Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:05:07 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for CompoundDb on nebbiolo2


To the developers/maintainers of the CompoundDb package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 388/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CompoundDb 1.1.3  (landing page)
Johannes Rainer
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/CompoundDb
git_branch: master
git_last_commit: f8289dc
git_last_commit_date: 2022-05-30 02:35:15 -0400 (Mon, 30 May 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CompoundDb
Version: 1.1.3
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CompoundDb.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings CompoundDb_1.1.3.tar.gz
StartedAt: 2022-06-23 19:19:33 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 19:21:47 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 134.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CompoundDb.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CompoundDb.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings CompoundDb_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/CompoundDb.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CompoundDb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CompoundDb’ version ‘1.1.3’
* 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 R 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CompoundDb.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL CompoundDb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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/RtmpDpnI5w/CompDb.Hsapiens.ChEBI.unknown 
[ FAIL 0 | WARN 5 | SKIP 1 | PASS 654 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 5 | SKIP 1 | PASS 654 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 14.961   0.593  15.540 

Example timings

CompoundDb.Rcheck/CompoundDb-Ex.timings

nameusersystemelapsed
CompDb0.7210.0760.798
Filter-classes0.0130.0010.014
IonDb0.2400.0080.248
MsBackendCompDb0.1030.0030.107
compound_tbl_lipidblast0.0260.0010.028
compound_tbl_sdf0.1210.0040.125
createCompDb0.3040.0040.308
expandMzIntensity0.0170.0000.017
import_mona_sdf0.0200.0000.019
msms_spectra_hmdb0.0260.0000.027
msms_spectra_mona0.0340.0080.043