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This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1982/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Spectra 1.10.3  (landing page)
RforMassSpectrometry Package Maintainer
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Spectra
git_branch: RELEASE_3_17
git_last_commit: ff96a62
git_last_commit_date: 2023-09-25 08:25:57 -0400 (Mon, 25 Sep 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Spectra on kjohnson2


To the developers/maintainers of the Spectra package:
- 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: 1.10.3
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_1.10.3.tar.gz
StartedAt: 2023-10-19 03:37:35 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 03:50:15 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 760.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Spectra.Rcheck
Warnings: 0

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_1.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Spectra.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Spectra/DESCRIPTION’ ... OK
* this is package ‘Spectra’ version ‘1.10.3’
* 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 ‘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 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 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 ... 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 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
Spectra     11.347  1.557  24.555
plotMzDelta 11.947  0.709  25.626
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘Spectra’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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("Spectra")
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, sort, 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

Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

> 
> 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])
> 
> 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 | spectra_subsetting                                              
⠋ |         1 | spectra_subsetting                                              
⠦ |         7 | spectra_subsetting                                              
⠸ |        14 | spectra_subsetting                                              
⠇ |        19 | spectra_subsetting                                              
⠴ |        26 | spectra_subsetting                                              
⠙ |        32 | spectra_subsetting                                              
⠼ |        35 | spectra_subsetting                                              
⠴ |        36 | spectra_subsetting                                              
⠦ |        37 | spectra_subsetting                                              
⠧ |        38 | spectra_subsetting                                              
⠇ |        39 | spectra_subsetting                                              
⠏ |        40 | spectra_subsetting                                              
⠋ |        41 | spectra_subsetting                                              
⠙ |        42 | spectra_subsetting                                              
⠹ |        43 | spectra_subsetting                                              
⠸ |        44 | spectra_subsetting                                              
⠦ |        47 | spectra_subsetting                                              
⠧ |        48 | spectra_subsetting                                              
⠏ |        50 | spectra_subsetting                                              
⠸ |        54 | spectra_subsetting                                              
⠧ |        58 | spectra_subsetting                                              
⠋ |        61 | spectra_subsetting                                              
✔ |        61 | spectra_subsetting [4.0s]

⠏ |         0 | spectra_variables                                               
⠸ |         4 | spectra_variables                                               
⠙ |        12 | spectra_variables                                               
⠴ |        16 | spectra_variables                                               
⠦ |        27 | spectra_variables                                               
⠙ |        32 | spectra_variables                                               
⠹ |        43 | spectra_variables                                               
⠸ |        54 | spectra_variables                                               
⠙ |     1  61 | spectra_variables                                               
✔ |     1  62 | spectra_variables [1.0s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 5.1 s

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 123 ]
> 
> be <- backendInitialize(MsBackendDataFrame(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S  OK | Context

⠏ |         0 | spectra_subsetting                                              
⠸ |         4 | spectra_subsetting                                              
⠏ |        10 | spectra_subsetting                                              
⠴ |        16 | spectra_subsetting                                              
⠙ |        22 | spectra_subsetting                                              
⠼ |        25 | spectra_subsetting                                              
⠋ |        31 | spectra_subsetting                                              
⠸ |        34 | spectra_subsetting                                              
⠴ |        36 | spectra_subsetting                                              
⠏ |        40 | spectra_subsetting                                              
⠹ |        43 | spectra_subsetting                                              
⠴ |        46 | spectra_subsetting                                              
⠹ |        53 | spectra_subsetting                                              
⠴ |        56 | spectra_subsetting                                              
⠏ |        60 | spectra_subsetting                                              
✔ |        61 | spectra_subsetting [2.0s]

⠏ |         0 | spectra_variables                                               
⠸ |         4 | spectra_variables                                               
⠦ |         7 | spectra_variables                                               
⠋ |        11 | spectra_variables                                               
⠦ |        17 | spectra_variables                                               
⠼ |        25 | spectra_variables                                               
⠇ |        29 | spectra_variables                                               
⠸ |        34 | spectra_variables                                               
⠦ |        37 | spectra_variables                                               
⠧ |        38 | spectra_variables                                               
⠼ |        45 | spectra_variables                                               
⠴ |        56 | spectra_variables                                               
⠇ |        59 | spectra_variables                                               
⠹ |        63 | spectra_variables                                               
⠦ |        67 | spectra_variables                                               
⠏ |        70 | spectra_variables                                               
⠙ |        72 | spectra_variables                                               
✔ |        78 | spectra_variables [2.3s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 4.4 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 139 ]
> 
> be <- backendInitialize(MsBackendMemory(), spectraData(be))
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S  OK | Context

⠏ |         0 | spectra_subsetting                                              
⠏ |        10 | spectra_subsetting                                              
⠼ |        25 | spectra_subsetting                                              
⠸ |        34 | spectra_subsetting                                              
⠦ |        37 | spectra_subsetting                                              
⠏ |        40 | spectra_subsetting                                              
⠸ |        44 | spectra_subsetting                                              
⠇ |        49 | spectra_subsetting                                              
⠴ |        56 | spectra_subsetting                                              
⠋ |        61 | spectra_subsetting                                              
✔ |        61 | spectra_subsetting [1.0s]

⠏ |         0 | spectra_variables                                               
⠋ |        11 | spectra_variables                                               
⠏ |        20 | spectra_variables                                               
⠼ |        35 | spectra_variables                                               
⠇ |        39 | spectra_variables                                               
⠸ |        54 | spectra_variables                                               
⠧ |        68 | spectra_variables                                               
⠏ |        70 | spectra_variables                                               
✔ |        80 | spectra_variables [1.0s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.1 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 141 ]
> 
> ## 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
 ... 33 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)
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
 ... 33 more variables/columns.

file(s):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
NULL
[ FAIL 0 | WARN 7 | SKIP 7 | PASS 2292 ]

══ 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'

[ FAIL 0 | WARN 7 | SKIP 7 | PASS 2292 ]
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
> 
> proc.time()
   user  system elapsed 
238.622   9.023 502.796 

Example timings

Spectra.Rcheck/Spectra-Ex.timings

nameusersystemelapsed
MsBackend0.2760.0080.580
Spectra11.347 1.55724.555
chunkapply0.4190.0650.972
combinePeaks0.0350.0040.082
countIdentifications0.0540.0430.199
filterFourierTransformArtefacts0.0620.0190.163
joinPeaks0.0030.0040.015
neutralLoss0.2320.0370.547
plotMzDelta11.947 0.70925.626
spectra-plotting0.2850.1180.841