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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CompoundDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CompoundDb_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CompoundDb.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CompoundDb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CompoundDb’ version ‘1.11.0’
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CompDb.Rd: SQLite, AnnotationFilter, tibble, Spectra,
    supportedFilters
  Filter-classes.Rd: supportedFilters
  IonDb.Rd: AnnotationFilter, tibble, supportedFilters
  MsBackendCompDb.Rd: MsBackendCached, Spectra, bpparam, MsBackend,
    DataFrame, MsBackendMemory, setBackend
  compound_tbl_sdf.Rd: read.SDFset
  expandMzIntensity.Rd: spectra, compounds
  import_mona_sdf.Rd: read.SDFset
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/CompoundDb.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CompoundDb
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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
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

> 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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXYOJPL/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                                             
⠇ |         19 | spectra_subsetting                                             
⠼ |         25 | spectra_subsetting                                             
✔ |      1  43 | spectra_subsetting

⠏ |          0 | spectra_variables                                              
⠙ |         52 | spectra_variables                                              
✔ |         64 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
── 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 
  6.289   1.095   6.799