Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cTRAP_1.28.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cTRAP.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-apple-darwin20* R was compiled by    Apple clang version 14.0.0 (clang-1400.0.29.202)    GNU Fortran (GCC) 14.2.0* running under: macOS Monterey 12.7.6* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘cTRAP/DESCRIPTION’ ... OK* this is package ‘cTRAP’ version ‘1.28.0’* package encoding: UTF-8* checking package namespace information ... OK* checking package dependencies ... INFOImports includes 27 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 ... NOTEFound the following hidden files and directories:  .devcontainerThese were most likely included in error. See section ‘Packagestructure’ in the ‘Writing R Extensions’ manual.* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘cTRAP’ can be installed ... OK* checking installed package size ... OK* checking package directory ... OK* checking DESCRIPTION meta-information ... NOTELicense stub is invalid DCF.* 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 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 ... NOTEFound the following possibly unsafe calls:File ‘cTRAP/R/shinyInterface_session.R’:  assignInNamespace("dataTablesFilter", dt_mod, "DT")plotComparison: no visible binding for global variable ‘.data’plotMetricDistribution: no visible binding for global variable ‘.data’plotSingleCorr: no visible binding for global variable ‘.data’plotTargetingDrug: no visible binding for global variable ‘.data’plotTargetingDrugsVSsimilarPerturbations: no visible binding for global  variable ‘.data’Undefined global functions or variables:  .data* 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 ... NOTEDocumented arguments not in \usage in Rd file 'compareWithAllMethods.Rd':  ‘rankByAscending’Functions with \usage entries need to have the appropriate \aliasentries, and all their arguments documented.The \usage entries must correspond to syntactically valid R code.See chapter ‘Writing R documentation files’ in the ‘Writing RExtensions’ manual.* 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 R/sysdata.rda ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                                            user system elapsedplotDrugSetEnrichment                    660.069  4.805 704.454plot.referenceComparison                  40.673  1.542  42.717convertGeneIdentifiers                    30.018  3.491  37.350plot.perturbationChanges                  29.285  0.984  34.448analyseDrugSetEnrichment                  23.526  2.921  35.115prepareDrugSets                           11.548 13.111  26.003plotTargetingDrugsVSsimilarPerturbations  10.136  1.414  12.972filterCMapMetadata                         7.939  1.443  11.403predictTargetingDrugs                      6.459  0.739   7.336downloadENCODEknockdownMetadata            3.730  1.340  20.409loadExpressionDrugSensitivityAssociation   1.337  2.281   5.256* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘spelling.R’  Running ‘testthat.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking running R code from vignettes ... SKIPPED* checking re-building of vignette outputs ... SKIPPED* checking PDF version of manual ... OK* DONEStatus: 4 NOTEsSee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/cTRAP.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cTRAP###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’* installing *source* package ‘cTRAP’ ...** this is package ‘cTRAP’ version ‘1.28.0’** 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 (cTRAP)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-apple-darwin20R 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.> if(requireNamespace('spelling', quietly = TRUE))+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,+                              skip_on_cran = TRUE)All Done!> > proc.time()   user  system elapsed   0.350   0.115   0.435

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-apple-darwin20R 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(cTRAP)> > test_check("cTRAP")trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs'downloaded 31.6 MBtrying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs'downloaded 2.1 MB[ FAIL 0 | WARN 0 | SKIP 2 | PASS 243 ]══ Skipped tests (2) ═══════════════════════════════════════════════════════════• On Bioconductor (1): 'test_ENCODE.R:16:5'• empty test (1): 'test_drugSetEnrichment.R:88:1'[ FAIL 0 | WARN 0 | SKIP 2 | PASS 243 ]> > proc.time()   user  system elapsed 103.922   7.230 123.467