "organism"), + value = c("HMDB_spctra", "http://www.hmdb.ca", + "v4", "2017-08-27", "Hsapiens")) > db_spctra_file <- createCompDb(cmps, metadata = metad2, path = tempdir(), + msms_spectra = msms_spctra) > cmp_spctra_db <- CompDb(db_spctra_file) > > cdb <- CompDb(system.file("sql/CompDb.MassBank.sql", package = "CompoundDb")) > > ions <- data.frame(compound_id = paste0("HMDB000000", + c("1", "1", "2", "2", "5")), + ion_adduct = c("A", "B", "B", "C", "D"), + ion_mz = c(100, 110, 150, 170, 200), + ion_rt = c(50, 60, 100, 110, 90)) > ion_db <- IonDb(paste0(tempdir(), "/ion_db.db"), cmp_db, ions) > > ion_spctra_db <- IonDb(paste0(tempdir(), "/ion_spctra_db.db"), + cmp_spctra_db, ions) > > test_check("CompoundDb") Creating package in /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpnUrAQw/CompDb.Hsapiens.ChEBI.unknown [ FAIL 0 | WARN 5 | SKIP 0 | PASS 697 ] [ FAIL 0 | WARN 5 | SKIP 0 | PASS 697 ] Warning message: call dbDisconnect() when finished working with a connection > > library(Spectra) Loading required package: BiocParallel > be <- backendInitialize(MsBackendCompDb(), cmp_spctra_db) > test_suite <- system.file("test_backends", "test_MsBackend", + package = "Spectra") > test_dir(test_suite, stop_on_failure = TRUE) ✔ | F W S OK | Context ⠏ | 0 | peaks_variables ✔ | 4 | peaks_variables ⠏ | 0 | spectra_subsetting ⠦ | 17 | spectra_subsetting ⠧ | 18 | spectra_subsetting ⠇ | 19 | spectra_subsetting ⠏ | 20 | spectra_subsetting ⠹ | 23 | spectra_subsetting ⠼ | 25 | spectra_subsetting ⠦ | 37 | spectra_subsetting ✔ | 1 43 | spectra_subsetting [1.1s] ⠏ | 0 | spectra_variables ⠸ | 14 | spectra_variables ⠇ | 29 | spectra_variables ⠧ | 48 | spectra_variables ⠧ | 58 | spectra_variables ✔ | 64 | spectra_variables ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 1.6 s ── Skipped tests (1) ─────────────────────────────────────────────────────────── • empty test (1): 'test_spectra_subsetting.R:109:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 111 ] > > proc.time() user system elapsed 18.306 3.293 19.500
CompoundDb.Rcheck/CompoundDb-Ex.timings
name | user | system | elapsed | |
CompDb | 0.705 | 0.010 | 0.716 | |
Filter-classes | 0.010 | 0.006 | 0.016 | |
IonDb | 0.546 | 0.046 | 0.591 | |
MsBackendCompDb | 0.095 | 0.001 | 0.096 | |
compound_tbl_lipidblast | 1.437 | 0.148 | 1.464 | |
compound_tbl_sdf | 0.099 | 0.007 | 0.106 | |
createCompDb | 0.276 | 0.044 | 0.321 | |
expandMzIntensity | 0.015 | 0.002 | 0.018 | |
import_mona_sdf | 0.018 | 0.003 | 0.022 | |
msms_spectra_hmdb | 0.025 | 0.002 | 0.027 | |
msms_spectra_mona | 0.038 | 0.004 | 0.042 | |