Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ASICS_2.26.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ASICS.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 ‘ASICS/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘ASICS’ version ‘2.26.0’* 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 ‘ASICS’ can be installed ... OK* checking installed package size ... INFO  installed size is  6.2Mb  sub-directories of 1Mb or more:    doc       2.7Mb    extdata   1.6Mb* 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 dependencies in R code ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... OK* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  AnalysisResults-class.Rd: SummarizedExperiment, opls, ropls  formatForAnalysis.Rd: SummarizedExperiment  kruskalWallis.Rd: SummarizedExperiment  oplsda.Rd: SummarizedExperiment, ropls, opls  pca.Rd: SummarizedExperiment, roplsPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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 LazyData ... OK* checking data for ASCII and uncompressed saves ... WARNING    Note: significantly better compression could be obtained        by using R CMD build --resave-data              old_size new_size compress  sysdata.rda    1.0Mb    661Kb       xz* checking installed files from ‘inst/doc’ ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                   user system elapsedsimulate_spectra 58.815  4.582  63.400ASICS            34.876  0.487  35.365* 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: 1 WARNING, 1 NOTESee  ‘/home/biocbuild/bbs-3.22-bioc/meat/ASICS.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ASICS###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘ASICS’ ...** this is package ‘ASICS’ version ‘2.26.0’** using staged installation** R** data*** moving datasets to lazyload DB** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** 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 (ASICS)

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(ASICS)> > test_check("ASICS")Binning   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   2%  |     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|===============================================================       |  90%  |                                                                              |================================================================      |  92%  |                                                                              |==================================================================    |  94%  |                                                                              |===================================================================   |  96%  |                                                                              |===================================================================== |  98%  |                                                                              |======================================================================| 100%Normalisation method : CS   |                                                                              |                          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|                                                                              |===================================                                   |  50%  |                                                                              |======================================================================| 100%Import spectra from txt or csv files... Normalisation method : CS Import spectra from fid files...  Begin PreprocessingChain Begin ReadFids dim Fid_data:  2 16384 IDs:  AG_faq_Beck01 AG_faq_Beck051 non-unique IDs? 0 End ReadFids It lasted 0.009 s user time, 0.002 s system time and 0.011 s elapsed time.Begin GroupDelayCorrection End GroupDelayCorrection It lasted 0.02 s user time, 0.003 s system time and 0.023 s elapsed time.Begin SolventSuppression End SolventSuppression It lasted 0.038 s user time, 0.006 s system time and 0.044 s elapsed time.Begin Apodization End Apodization It lasted 0.001 s user time, 0 s system time and 0 s elapsed time.Begin ZeroFilling End ZeroFilling It lasted 0.022 s user time, 0 s system time and 0.021 s elapsed time.Begin FourierTransform End FourierTransform It lasted 0.007 s user time, 0 s system time and 0.008 s elapsed time.Begin ZeroOrderPhaseCorrection End ZeroOrderPhaseCorrection It lasted 0.089 s user time, 0.003 s system time and 0.092 s elapsed time.Begin InternalReferencing End InternalReferencing It lasted 0.008 s user time, 0 s system time and 0.008 s elapsed time.Begin WindowSelection End WindowSelection It lasted 0.037 s user time, 0 s system time and 0.036 s elapsed time.End PreprocessingChain It lasted 0.233 s user time, 0.015 s system time and 0.248 s elapsed time.Normalisation method : CS Import spectra from txt or csv files... Normalisation method : CS Normalisation method : CS Alignment... Peak detection   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Finding reference spectrum Compute FFT correlations   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%The reference spectrum is the number 3 : AG_faq_Beck139 Align spectra   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Import spectra from txt or csv files... Normalisation method : CS Binning   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Normalisation method : CS Import spectra from txt or csv files... Normalisation method : CS Remove areas from spectrum and library   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Compute weights   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Remove metabolites that cannot belong to the mixture   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Translate library   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Deform library peaks   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Compute quantifications   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%Format global results... Import spectra from 1r files...   |                                                                              |                                                                      |   0%  |                                                                              |===================================                                   |  50%  |                                                                              |======================================================================| 100%Normalisation method : CS Remove areas from spectrum and library   |                                                                              |                                                                      |   0%  |                                                                              |===================================                                   |  50%  |                                                                              |======================================================================| 100%Compute weights   |                                                                              |                                                                      |   0%  |                                                                              |===================================                                   |  50%  |                                                                              |======================================================================| 100%Remove metabolites that cannot belong to the mixture   |                                                                              |                                                                      |   0%  |                                                                              |===================================                                   |  50%  |                                                                              |======================================================================| 100%Translate library Compute shifts for all maximum shift values   |                                                                              |                                                                      |   0%  |                                                                              |===================================                                   |  50%  |                                                                              |======================================================================| 100%  |                                                                              |                                                                      |   0%  |                                                                              |==============                                                        |  20%  |                                                     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|============================                                          |  40%  |                                                                              |==========================================                            |  60%  |                                                                              |========================================================              |  80%  |                                                                              |======================================================================| 100%Put the median shift for extreme shift values   |                                                                              |                                                                      |   0%  |                                                                              |==============                                                        |  20%  |                                                                              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                                                    |==========================================                            |  60%  |                                                                              |========================================================              |  80%  |                                                                              |======================================================================| 100%Compute correlations between buckets and quantifications   |                                                                              |                                                                      |   0%  |                                                                              |==============                                                        |  20%  |                                                                              |============================                                          |  40%  |                                                                              |==========================================                            |  60%  |                                                                              |========================================================              |  80%  |                                                                              |======================================================================| 100%Shift all spectra according to the best shift   |                                                                              |                                                                      |   0%  |                                                                              |===================================                                   |  50%  |                                                                              |======================================================================| 100%Deform library peaks   |        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[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ][ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]> > proc.time()   user  system elapsed 211.779   5.212 216.988