Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2027/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Spectra 1.16.0 (landing page) RforMassSpectrometry Package Maintainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: Spectra |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Spectra_1.16.0.tar.gz |
StartedAt: 2024-11-20 10:07:48 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 10:13:42 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 354.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Spectra.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Spectra_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Spectra.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘Spectra/DESCRIPTION’ ... OK * this is package ‘Spectra’ version ‘1.16.0’ * 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 ... 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 estimatePrecursorMz 47.638 0.946 48.481 addProcessing 8.686 0.950 9.535 plotMzDelta 7.347 1.037 8.018 combinePeaks 6.786 1.265 5.032 Spectra 4.249 1.349 3.909 * 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: 1 NOTE See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Spectra.Rcheck/00check.log’ for details.
Spectra.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Spectra ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘Spectra’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 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, saveRDS, setdiff, 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 > > 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 ⠇ | 19 | spectra_subsetting ⠼ | 35 | spectra_subsetting ⠧ | 38 | spectra_subsetting ⠋ | 41 | spectra_subsetting ⠸ | 44 | spectra_subsetting ⠇ | 49 | spectra_subsetting ⠹ | 63 | spectra_subsetting ✔ | 68 | spectra_subsetting ⠏ | 0 | spectra_variables ⠦ | 27 | spectra_variables ⠼ | 55 | spectra_variables ✔ | 1 62 | spectra_variables ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 1.2 s ── Skipped tests (1) ─────────────────────────────────────────────────────────── • empty test (1): 'test_spectra_variables.R:262:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 134 ] > > 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 ⠸ | 14 | spectra_subsetting ⠋ | 31 | spectra_subsetting ⠙ | 42 | spectra_subsetting ⠴ | 56 | spectra_subsetting ✔ | 68 | spectra_subsetting ⠏ | 0 | spectra_variables ⠼ | 15 | spectra_variables ⠋ | 31 | spectra_variables ⠼ | 45 | spectra_variables ⠙ | 62 | spectra_variables ✔ | 78 | spectra_variables ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 1.1 s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 150 ] > > 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 ⠧ | 68 | spectra_subsetting ✔ | 68 | spectra_subsetting ⠏ | 0 | spectra_variables ⠦ | 37 | spectra_variables ⠇ | 69 | spectra_variables ✔ | 80 | spectra_variables ══ Results ═════════════════════════════════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 152 ] > > ## 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 10 | SKIP 7 | PASS 2794 ] ══ 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 10 | SKIP 7 | PASS 2794 ] 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 169.993 5.217 174.776
Spectra.Rcheck/Spectra-Ex.timings
name | user | system | elapsed | |
MsBackend | 0.251 | 0.003 | 0.255 | |
Spectra | 4.249 | 1.349 | 3.909 | |
addProcessing | 8.686 | 0.950 | 9.535 | |
chunkapply | 0.513 | 0.080 | 0.597 | |
combinePeaks | 6.786 | 1.265 | 5.032 | |
combinePeaksData | 0.021 | 0.004 | 0.025 | |
combineSpectra | 2.455 | 0.709 | 1.102 | |
compareSpectra | 3.355 | 0.263 | 3.558 | |
countIdentifications | 0.017 | 0.020 | 0.070 | |
estimatePrecursorIntensity | 2.256 | 0.453 | 2.612 | |
estimatePrecursorMz | 47.638 | 0.946 | 48.481 | |
filterFourierTransformArtefacts | 0.069 | 0.008 | 0.077 | |
filterMsLevel | 4.006 | 0.467 | 4.361 | |
filterPeaksRanges | 0.045 | 0.002 | 0.048 | |
joinPeaks | 0.002 | 0.000 | 0.003 | |
neutralLoss | 0.120 | 0.002 | 0.121 | |
plotMzDelta | 7.347 | 1.037 | 8.018 | |
spectra-plotting | 0.222 | 0.082 | 0.217 | |
spectraData | 2.080 | 1.154 | 1.718 | |