Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-10 12:05 -0400 (Fri, 10 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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 2072/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Spectra 1.19.8  (landing page)
RforMassSpectrometry Package Maintainer
Snapshot Date: 2025-10-09 13:45 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/Spectra
git_branch: devel
git_last_commit: 3540c00
git_last_commit_date: 2025-10-06 01:38:50 -0400 (Mon, 06 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Spectra on lconway

To the developers/maintainers of the Spectra package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Spectra.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: Spectra
Version: 1.19.8
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_1.19.8.tar.gz
StartedAt: 2025-10-10 01:24:12 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 01:33:51 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 578.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Spectra.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.19.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Spectra.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Spectra/DESCRIPTION’ ... OK
* this is package ‘Spectra’ version ‘1.19.8’
* package encoding: UTF-8
* 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 ‘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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
estimatePrecursorMz 93.975  3.355  98.057
addProcessing       14.390  1.751  15.961
combinePeaks        11.756  2.088   7.937
plotMzDelta         10.071  1.138  10.628
Spectra              5.789  2.169   5.789
filterMsLevel        6.932  0.716   7.528
compareSpectra       7.063  0.566   7.678
spectraData          3.537  2.091   3.196
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • plotting-functions/plot-single-spectrum-labels-ass.svg
  • plotting-functions/plot-single-spectrum-labels.svg
  • plotting-functions/plot-single-spectrum-xlim.svg
  • plotting-functions/plotspectra-asp05.svg
  • plotting-functions/plotspectra-asp2.svg
  • plotting-functions/plotspectra-color-peaks-label-labelcol.svg
  • plotting-functions/plotspectra-color-peaks-label.svg
  • plotting-functions/plotspectra-color-peaks.svg
  • plotting-functions/plotspectramirror-match-color-labelcol.svg
  • plotting-functions/plotspectramirror-match-color.svg
  • plotting-functions/plotspectramirror-same.svg
  • plotting-functions/plotspectraoverlay-no-axes.svg
  • plotting-functions/plotspectraoverlay-xlim.svg
  Error: Test failures
  Execution halted
* 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-3.22-bioc/meat/Spectra.Rcheck/00check.log’
for details.


Installation output

Spectra.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Spectra
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Spectra’ ...
** this is package ‘Spectra’ version ‘1.19.8’
** 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)

Tests output

Spectra.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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("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
> 
> register(SerialParam())
> 
> sciex_file <- normalizePath(
+     dir(system.file("sciex", package = "msdata"), full.names = TRUE))
> cdf_file <- normalizePath(
+     dir(system.file("cdf", package = "msdata"), full.names = TRUE))
> 
> sciex_mzr <- backendInitialize(MsBackendMzR(), files = sciex_file)
> sciex_pks <- peaksData(sciex_mzr)
> fl <- normalizePath(
+     dir(system.file("proteomics", package = "msdata"), full.names = TRUE))
> tmt_mzr <- backendInitialize(MsBackendMzR(), files = fl[5])
> 
> fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML",
+                   package = "msdata")
> sps_dia <- Spectra(fl)
> 
> fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML",
+                   package = "msdata")
> 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                                                
✔ |          4 | peaks_variables

⠏ |          0 | spectra_subsetting                                             
⠏ |         10 | spectra_subsetting                                             
⠙ |         22 | spectra_subsetting                                             
⠹ |         33 | spectra_subsetting                                             
⠴ |         36 | spectra_subsetting                                             
⠧ |         38 | spectra_subsetting                                             
⠏ |         40 | spectra_subsetting                                             
⠙ |         42 | spectra_subsetting                                             
⠸ |         44 | spectra_subsetting                                             
⠧ |         48 | spectra_subsetting                                             
⠴ |         56 | spectra_subsetting                                             
⠙ |         62 | spectra_subsetting                                             
⠏ |         70 | spectra_subsetting                                             
⠼ |         75 | spectra_subsetting                                             
⠧ |         78 | spectra_subsetting                                             
✔ |         86 | spectra_subsetting [1.9s]

⠏ |          0 | spectra_variables                                              
⠹ |         13 | spectra_variables                                              
⠦ |         27 | spectra_variables                                              
⠹ |         43 | spectra_variables                                              
⠦ |      1  56 | spectra_variables                                              
✔ |      1  62 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.6 s

── 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                                             
⠦ |          7 | spectra_subsetting                                             
⠴ |         16 | spectra_subsetting                                             
⠼ |         25 | spectra_subsetting                                             
⠸ |         34 | spectra_subsetting                                             
⠋ |         41 | spectra_subsetting                                             
⠇ |         49 | spectra_subsetting                                             
⠴ |         56 | spectra_subsetting                                             
⠴ |         66 | spectra_subsetting                                             
⠹ |         73 | spectra_subsetting                                             
⠋ |         81 | spectra_subsetting                                             
✔ |         86 | spectra_subsetting [1.2s]

⠏ |          0 | spectra_variables                                              
⠴ |          6 | spectra_variables                                              
⠼ |         15 | spectra_variables                                              
⠼ |         25 | spectra_variables                                              
⠸ |         34 | spectra_variables                                              
⠇ |         39 | spectra_variables                                              
⠸ |         54 | spectra_variables                                              
⠙ |         62 | spectra_variables                                              
⠏ |         70 | spectra_variables                                              
✔ |         78 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.2 s

[ 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                                             
⠋ |         21 | spectra_subsetting                                             
⠴ |         36 | spectra_subsetting                                             
⠋ |         41 | spectra_subsetting                                             
⠇ |         49 | spectra_subsetting                                             
⠼ |         65 | spectra_subsetting                                             
⠹ |         73 | spectra_subsetting                                             
✔ |         86 | spectra_subsetting

⠏ |          0 | spectra_variables                                              
⠧ |         18 | spectra_variables                                              
⠧ |         38 | spectra_variables                                              
⠙ |         62 | spectra_variables                                              
⠏ |         70 | spectra_variables                                              
✔ |         80 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.3 s

[ 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):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
MSn data (Spectra) with 0 spectra in a MsBackendMemory backend:
Lazy evaluation queue: 2 processing step(s)
Sizes of mz and intensity arrays don't match.
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):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
NULL
[ FAIL 1 | WARN 11 | SKIP 7 | PASS 2934 ]

══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test_plotMzDelta.R:30:5', 'test_plotting-functions.R:17:5',
  'test_plotting-functions.R:50:5', 'test_plotting-functions.R:69:5',
  'test_plotting-functions.R:99:5', 'test_plotting-functions.R:144:5'
• empty test (1): 'test_MsBackendMzR.R:464:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_Spectra-functions.R:389:5'): joinSpectraData works ─────────────
Error in `object@backend$getPeakList(scans)`: dims [product 90028] do not match the length of object [45014]
Backtrace:
     ▆
  1. ├─ProtGenerics::setBackend(ms, MsBackendMemory(), BPPARAM = SerialParam()) at test_Spectra-functions.R:389:5
  2. └─Spectra::setBackend(ms, MsBackendMemory(), BPPARAM = SerialParam())
  3.   └─Spectra (local) .local(object, backend, ...)
  4.     ├─ProtGenerics::backendInitialize(...)
  5.     ├─Spectra::backendInitialize(...)
  6.     │ └─Spectra (local) .local(object, ...)
  7.     │   └─methods::is(data, "DataFrame")
  8.     ├─ProtGenerics::spectraData(object@backend)
  9.     └─Spectra::spectraData(object@backend)
 10.       └─Spectra (local) .local(object, ...)
 11.         └─Spectra:::.spectra_data_mzR(object, columns)
 12.           ├─ProtGenerics::peaksData(x)
 13.           └─Spectra::peaksData(x)
 14.             └─Spectra (local) .local(object, ...)
 15.               └─Spectra:::.mzR_peaks(...)
 16.                 ├─mzR::peaks(msd, scanIndex)
 17.                 └─mzR::peaks(msd, scanIndex)
 18.                   └─mzR (local) .local(object, ...)
 19.                     └─mzR:::.peaks(object, scans)
 20.                       └─object@backend$getPeakList(scans)

[ FAIL 1 | WARN 11 | SKIP 7 | PASS 2934 ]
Deleting unused snapshots:
• plotting-functions/plot-single-spectrum-labels-ass.svg
• plotting-functions/plot-single-spectrum-labels.svg
• plotting-functions/plot-single-spectrum-xlim.svg
• plotting-functions/plotspectra-asp05.svg
• plotting-functions/plotspectra-asp2.svg
• plotting-functions/plotspectra-color-peaks-label-labelcol.svg
• plotting-functions/plotspectra-color-peaks-label.svg
• plotting-functions/plotspectra-color-peaks.svg
• plotting-functions/plotspectramirror-match-color-labelcol.svg
• plotting-functions/plotspectramirror-match-color.svg
• plotting-functions/plotspectramirror-same.svg
• plotting-functions/plotspectraoverlay-no-axes.svg
• plotting-functions/plotspectraoverlay-xlim.svg
Error: Test failures
Execution halted

Example timings

Spectra.Rcheck/Spectra-Ex.timings

nameusersystemelapsed
MsBackend0.2760.0090.285
Spectra5.7892.1695.789
addProcessing14.390 1.75115.961
chunkapply0.6310.0940.727
combinePeaks11.756 2.088 7.937
combinePeaksData0.0320.0270.060
combineSpectra1.6950.2591.828
compareSpectra7.0630.5667.678
countIdentifications0.0800.1190.193
estimatePrecursorIntensity3.7810.7294.557
estimatePrecursorMz93.975 3.35598.057
fillCoreSpectraVariables0.0110.0010.012
filterFourierTransformArtefacts0.0950.0060.103
filterMsLevel6.9320.7167.528
filterPeaksRanges0.0490.0040.054
fragmentGroupIndex0.2630.1650.424
joinPeaks0.0040.0050.008
neutralLoss0.2490.0280.278
plotMzDelta10.071 1.13810.628
precursorPurity1.6260.7343.680
spectra-plotting1.2570.6090.463
spectraData3.5372.0913.196