Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 20/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
adverSCarial 1.2.0 (landing page) Ghislain FIEVET
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 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: 1.2.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings adverSCarial_1.2.0.tar.gz |
StartedAt: 2024-07-21 21:32:37 -0400 (Sun, 21 Jul 2024) |
EndedAt: 2024-07-21 21:34:01 -0400 (Sun, 21 Jul 2024) |
EllapsedTime: 84.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: adverSCarial.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings adverSCarial_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/adverSCarial.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘adverSCarial/DESCRIPTION’ ... OK * this is package ‘adverSCarial’ 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 for sufficient/correct file permissions ... 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 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 ... 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 20.412 2.027 23.219 sceConvertToHGNC 9.133 2.089 11.704 matrixFromSCE 7.376 1.372 9.115 advChar 7.657 0.980 8.637 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/adverSCarial.Rcheck/00check.log’ for details.
adverSCarial.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL adverSCarial ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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: 0.000164270401000977 Split number: 8/100 Split time: 0.00014185905456543 Split number: 16/100 Split time: 0.000101327896118164 Split number: 32/100 Split time: 0.000101804733276367 Split number: 64/100 Split time: 0.000107765197753906 Split number: 100/100 Split time: 0.000104665756225586 result length: 3 result length: 3 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.000163078308105469 Split number: 8/100 Split time: 0.000105142593383789 Split number: 16/100 Split time: 0.000118255615234375 Split number: 32/100 Split time: 0.000100374221801758 Split number: 64/100 Split time: 0.000101327896118164 Split number: 100/100 Split time: 0.000105619430541992 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.000146627426147461 Split number: 8/100 Split time: 0.000102996826171875 Split number: 16/100 Split time: 0.000113010406494141 Split number: 32/100 Split time: 9.87052917480469e-05 Split number: 64/100 Split time: 0.000106096267700195 Split number: 100/100 Split time: 0.000122308731079102 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.000148296356201172 Split number: 8/100 Split time: 0.000106096267700195 Split number: 16/100 Split time: 9.89437103271484e-05 Split number: 32/100 Split time: 9.918212890625e-05 Split number: 64/100 Split time: 0.000107526779174805 Split number: 100/100 Split time: 0.000105142593383789 Split number: 1/100 Split number: 2/100 Split number: 4/100 Split time: 0.000144004821777344 Split number: 8/100 Split time: 0.000123977661132812 Split number: 16/100 Split time: 9.84668731689453e-05 Split number: 32/100 Split time: 9.98973846435547e-05 Split number: 64/100 Split time: 0.000102519989013672 Split number: 100/100 Split time: 0.000118255615234375 RUNIT TEST PROTOCOL -- Sun Jul 21 21:33:55 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 4.647 0.252 4.888
adverSCarial.Rcheck/adverSCarial-Ex.timings
name | user | system | elapsed | |
MClassifier | 20.412 | 2.027 | 23.219 | |
advChar | 7.657 | 0.980 | 8.637 | |
advGridMinChange | 0.282 | 0.008 | 0.290 | |
advList | 0.010 | 0.001 | 0.010 | |
advMaxChange | 0.120 | 0.023 | 0.142 | |
advModifications | 0.136 | 0.016 | 0.152 | |
advRandWalkMinChange | 0.308 | 0.004 | 0.311 | |
advSingleGene | 0.131 | 0.008 | 0.138 | |
matrixFromSCE | 7.376 | 1.372 | 9.115 | |
maxChangeOverview | 0.187 | 0.024 | 0.211 | |
predictWithNewValue | 0.205 | 0.008 | 0.213 | |
sceConvertToHGNC | 9.133 | 2.089 | 11.704 | |
singleGeneOverview | 0.215 | 0.072 | 0.288 | |