| Back to Rapid builds (Linux only) of a subset of BioC 3.22 Report updated every 6 hours |
This page was generated on 2025-10-30 14:25 -0400 (Thu, 30 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 896 |
| 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 209/229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| Spectra 1.21.0 (landing page) RforMassSpectrometry Package Maintainer
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||
|
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. |
| Package: Spectra |
| Version: 1.21.0 |
| Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings Spectra_1.21.0.tar.gz |
| StartedAt: 2025-10-30 13:59:33 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 14:05:42 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 369.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Spectra.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings Spectra_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Spectra.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Spectra/DESCRIPTION’ ... OK
* this is package ‘Spectra’ version ‘1.21.0’
* 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 loading without being on the library search path ... 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 51.090 0.897 50.050
addProcessing 8.401 0.832 9.078
plotMzDelta 7.476 0.843 7.779
combinePeaks 6.283 1.260 4.717
Spectra 3.742 1.274 3.611
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Spectra.Rcheck/00check.log’
for details.
Spectra.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL Spectra ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’ * installing *source* package ‘Spectra’ ... ** this is package ‘Spectra’ version ‘1.21.0’ ** 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)
Spectra.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
⠏ | 0 | spectra_subsetting
⠙ | 22 | spectra_subsetting
⠼ | 35 | spectra_subsetting
⠧ | 38 | spectra_subsetting
⠋ | 41 | spectra_subsetting
⠸ | 44 | spectra_subsetting
⠇ | 49 | spectra_subsetting
⠙ | 62 | spectra_subsetting
⠹ | 73 | spectra_subsetting
⠋ | 81 | spectra_subsetting
✔ | 86 | spectra_subsetting [1.0s]
⠏ | 0 | spectra_variables
⠦ | 27 | spectra_variables
⠸ | 54 | spectra_variables
✔ | 1 62 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.3 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
⠴ | 16 | spectra_subsetting
⠸ | 34 | spectra_subsetting
⠦ | 47 | spectra_subsetting
⠙ | 62 | spectra_subsetting
⠼ | 75 | spectra_subsetting
✔ | 86 | spectra_subsetting
⠏ | 0 | spectra_variables
⠏ | 10 | spectra_variables
⠇ | 29 | spectra_variables
⠋ | 41 | spectra_variables
⠙ | 62 | spectra_variables
✔ | 78 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.2 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
⠴ | 36 | spectra_subsetting
⠦ | 47 | spectra_subsetting
⠹ | 73 | spectra_subsetting
✔ | 86 | spectra_subsetting
⠏ | 0 | spectra_variables
⠧ | 38 | spectra_variables
⠏ | 70 | 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):
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
... 34 more variables/columns.
file(s):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
NULL
[ FAIL 0 | WARN 11 | SKIP 7 | PASS 2964 ]
══ 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 11 | SKIP 7 | PASS 2964 ]
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
180.405 4.979 184.749
Spectra.Rcheck/Spectra-Ex.timings
| name | user | system | elapsed | |
| MsBackend | 0.155 | 0.005 | 0.161 | |
| Spectra | 3.742 | 1.274 | 3.611 | |
| addProcessing | 8.401 | 0.832 | 9.078 | |
| chunkapply | 0.441 | 0.058 | 0.498 | |
| combinePeaks | 6.283 | 1.260 | 4.717 | |
| combinePeaksData | 0.718 | 0.261 | 0.024 | |
| combineSpectra | 1.682 | 0.432 | 1.052 | |
| compareSpectra | 3.613 | 0.230 | 3.782 | |
| countIdentifications | 0.018 | 0.020 | 0.073 | |
| estimatePrecursorIntensity | 0.552 | 0.177 | 2.503 | |
| estimatePrecursorMz | 51.090 | 0.897 | 50.050 | |
| fillCoreSpectraVariables | 0.007 | 0.001 | 0.008 | |
| filterFourierTransformArtefacts | 0.063 | 0.002 | 0.066 | |
| filterMsLevel | 4.163 | 0.520 | 4.569 | |
| filterPeaksRanges | 0.037 | 0.001 | 0.038 | |
| fragmentGroupIndex | 0.146 | 0.142 | 0.257 | |
| joinPeaks | 0.003 | 0.000 | 0.003 | |
| neutralLoss | 0.146 | 0.024 | 0.170 | |
| plotMzDelta | 7.476 | 0.843 | 7.779 | |
| precursorPurity | 0.851 | 0.506 | 1.821 | |
| spectra-plotting | 0.630 | 0.274 | 0.212 | |
| spectraData | 2.193 | 1.276 | 1.838 | |