Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 20/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
adverSCarial 1.3.0 (landing page) Ghislain FIEVET
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.3.0 |
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_1.3.0.tar.gz |
StartedAt: 2024-06-09 23:20:51 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 23:24:21 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 209.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: adverSCarial.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 '1.3.0' * 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 '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' 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 counts is lastResLength new Consider adding importFrom("methods", "is", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) advGridMinChange.Rd:34-37: Lost braces 34 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advMaxChange.Rd:38-41: Lost braces 38 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advRandWalkMinChange.Rd:36-39: Lost braces 36 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advSingleGene.Rd:42-45: Lost braces 42 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) maxChangeOverview.Rd:35-38: Lost braces 35 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) predictWithNewValue.Rd:35-38: Lost braces 35 | 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 ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'advGridMinChange.Rd': advGridMinChange Code: function(exprs, clusters, target, classifier, genes, modifications = list(c("perc1"), c("perc99")), returnFirstFound = FALSE, argForClassif = "data.frame", argForModif = "data.frame", verbose = FALSE, iamsure = FALSE) Docs: function(exprs, clusters, target, classifier, genes, modifications = list(c("perc1"), c("perc99")), returnFirstFound = FALSE, argForClassif = "DelayedMatrix", argForModif = "DelayedMatrix", verbose = FALSE, iamsure = FALSE) Mismatches in argument default values: Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix" Name: 'argForModif' Code: "data.frame" Docs: "DelayedMatrix" Codoc mismatches from Rd file 'advMaxChange.Rd': advMaxChange Code: function(exprs, clusters, target, classifier, exclGenes = c(), genes = c(), advMethod = "perc99", advFixedValue = 3, advFct = NULL, maxSplitSize = 1, argForClassif = "data.frame", argForModif = "data.frame", verbose = FALSE) Docs: function(exprs, clusters, target, classifier, exclGenes = c(), genes = c(), advMethod = "perc99", advFixedValue = 3, advFct = NULL, maxSplitSize = 1, argForClassif = "DelayedMatrix", argForModif = "data.frame", verbose = FALSE) Mismatches in argument default values: Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix" Codoc mismatches from Rd file 'advRandWalkMinChange.Rd': advRandWalkMinChange Code: function(exprs, clusters, target, classifier, genes, modifications = list(c("perc1"), c("perc99")), firstBatch = 100, walkLength = 100, stepChangeRatio = 0.2, whileMaxCount = 10000, changeType = "any", argForClassif = "data.frame", argForModif = "data.frame", verbose = FALSE) Docs: function(exprs, clusters, target, classifier, genes, modifications = list(c("perc1"), c("perc99")), firstBatch = 100, walkLength = 100, stepChangeRatio = 0.2, whileMaxCount = 10000, changeType = "any", argForClassif = "DelayedMatrix", argForModif = "DelayedMatrix", verbose = FALSE) Mismatches in argument default values: Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix" Name: 'argForModif' Code: "data.frame" Docs: "DelayedMatrix" Codoc mismatches from Rd file 'advSingleGene.Rd': advSingleGene Code: function(exprs, clusters, target, classifier, exclGenes = c(), genes = c(), advMethod = "perc99", advFixedValue = 3, advFct = NULL, firstDichot = 100, maxSplitSize = 1, returnFirstFound = FALSE, changeType = "any", argForClassif = "data.frame", argForModif = "data.frame", verbose = FALSE) Docs: function(exprs, clusters, target, classifier, exclGenes = c(), genes = c(), advMethod = "perc99", advFixedValue = 3, advFct = NULL, firstDichot = 100, maxSplitSize = 1, returnFirstFound = FALSE, changeType = "any", argForClassif = "DelayedMatrix", argForModif = "data.frame", verbose = FALSE) Mismatches in argument default values: Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix" Codoc mismatches from Rd file 'maxChangeOverview.Rd': maxChangeOverview Code: function(exprs, clusters, classifier, exclGenes = c(), genes = c(), modifications = list(c("perc1"), c("perc99")), advMethod = "perc99", advFixedValue = 3, advFct = NULL, maxSplitSize = 100, argForClassif = "data.frame", argForModif = "data.frame", verbose = FALSE) Docs: function(exprs, clusters, classifier, exclGenes = c(), genes = c(), modifications = list(c("perc1"), c("perc99")), advMethod = "perc99", advFixedValue = 3, advFct = NULL, maxSplitSize = 100, argForClassif = "DelayedMatrix", argForModif = "data.frame", verbose = FALSE) Mismatches in argument default values: Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix" Codoc mismatches from Rd file 'singleGeneOverview.Rd': singleGeneOverview Code: function(exprs, clusters, classifier, exclGenes = c(), genes = c(), modifications = list(c("perc1"), c("perc99")), advMethod = "perc99", advFixedValue = 3, advFct = NULL, firstDichot = 100, maxSplitSize = 100, changeType = "any", argForClassif = "data.frame", argForModif = "data.frame", verbose = FALSE) Docs: function(exprs, clusters, classifier, exclGenes = c(), genes = c(), modifications = list(c("perc1"), c("perc99")), advMethod = "perc99", advFixedValue = 3, advFct = NULL, firstDichot = 100, maxSplitSize = 100, changeType = "any", argForClassif = "DelayedMatrix", argForModif = "data.frame", verbose = FALSE) Mismatches in argument default values: Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix" * checking Rd \usage sections ... OK * 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 23.47 13.04 37.45 sceConvertToHGNC 10.41 4.51 15.29 matrixFromSCE 7.76 4.35 12.31 advChar 9.22 1.44 10.66 * 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: 1 WARNING, 3 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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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 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 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.000193119049072266 Split number: 8/100 Split time: 0.000182867050170898 Split number: 16/100 Split time: 0.00014805793762207 Split number: 32/100 Split time: 0.000155925750732422 Split number: 64/100 Split time: 0.000161886215209961 Split number: 100/100 Split time: 0.000169992446899414 result length: 3 result length: 3 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.000185012817382812 Split number: 8/100 Split time: 0.00011897087097168 Split number: 16/100 Split time: 0.000114917755126953 Split number: 32/100 Split time: 0.000114917755126953 Split number: 64/100 Split time: 0.000126838684082031 Split number: 100/100 Split time: 0.000123023986816406 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.00017094612121582 Split number: 8/100 Split time: 0.000118017196655273 Split number: 16/100 Split time: 0.000117063522338867 Split number: 32/100 Split time: 0.000115156173706055 Split number: 64/100 Split time: 0.000123023986816406 Split number: 100/100 Split time: 0.000118017196655273 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.000169992446899414 Split number: 8/100 Split time: 0.000114917755126953 Split number: 16/100 Split time: 0.00010991096496582 Split number: 32/100 Split time: 0.000113964080810547 Split number: 64/100 Split time: 0.000117063522338867 Split number: 100/100 Split time: 0.000121831893920898 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.000166893005371094 Split number: 8/100 Split time: 0.000117063522338867 Split number: 16/100 Split time: 0.000110864639282227 Split number: 32/100 Split time: 0.000114917755126953 Split number: 64/100 Split time: 0.000124931335449219 Split number: 100/100 Split time: 0.0001220703125 RUNIT TEST PROTOCOL -- Sun Jun 9 23:24:06 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 4.64 3.71 8.60
adverSCarial.Rcheck/adverSCarial-Ex.timings
name | user | system | elapsed | |
MClassifier | 23.47 | 13.04 | 37.45 | |
advChar | 9.22 | 1.44 | 10.66 | |
advGridMinChange | 0.41 | 1.44 | 1.85 | |
advList | 0.01 | 0.00 | 0.01 | |
advMaxChange | 0.13 | 1.36 | 1.50 | |
advModifications | 0.24 | 1.28 | 1.59 | |
advRandWalkMinChange | 0.40 | 1.26 | 1.80 | |
advSingleGene | 0.21 | 1.33 | 1.64 | |
matrixFromSCE | 7.76 | 4.35 | 12.31 | |
maxChangeOverview | 0.22 | 1.45 | 1.75 | |
predictWithNewValue | 0.20 | 1.36 | 1.67 | |
sceConvertToHGNC | 10.41 | 4.51 | 15.29 | |
singleGeneOverview | 0.27 | 1.25 | 1.62 | |