Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 420/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CompoundDb 1.8.0  (landing page)
Johannes Rainer
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/CompoundDb
git_branch: RELEASE_3_19
git_last_commit: c4266c8
git_last_commit_date: 2024-04-30 11:40:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CompoundDb on nebbiolo1

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.

raw results


Summary

Package: CompoundDb
Version: 1.8.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CompoundDb.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CompoundDb_1.8.0.tar.gz
StartedAt: 2024-06-19 21:55:13 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 21:57:54 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 160.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CompoundDb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CompoundDb.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CompoundDb_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CompoundDb.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CompoundDb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CompoundDb’ version ‘1.8.0’
* 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 ‘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


Installation output

CompoundDb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CompoundDb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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)

Tests output

CompoundDb.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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, 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")
MsBackendCompDb with 0 spectra
MsBackendCompDb with 4 spectra
    msLevel precursorMz  polarity
  <integer>   <numeric> <integer>
1        NA          NA         1
2        NA          NA         1
3        NA          NA         1
4        NA          NA         0
 ... 32 more variables/columns.
 Use  'spectraVariables' to list all of them.
 data source: HMDB_spctra 
 version: v4 
 organism: Hsapiens 
Creating package in /tmp/RtmpNYlAmA/CompDb.Hsapiens.ChEBI.unknown 
[ FAIL 0 | WARN 11 | SKIP 1 | PASS 660 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_MsBackendCompDb.R:165:1'

[ FAIL 0 | WARN 11 | SKIP 1 | PASS 660 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> library(Spectra)
Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth

> 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                                             
⠸ |         34 | spectra_subsetting                                             
✔ |      1  36 | spectra_subsetting

⠏ |          0 | spectra_variables                                              
⠸ |         14 | spectra_variables                                              
⠧ |         28 | spectra_variables                                              
⠸ |         44 | spectra_variables                                              
⠸ |         54 | spectra_variables                                              
✔ |         64 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.5 s

── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_subsetting.R:90:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 104 ]
> 
> proc.time()
   user  system elapsed 
 16.302   1.186  17.478 

Example timings

CompoundDb.Rcheck/CompoundDb-Ex.timings

nameusersystemelapsed
CompDb0.7610.0320.793
Filter-classes0.0140.0000.014
IonDb0.6260.0440.670
MsBackendCompDb0.1020.0040.106
compound_tbl_lipidblast0.0290.0000.029
compound_tbl_sdf0.1020.0080.110
createCompDb0.2700.0280.298
expandMzIntensity0.0180.0040.021
import_mona_sdf0.0180.0030.023
msms_spectra_hmdb0.0150.0150.031
msms_spectra_mona0.0220.0350.059