Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MSnID_1.44.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MSnID.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 ‘MSnID/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘MSnID’ version ‘1.44.0’* checking package namespace information ... OK* checking package dependencies ... INFOImports includes 25 non-default packages.Importing from so many packages makes the package vulnerable to any ofthem becoming unavailable.  Move as many as possible to Suggests anduse conditionally.* 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 ‘MSnID’ 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 dependencies in R code ... NOTENamespaces in Imports field not imported from:  ‘BiocGenerics’ ‘BiocStyle’ ‘RUnit’ ‘ggplot2’ ‘msmsTests’ ‘xtable’  All declared Imports should be used.* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTE.read_mzIDs.mzR.engine.single.file: no visible binding for global  variable ‘peptideRef’Undefined global functions or variables:  peptideRef* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  MSnID-class.Rd: MSnSet  MSnID-package.Rd: mzIDPlease 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 ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                          user system elapsedfetch_conversion_table  11.630  0.875  13.180remap_accessions-method  6.524  0.234   7.098remap_fasta_entry_names  6.211  0.528   7.001optimize_filter          3.927  0.696  22.182* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘runTests.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: 3 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/MSnID.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MSnID###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘MSnID’ ...** this is package ‘MSnID’ version ‘1.44.0’** using staged installation** R** data*** moving datasets to lazyload DB** demo** 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 (MSnID)

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.> BiocGenerics:::testPackage("MSnID")Note, the anticipated/suggested columns in thepeptide-to-spectrum matching results are:-----------------------------------------------accessioncalculatedMassToChargechargeStateexperimentalMassToChargeisDecoypeptidespectrumFilespectrumIDReading from mzIdentMLs ...reading c_elegans.mzid.gz... DONE!Reading from mzIdentMLs ...RUNIT TEST PROTOCOL -- Fri Dec 12 02:48:36 2025 *********************************************** Number of test functions: 19 Number of errors: 0 Number of failures: 0  1 Test Suite : MSnID RUnit Tests - 19 test functions, 0 errors, 0 failuresNumber of test functions: 19 Number of errors: 0 Number of failures: 0 There were 12 warnings (use warnings() to see them)> > proc.time()   user  system elapsed  39.550   1.462  56.286