Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Spectra_1.20.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Spectra.Rcheck’* using R version 4.5.2 (2025-10-31)* 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 ‘1.20.0’* 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 ... NOTEForeign 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 RExtensions’ manual.* checking R code for possible problems ... OK* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTENon-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 ... OKExamples with CPU (user + system) or elapsed time > 5s                      user system elapsedestimatePrecursorMz 74.118  1.087  75.172addProcessing       11.599  0.814  12.273combinePeaks        10.055  1.358   6.372plotMzDelta         10.200  0.946  10.509filterMsLevel        5.607  0.393   5.920Spectra              4.527  1.160   4.120compareSpectra       5.334  0.259   5.549* 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* DONEStatus: 2 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/Spectra.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Spectra###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘Spectra’ ...** this is package ‘Spectra’ version ‘1.20.0’** using staged installation** R** data** inst** byte-compile and prepare package for lazy loadingCreating 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnuR 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: S4VectorsLoading required package: stats4Loading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe 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.minAttaching package: 'S4Vectors'The following object is masked from 'package:utils':    findMatchesThe following objects are masked from 'package:base':    I, expand.grid, unnameLoading 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                                             ⠼ |         25 | spectra_subsetting                                             ⠼ |         35 | spectra_subsetting                                             ⠦ |         37 | spectra_subsetting                                             ⠇ |         39 | spectra_subsetting                                             ⠋ |         41 | spectra_subsetting                                             ⠹ |         43 | spectra_subsetting                                             ⠦ |         47 | spectra_subsetting                                             ⠼ |         55 | spectra_subsetting                                             ⠙ |         62 | spectra_subsetting                                             ⠋ |         71 | spectra_subsetting                                             ⠧ |         78 | spectra_subsetting                                             ✔ |         86 | spectra_subsetting [1.5s]⠏ |          0 | spectra_variables                                              ⠴ |         16 | spectra_variables                                              ⠴ |         36 | spectra_variables                                              ⠸ |         54 | spectra_variables                                              ✔ |      1  62 | spectra_variables══ Results ═════════════════════════════════════════════════════════════════════Duration: 2.0 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                                             ⠏ |         10 | spectra_subsetting                                             ⠙ |         22 | spectra_subsetting                                             ⠸ |         34 | spectra_subsetting                                             ⠹ |         43 | spectra_subsetting                                             ⠹ |         53 | spectra_subsetting                                             ⠙ |         62 | spectra_subsetting                                             ⠋ |         71 | spectra_subsetting                                             ⠋ |         81 | spectra_subsetting                                             ✔ |         86 | spectra_subsetting⠏ |          0 | spectra_variables                                              ⠧ |          8 | spectra_variables                                              ⠦ |         17 | spectra_variables                                              ⠋ |         31 | spectra_variables                                              ⠧ |         38 | spectra_variables                                              ⠙ |         52 | spectra_variables                                              ⠙ |         62 | spectra_variables                                              ⠋ |         71 | spectra_variables                                              ✔ |         78 | spectra_variables══ Results ═════════════════════════════════════════════════════════════════════Duration: 1.8 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                                             ⠹ |         33 | spectra_subsetting                                             ⠏ |         40 | spectra_subsetting                                             ⠇ |         49 | spectra_subsetting                                             ⠏ |         70 | spectra_subsetting                                             ⠴ |         86 | spectra_subsetting                                             ✔ |         86 | spectra_subsetting⠏ |          0 | spectra_variables                                              ⠼ |         25 | spectra_variables                                              ⠧ |         48 | spectra_variables                                              ⠏ |         70 | spectra_variables                                              ✔ |         80 | spectra_variables══ Results ═════════════════════════════════════════════════════════════════════Duration: 1.0 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         12         2        NA         13         2        NA         2 ... 16 more variables/columns.file(s): c dMsBackendMzR with 0 spectraMsBackendMzR with 1862 spectra       msLevel     rtime scanIndex     <integer> <numeric> <integer>1            1     0.280         12            1     0.559         23            1     0.838         34            1     1.117         45            1     1.396         5...        ...       ...       ...1858         1   258.636       9271859         1   258.915       9281860         1   259.194       9291861         1   259.473       9301862         1   259.752       931 ... 34 more variables/columns.file(s):20171016_POOL_POS_1_105-134.mzML20171016_POOL_POS_3_105-134.mzMLMSn 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         12            1     0.559         23            1     0.838         34            1     1.117         45            1     1.396         5...        ...       ...       ...1858         1   258.636       9271859         1   258.915       9281860         1   259.194       9291861         1   259.473       9301862         1   259.752       931 ... 34 more variables/columns.file(s):20171016_POOL_POS_1_105-134.mzML20171016_POOL_POS_3_105-134.mzMLNULL[ FAIL 0 | WARN 11 | SKIP 7 | PASS 2966 ]══ 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:464:1'[ FAIL 0 | WARN 11 | SKIP 7 | PASS 2966 ]> > proc.time()   user  system elapsed 252.021   6.719 258.148