Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 484/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cypress 1.2.0 (landing page) Shilin Yu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the cypress package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cypress.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: cypress |
Version: 1.2.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cypress.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cypress_1.2.0.tar.gz |
StartedAt: 2024-12-20 00:33:39 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:50:08 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 989.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cypress.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cypress.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cypress_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/cypress.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'cypress/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'cypress' version '1.2.0' * 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 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed simFromParam 4.22 0.08 136.92 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
cypress.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL cypress ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'cypress' ... ** 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)
cypress.Rcheck/tests/runTest.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R 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() function estimating size factors estimating dispersions gene-wise dispersion estimates mean-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 estimates fitting 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() function estimating size factors estimating dispersions gene-wise dispersion estimates mean-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 estimates fitting model and testing 15 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest LFC: 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() function estimating size factors estimating dispersions gene-wise dispersion estimates mean-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 estimates fitting 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() function estimating size factors estimating dispersions gene-wise dispersion estimates mean-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 estimates fitting model and testing LFC: 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() function estimating size factors estimating dispersions gene-wise dispersion estimates mean-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 estimates fitting 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() function estimating size factors estimating dispersions gene-wise dispersion estimates mean-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 estimates fitting model and testing 137 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest LFC: 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() function estimating size factors estimating dispersions gene-wise dispersion estimates mean-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 estimates fitting 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() function estimating size factors estimating dispersions gene-wise dispersion estimates mean-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 estimates fitting model and testing 5 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest Complete simulation for CYPRESS. Complete experiment design for CYPRESS. LFC: 1 Sample Size: 8 No prior inference information, run TOAST for first round inference inference with tree: single inference with tree: full No prior inference information, run TOAST for first round inference inference with tree: single inference with tree: full LFC: 1 Sample Size: 10 No prior inference information, run TOAST for first round inference inference with tree: single inference with tree: full No prior inference information, run TOAST for first round inference inference with tree: single inference with tree: full LFC: 1.5 Sample Size: 8 No prior inference information, run TOAST for first round inference inference with tree: single inference with tree: full No prior inference information, run TOAST for first round inference inference with tree: single inference with tree: full LFC: 1.5 Sample Size: 10 No prior inference information, run TOAST for first round inference inference with tree: single inference with tree: full No prior inference information, run TOAST for first round inference inference with tree: single inference with tree: full Complete simulation for CYPRESS. RUNIT TEST PROTOCOL -- Fri Dec 20 00:49:57 2024 *********************************************** 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 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > > proc.time() user system elapsed 210.59 2.00 633.48
cypress.Rcheck/cypress-Ex.timings
name | user | system | elapsed | |
ASD_prop | 0.14 | 0.06 | 0.21 | |
GSE60424Power | 0.01 | 0.00 | 0.02 | |
GSE60424_param | 0.00 | 0.01 | 0.02 | |
asdPower | 0 | 0 | 0 | |
asd_param | 0.04 | 0.10 | 0.14 | |
cypress-class | 0.00 | 0.01 | 0.02 | |
cypress-methods | 0.02 | 0.02 | 0.03 | |
ibdPower | 0 | 0 | 0 | |
ibd_param | 0.08 | 0.08 | 0.15 | |
plotFDC | 0.06 | 0.00 | 0.07 | |
plotPower | 0.05 | 0.00 | 0.04 | |
plotTDR | 0.03 | 0.00 | 0.03 | |
quickPower | 0.01 | 0.00 | 0.00 | |
simFromData | 0 | 0 | 0 | |
simFromParam | 4.22 | 0.08 | 136.92 | |