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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Spectra.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Spectra_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/Spectra.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-22 02:40:34 UTC
* using option ‘--no-vignettes’
* checking for file ‘Spectra/DESCRIPTION’ ... OK
* this is package ‘Spectra’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.23/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.23/bioc/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 ‘Spectra’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("_H5Dclose", ..., PACKAGE = "rhdf5")
  .Call("_H5Dopen", ..., PACKAGE = "rhdf5")
  .Call("_H5Dread", ..., PACKAGE = "rhdf5")
  .Call("_H5Fclose", ..., PACKAGE = "rhdf5")
  .Call("_H5Fopen", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'MsBackend.Rd':
  ‘[MsCoreUtils:matching]{MsCoreUtils::closest()}’

Non-topic package-anchored link(s) in Rd file 'addProcessing.Rd':
  ‘[MsCoreUtils:matching]{MsCoreUtils::common()}’

Non-topic package-anchored link(s) in Rd file 'joinPeaks.Rd':
  ‘[MsCoreUtils:matching]{MsCoreUtils::join()}’

Non-topic package-anchored link(s) in Rd file 'spectra-plotting.Rd':
  ‘[MsCoreUtils:matching]{MsCoreUtils::common()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Spectra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Spectra
> ### Title: The Spectra class to manage and access MS data
> ### Aliases: Spectra Spectra-class setBackend export Spectra,missing-method
> ###   Spectra,MsBackend-method Spectra,character-method Spectra,ANY-method
> ###   setBackend,Spectra,MsBackend-method export,Spectra-method
> ###   dataStorageBasePath,Spectra-method
> ###   dataStorageBasePath<-,Spectra-method
> 
> ### ** Examples
> 
> 
> ##  --------  CREATION OF SPECTRA OBJECTS  --------
> 
> ## Create a Spectra providing a `DataFrame` containing the spectrum data.
> 
> spd <- DataFrame(msLevel = c(1L, 2L), rtime = c(1.1, 1.2))
> spd$mz <- list(c(100, 103.2, 104.3, 106.5), c(45.6, 120.4, 190.2))
> spd$intensity <- list(c(200, 400, 34.2, 17), c(12.3, 15.2, 6.8))
> 
> data <- Spectra(spd)
> data
MSn data (Spectra) with 2 spectra in a MsBackendMemory backend:
    msLevel     rtime scanIndex
  <integer> <numeric> <integer>
1         1       1.1        NA
2         2       1.2        NA
 ... 16 more variables/columns.
> 
> ## Create a Spectra from mzML files and use the `MsBackendMzR` on-disk
> ## backend. Example mzML files are provided by the *MsDataHub* package.
> sciex_file <- c(MsDataHub::X20171016_POOL_POS_1_105.134.mzML(),
+                 MsDataHub::X20171016_POOL_POS_3_105.134.mzML())
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
Connection timed out after 10011 milliseconds
  Consider rerunning with 'localHub=TRUE'
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/Spectra.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Spectra
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘Spectra’ ...
** this is package ‘Spectra’ version ‘1.23.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘entropy’ in package ‘Spectra’
** 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 (Spectra)

R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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("patrick")
> library("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("MsDataHub")
> 
> register(SerialParam())
> 
> ## MsDataHub
> cdf_file <- unname(MsDataHub::ko15.CDF())
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> 
> sciex_file <- unname(c(MsDataHub::X20171016_POOL_POS_1_105.134.mzML(),
+                        MsDataHub::X20171016_POOL_POS_3_105.134.mzML()))
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> sciex_mzr <- backendInitialize(MsBackendMzR(), files = sciex_file)
> sciex_pks <- peaksData(sciex_mzr)
> 
> fl <- MsDataHub::TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzML.gz()
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> tmt_mzr <- backendInitialize(MsBackendMzR(), files = fl)
> sps_tmt <- setBackend(Spectra(tmt_mzr), MsBackendMemory())
> 
> fl <- MsDataHub::PestMix1_SWATH.mzML()
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> sps_dia <- Spectra(fl)
> 
> fl <- MsDataHub::PestMix1_DDA.mzML()
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> sps_dda <- Spectra(fl)
> 
> sciex_hd5 <- backendInitialize(MsBackendHdf5Peaks(),
+                                data = spectraData(sciex_mzr),
+                                hdf5path = tempdir())
> 
> test_suite <- system.file("test_backends", "test_MsBackend",
+                           package = "Spectra")
> be <- sciex_mzr[1:10]
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

⠏ |          0 | peaks_variables                                                
✔ |          4 | peaks_variables

⠏ |          0 | spectra_subsetting                                             
⠼ |         35 | spectra_subsetting                                             
⠋ |         41 | spectra_subsetting                                             
⠹ |         53 | spectra_subsetting                                             
⠸ |         74 | spectra_subsetting                                             
✔ |         86 | spectra_subsetting

⠏ |          0 | spectra_variables                                              
⠸ |         54 | spectra_variables                                              
✔ |      1  62 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_variables.R:262:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 152 ]
> 
> be <- backendInitialize(MsBackendDataFrame(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

⠏ |          0 | peaks_variables                                                
✔ |          4 | peaks_variables

⠏ |          0 | spectra_subsetting                                             
⠧ |         28 | spectra_subsetting                                             
⠹ |         53 | spectra_subsetting                                             
⠸ |         74 | spectra_subsetting                                             
✔ |         86 | spectra_subsetting

⠏ |          0 | spectra_variables                                              
⠋ |         31 | spectra_variables                                              
⠙ |         62 | spectra_variables                                              
✔ |         78 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
> 
> be <- backendInitialize(MsBackendMemory(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

⠏ |          0 | peaks_variables                                                
✔ |          4 | peaks_variables

⠏ |          0 | spectra_subsetting                                             
⠴ |         56 | spectra_subsetting                                             
✔ |         86 | spectra_subsetting

⠏ |          0 | spectra_variables                                              
⠸ |         74 | spectra_variables                                              
✔ |         80 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 170 ]
> 
> ## be <- sciex_hd5[1:10]
> ## test_dir(test_suite, stop_on_failure = TRUE)
> 
> test_check("Spectra")
Error in .h5_read_bare(fid, "/header/modcount") : 
  HDF5. Dataset. Can't open object.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibility. Unable to open file.
MsBackendHdf5Peaks with 3 spectra
    msLevel     rtime scanIndex
  <integer> <numeric> <integer>
1         1        NA         1
2         2        NA         1
3         2        NA         2
 ... 16 more variables/columns.

file(s):
 c
 d
MsBackendMzR with 0 spectra
MsBackendMzR with 1862 spectra
       msLevel     rtime scanIndex
     <integer> <numeric> <integer>
1            1     0.280         1
2            1     0.559         2
3            1     0.838         3
4            1     1.117         4
5            1     1.396         5
...        ...       ...       ...
1858         1   258.636       927
1859         1   258.915       928
1860         1   259.194       929
1861         1   259.473       930
1862         1   259.752       931
 ... 34 more variables/columns.

file(s):
ea1b8f78976_7859
ea1b3361a693_7860
MSn data (Spectra) with 0 spectra in a MsBackendMemory backend:
Lazy evaluation queue: 2 processing step(s)
MSn data (Spectra) with 1862 spectra in a MsBackendMzR backend:
       msLevel     rtime scanIndex
     <integer> <numeric> <integer>
1            1     0.280         1
2            1     0.559         2
3            1     0.838         3
4            1     1.117         4
5            1     1.396         5
...        ...       ...       ...
1858         1   258.636       927
1859         1   258.915       928
1860         1   259.194       929
1861         1   259.473       930
1862         1   259.752       931
 ... 34 more variables/columns.

file(s):
ea1b8f78976_7859
ea1b3361a693_7860
NULL
[ FAIL 0 | WARN 7 | SKIP 7 | PASS 3025 ]

══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test_plotMzDelta.R:26:1', 'test_plotting-functions.R:16:1',
  'test_plotting-functions.R:49:1', 'test_plotting-functions.R:68:1',
  'test_plotting-functions.R:98:1', 'test_plotting-functions.R:139:1'
• empty test (1): 'test_MsBackendMzR.R:467:1'

[ FAIL 0 | WARN 7 | SKIP 7 | PASS 3025 ]
> 
> proc.time()
   user  system elapsed 
126.758   3.981 131.533