Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cypress.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cypress_1.6.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cypress.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 ‘cypress/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘cypress’ version ‘1.6.0’* 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 ‘cypress’ 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 ... 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 ... 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 ... OKExamples with CPU (user + system) or elapsed time > 5s                user system elapsedsimFromParam 136.116 17.524  60.298* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘runTest.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: OK

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL cypress###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘cypress’ ...** this is package ‘cypress’ version ‘1.6.0’** using staged installation** R** data** 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 (cypress)

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("cypress")Complete experiment design for CYPRESS.LFC: 1 Sample Size: 8  the design formula contains one or more numeric variables with integer values,  specifying a model with increasing fold change for higher values.  did you mean for this to be a factor? if so, first convert  this variable to a factor using the factor() functionestimating size factorsestimating dispersionsgene-wise dispersion estimatesmean-dispersion relationship-- note: fitType='parametric', but the dispersion trend was not well captured by the   function: y = a/x + b, and a local regression fit was automatically substituted.   specify fitType='local' or 'mean' to avoid this message next time.final dispersion estimatesfitting model and testing3 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest  the design formula contains one or more numeric variables with integer values,  specifying a model with increasing fold change for higher values.  did you mean for this to be a factor? if so, first convert  this variable to a factor using the factor() functionestimating size factorsestimating dispersionsgene-wise dispersion estimatesmean-dispersion relationshipfinal dispersion estimatesfitting model and testing3 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTestLFC: 1 Sample Size: 10  the design formula contains one or more numeric variables with integer values,  specifying a model with increasing fold change for higher values.  did you mean for this to be a factor? if so, first convert  this variable to a factor using the factor() functionestimating size factorsestimating dispersionsgene-wise dispersion estimatesmean-dispersion relationship-- note: fitType='parametric', but the dispersion trend was not well captured by the   function: y = a/x + b, and a local regression fit was automatically substituted.   specify fitType='local' or 'mean' to avoid this message next time.final dispersion estimatesfitting model and testing  the design formula contains one or more numeric variables with integer values,  specifying a model with increasing fold change for higher values.  did you mean for this to be a factor? if so, first convert  this variable to a factor using the factor() functionestimating size factorsestimating dispersionsgene-wise dispersion estimatesmean-dispersion relationship-- note: fitType='parametric', but the dispersion trend was not well captured by the   function: y = a/x + b, and a local regression fit was automatically substituted.   specify fitType='local' or 'mean' to avoid this message next time.final dispersion estimatesfitting model and testingLFC: 1.5 Sample Size: 8  the design formula contains one or more numeric variables with integer values,  specifying a model with increasing fold change for higher values.  did you mean for this to be a factor? if so, first convert  this variable to a factor using the factor() functionestimating size factorsestimating dispersionsgene-wise dispersion estimatesmean-dispersion relationship-- note: fitType='parametric', but the dispersion trend was not well captured by the   function: y = a/x + b, and a local regression fit was automatically substituted.   specify fitType='local' or 'mean' to avoid this message next time.final dispersion estimatesfitting model and testing  the design formula contains one or more numeric variables with integer values,  specifying a model with increasing fold change for higher values.  did you mean for this to be a factor? if so, first convert  this variable to a factor using the factor() functionestimating size factorsestimating dispersionsgene-wise dispersion estimatesmean-dispersion relationship-- note: fitType='parametric', but the dispersion trend was not well captured by the   function: y = a/x + b, and a local regression fit was automatically substituted.   specify fitType='local' or 'mean' to avoid this message next time.final dispersion estimatesfitting model and testingLFC: 1.5 Sample Size: 10  the design formula contains one or more numeric variables with integer values,  specifying a model with increasing fold change for higher values.  did you mean for this to be a factor? if so, first convert  this variable to a factor using the factor() functionestimating size factorsestimating dispersionsgene-wise dispersion estimatesmean-dispersion relationship-- note: fitType='parametric', but the dispersion trend was not well captured by the   function: y = a/x + b, and a local regression fit was automatically substituted.   specify fitType='local' or 'mean' to avoid this message next time.final dispersion estimatesfitting model and testing  the design formula contains one or more numeric variables with integer values,  specifying a model with increasing fold change for higher values.  did you mean for this to be a factor? if so, first convert  this variable to a factor using the factor() functionestimating size factorsestimating dispersionsgene-wise dispersion estimatesmean-dispersion relationship-- note: fitType='parametric', but the dispersion trend was not well captured by the   function: y = a/x + b, and a local regression fit was automatically substituted.   specify fitType='local' or 'mean' to avoid this message next time.final dispersion estimatesfitting model and testing1 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTestComplete simulation for CYPRESS.Complete experiment design for CYPRESS.LFC: 1 Sample Size: 8No prior inference information, run TOAST for first round inference inference with tree: singleinference with tree: fullNo prior inference information, run TOAST for first round inference inference with tree: singleinference with tree: fullLFC: 1 Sample Size: 10No prior inference information, run TOAST for first round inference inference with tree: singleinference with tree: fullNo prior inference information, run TOAST for first round inference inference with tree: singleinference with tree: fullLFC: 1.5 Sample Size: 8No prior inference information, run TOAST for first round inference inference with tree: singleinference with tree: fullNo prior inference information, run TOAST for first round inference inference with tree: singleinference with tree: fullLFC: 1.5 Sample Size: 10No prior inference information, run TOAST for first round inference inference with tree: singleinference with tree: fullNo prior inference information, run TOAST for first round inference inference with tree: singleinference with tree: fullComplete simulation for CYPRESS.RUNIT TEST PROTOCOL -- Thu Dec 11 23:42:20 2025 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0  1 Test Suite : cypress RUnit Tests - 2 test functions, 0 errors, 0 failuresNumber of test functions: 2 Number of errors: 0 Number of failures: 0 > > > proc.time()   user  system elapsed 485.571  60.102 394.675