Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-24 11:39 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 20/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
adverSCarial 1.3.11 (landing page) Ghislain FIEVET
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the adverSCarial package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/adverSCarial.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: adverSCarial |
Version: 1.3.11 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:adverSCarial.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings adverSCarial_1.3.11.tar.gz |
StartedAt: 2024-07-23 21:52:14 -0400 (Tue, 23 Jul 2024) |
EndedAt: 2024-07-23 21:54:53 -0400 (Tue, 23 Jul 2024) |
EllapsedTime: 158.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: adverSCarial.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:adverSCarial.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings adverSCarial_1.3.11.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'adverSCarial/DESCRIPTION' ... OK * this is package 'adverSCarial' version '1.3.11' * 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 ... NOTE Found the following hidden files and directories: vignettes/.RData These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'adverSCarial' 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 ... NOTE .advModificationsFunction: no visible global function definition for 'is' .advModificationsFunction : <anonymous>: no visible global function definition for 'is' .advModificationsNotFunction: no visible global function definition for 'is' .advModificationsNotFunction: no visible global function definition for 'counts' .advModificationsNotFunction : <anonymous>: no visible global function definition for 'is' .randWalkGetSeed: no visible global function definition for 'SingleCellExperiment' .randWalkGetSeed: no visible global function definition for 'is' .randWalkTryNewVector: no visible global function definition for 'SingleCellExperiment' .randWalkTryNewVector: no visible global function definition for 'is' MClassifier: no visible global function definition for 'is' MClassifier: no visible global function definition for 'counts' advChar: no visible global function definition for 'new' advGridMinChange: no visible global function definition for 'is' advGridMinChange: no visible global function definition for 'counts' advGridMinChange: no visible global function definition for 'SingleCellExperiment' advList: no visible global function definition for 'new' advMaxChange: no visible global function definition for 'is' advMaxChange: no visible global function definition for 'counts' advMaxChange: no visible global function definition for 'new' advModifications: no visible global function definition for 'is' advModifications: no visible global function definition for 'counts' advModifications: no visible global function definition for 'SingleCellExperiment' advRandWalkMinChange: no visible global function definition for 'is' advRandWalkMinChange: no visible global function definition for 'counts' advSingleGene: no visible global function definition for 'is' advSingleGene: no visible global function definition for 'counts' advSingleGene: no visible binding for '<<-' assignment to 'lastResLength' advSingleGene : <anonymous>: no visible binding for global variable 'lastResLength' advSingleGene : <anonymous>: no visible binding for '<<-' assignment to 'lastResLength' advSingleGene: no visible global function definition for 'new' getDistantCouples: no visible global function definition for 'combn' getSignGenes : <anonymous>: no visible global function definition for 'wilcox.test' getSignGenes : <anonymous>: no visible global function definition for 't.test' matrixFromSCE: no visible global function definition for 'is' matrixFromSCE: no visible global function definition for 'colData' maxChangeOverview: no visible global function definition for 'is' maxChangeOverview: no visible global function definition for 'counts' predictWithNewValue: no visible global function definition for 'is' sceConvertToHGNC: no visible global function definition for 'is' sceConvertToHGNC: no visible global function definition for 'SingleCellExperiment' sceConvertToHGNC: no visible global function definition for 'colData' singleGeneOverview: no visible global function definition for 'is' singleGeneOverview: no visible global function definition for 'counts' Undefined global functions or variables: SingleCellExperiment colData combn counts is lastResLength new t.test wilcox.test Consider adding importFrom("methods", "is", "new") importFrom("stats", "t.test", "wilcox.test") importFrom("utils", "combn") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) advCGD.Rd:31-34: Lost braces 31 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advGridMinChange.Rd:34-37: Lost braces 34 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advMaxChange.Rd:39-42: Lost braces 39 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advRandWalkMinChange.Rd:36-39: Lost braces 36 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advSingleGene.Rd:43-46: Lost braces 43 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) maxChangeOverview.Rd:35-38: Lost braces 35 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) predictWithNewValue.Rd:36-39: Lost braces 36 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) singleGeneOverview.Rd:37-40: Lost braces 37 | classifier = function(expr, clusters, target){ | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'advTraining' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'advMaxChange.Rd' 'slot' Undocumented arguments in Rd file 'advModifications.Rd' 'slot' Undocumented arguments in Rd file 'advSingleGene.Rd' 'slot' Undocumented arguments in Rd file 'predictWithNewValue.Rd' 'slot' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... NOTE The following directory looks like a leftover from 'knitr': 'figure' Please remove from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MClassifier 26.59 4.77 71.22 advChar 10.64 1.77 12.41 sceConvertToHGNC 10.40 1.75 12.39 matrixFromSCE 8.37 1.50 10.12 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck/00check.log' for details.
adverSCarial.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL adverSCarial ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'adverSCarial' ... ** using staged installation ** R ** 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 (adverSCarial)
adverSCarial.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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("adverSCarial") Running combination: 1 on 3 Running combination: 2 on 3 Running combination: 3 on 3 predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame result length: 3 Running first batch to determine walk seed: 1 on 3 Running first batch to determine walk seed: 2 on 3 Running first batch to determine walk seed: 3 on 3 No modified type, try with a higher firstBatch argument predictWithNewValue data.frame data.frame Split number: 1/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b Split number: 2/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b Split number: 4/100 Split time: 0.000149011611938477 Split number: 8/100 Split time: 0.000179052352905273 Split number: 16/100 Split time: 0.000149965286254883 Split number: 32/100 Split time: 0.000149965286254883 Split number: 64/100 Split time: 0.000147819519042969 Split number: 100/100 Split time: 0.000157833099365234 predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame result length: 3 predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame result length: 3 predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame result length: 3 predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame result length: 3 predictWithNewValue data.frame data.frame predictWithNewValue data.frame data.frame Split number: 1/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b Split number: 2/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b Split number: 4/100 Split time: 0.000189065933227539 Split number: 8/100 Split time: 0.00018000602722168 Split number: 16/100 Split time: 0.000183820724487305 Split number: 32/100 Split time: 0.000195026397705078 Split number: 64/100 Split time: 0.00020599365234375 Split number: 100/100 Split time: 0.00020909309387207 predictWithNewValue data.frame data.frame Split number: 1/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: t Split number: 2/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: t predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: t Split number: 4/100 Split time: 0.00018000602722168 Split number: 8/100 Split time: 0.000164031982421875 Split number: 16/100 Split time: 0.000161886215209961 Split number: 32/100 Split time: 0.000203132629394531 Split number: 64/100 Split time: 0.000231027603149414 Split number: 100/100 Split time: 0.000195980072021484 predictWithNewValue data.frame data.frame Split number: 1/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b Split number: 2/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: b Split number: 4/100 Split time: 0.000119924545288086 Split number: 8/100 Split time: 0.000113964080810547 Split number: 16/100 Split time: 0.000107049942016602 Split number: 32/100 Split time: 0.00010991096496582 Split number: 64/100 Split time: 0.000119924545288086 Split number: 100/100 Split time: 0.000113010406494141 predictWithNewValue data.frame data.frame Split number: 1/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: t Split number: 2/100 predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: t predictWithNewValue data.frame data.frame cellType: b classifTarget: b target: t Split number: 4/100 Split time: 0.0001220703125 Split number: 8/100 Split time: 0.000110149383544922 Split number: 16/100 Split time: 0.000120878219604492 Split number: 32/100 Split time: 0.000112056732177734 Split number: 64/100 Split time: 0.00011897087097168 Split number: 100/100 Split time: 0.000117063522338867 RUNIT TEST PROTOCOL -- Tue Jul 23 21:54:42 2024 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : adverSCarial RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 4.93 0.25 5.17
adverSCarial.Rcheck/adverSCarial-Ex.timings
name | user | system | elapsed | |
MClassifier | 26.59 | 4.77 | 71.22 | |
advCGD | 0.04 | 0.00 | 0.03 | |
advChar | 10.64 | 1.77 | 12.41 | |
advGridMinChange | 0.36 | 0.03 | 0.40 | |
advList | 0.01 | 0.00 | 0.02 | |
advMaxChange | 0.20 | 0.03 | 0.23 | |
advModifications | 0.23 | 0.05 | 0.28 | |
advRandWalkMinChange | 0.38 | 0.04 | 0.42 | |
advSingleGene | 0.23 | 0.02 | 0.25 | |
getSignGenes | 0 | 0 | 0 | |
matrixFromSCE | 8.37 | 1.50 | 10.12 | |
maxChangeOverview | 0.22 | 0.04 | 0.26 | |
predictWithNewValue | 0.16 | 0.05 | 0.21 | |
sceConvertToHGNC | 10.40 | 1.75 | 12.39 | |
singleGeneOverview | 0.24 | 0.03 | 0.26 | |