Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 372/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ClustAll 1.2.0 (landing page) Asier Ortega-Legarreta
| 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 ClustAll package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClustAll.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: ClustAll |
Version: 1.2.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClustAll.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ClustAll_1.2.0.tar.gz |
StartedAt: 2024-12-20 00:07:32 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:11:36 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 243.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ClustAll.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClustAll.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ClustAll_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ClustAll.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 'ClustAll/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ClustAll' 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 'ClustAll' 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 summary_clusters 1.81 0.09 19.22 JACCARD_DISTANCE_F 1.18 0.11 18.97 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'createClustAll_example.R' Running 'runClustAll_example.R' 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: OK
ClustAll.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ClustAll ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ClustAll' ... ** 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 (ClustAll)
ClustAll.Rcheck/tests/createClustAll_example.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. > ########################################### > # All possibilities to create the object > ########################################### > require("ClustAll") Loading required package: ClustAll > data("BreastCancerWisconsin", package = "ClustAll") > data("BreastCancerWisconsinMISSING", package = "ClustAll") > > test_creatingClustAll1 <- function() { + # Scenario 1: 1.No NA, 2.No imputation, 3.No imputation implemented + createClustAll(data = wdbc, colValidation = "Diagnosis", + nImputation = NULL, dataImputed = NULL) + } > > test_creatingClustAll2 <- function() { + # Scenario 2: 1.Yes NA, 2.Yes imputation, 3.Imputations automatically (default) + createClustAll(wdbcNA, nImputation = 2, colValidation = "Diagnosis") + createClustAll(wdbcNA, dataImputed = wdbcMIDS, + colValidation = "Diagnosis") + } > > test_creatingClustAll3 <- function() { + # Scenario 3: 1.Yes NA, 2.Yes imputation, 3.Imputations manually + createClustAll(wdbcNA, dataImputed = wdbcMIDS, + colValidation = "Diagnosis") + } > > proc.time() user system elapsed 7.50 0.68 8.17
ClustAll.Rcheck/tests/runClustAll_example.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. > ########################################################## > # Running the pipeline with parallelization > ########################################################## > require("ClustAll") Loading required package: ClustAll > data("BreastCancerWisconsin", package = "ClustAll") # load example data > wdbc <- subset(wdbc,select=c(-ID, -Diagnosis)) > wdbc <- wdbc[1:15,1:8] # reduce the number of variables for a less computational time > obj <- createClustAll(data = wdbc, colValidation = NULL, + nImputation = NULL, dataImputed = NULL) Before continuing, check that the transformation has been processed correctly. ClustALL object was created successfully. You can run runClustAll. > > > test_pipeline1 <- function() { + # 1. No parallelization, 2. YES simplified (use all depth) + runClustAll(obj, threads = 1, simplify = TRUE) + } > # > test_pipeline2 <- function() { + # 1. YES parallelization, 2. YES simplified (one depth every four) + runClustAll(obj, threads = 2, simplify = TRUE) + } > > > > proc.time() user system elapsed 7.03 0.71 7.73
ClustAll.Rcheck/tests/runTests.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("ClustAll") The following cluster(s) do(es) not exist: NOTexist You may want to check the clusters using resStratification. The following cluster(s) do(es) not exist: NOTexist You may want to check the clusters using resStratification. The following cluster(s) do(es) not exist: NOTexist You may want to check the clusters using resStratification. The ClustALL Object does not include labels. Please create a new object or modidy the object with the original labelling data. For that check addValidationData method. The ClustALL Object does not include labels. Please create a new object or modify the object with the original labelling data. For that check addValidationData method Loading required package: mice Attaching package: 'mice' The following object is masked from 'package:stats': filter The following objects are masked from 'package:base': cbind, rbind iter imp variable 1 1 1 2 2 1 2 2 3 1 3 2 4 1 4 2 5 1 5 2 The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. The introduced column name is not present in the dataset. Please, make sure to introduce it correctly. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. ClustALL object was created successfully. You can run runClustAll. The introduced data and the original data labelling have different lengths. Make sure the introduced data is correct. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Categorical variables detected! Applying One-hot encoding... Before continuing, check that the transformation has been processed correctly. ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Categorical variables detected! Applying One-hot encoding... Before continuing, check that the transformation has been processed correctly. ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. The dataset does NOT contain NA values. The imputation process will not be applied. ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. Running default multiple imputation method. For more information check mice package. iter imp variable 1 1 1 2 2 1 2 2 3 1 3 2 4 1 4 2 5 1 5 2 ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. The decimal value will be rounded. Running default multiple imputation method. For more information check mice package. iter imp variable 1 1 1 2 2 1 2 2 3 1 3 2 4 1 4 2 5 1 5 2 ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. The decimal value will be rounded. Running default multiple imputation method. For more information check mice package. iter imp variable 1 1 1 2 1 3 2 1 2 2 2 3 3 1 3 2 3 3 4 1 4 2 4 3 5 1 5 2 5 3 ClustALL object was created successfully. You can run runClustAll. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. The dataset contains NA values. Specify the number of imputations (nImputation) to be computed. The dataset contains character values. They will be transformed into categorical (more than one class) or binary (one class). Before continuing, check that the transformation has been processed correctly. Parameter nImputation is not valid. Please introduce a positive number of imputations. RUNIT TEST PROTOCOL -- Fri Dec 20 00:11:24 2024 *********************************************** Number of test functions: 7 Number of errors: 0 Number of failures: 0 1 Test Suite : ClustAll RUnit Tests - 7 test functions, 0 errors, 0 failures Number of test functions: 7 Number of errors: 0 Number of failures: 0 Warning messages: 1: Number of logged events: 2 2: Number of logged events: 1 3: Number of logged events: 1 4: Number of logged events: 1 > > proc.time() user system elapsed 8.03 0.89 8.84
ClustAll.Rcheck/ClustAll-Ex.timings
name | user | system | elapsed | |
JACCARD_DISTANCE_F | 1.18 | 0.11 | 18.97 | |
addValidationData | 0.02 | 0.00 | 0.01 | |
cluster2data | 0.01 | 0.00 | 0.02 | |
createClustAll | 0.07 | 0.01 | 0.08 | |
dataImputed | 0.04 | 0.00 | 0.04 | |
dataOriginal | 0.22 | 0.06 | 0.28 | |
dataValidation | 0.02 | 0.02 | 0.04 | |
extractData | 0 | 0 | 0 | |
extractResults | 0.01 | 0.00 | 0.01 | |
nImputation | 0.02 | 0.02 | 0.03 | |
plotJACCARD | 0.02 | 0.00 | 0.02 | |
plotSANKEY | 0.01 | 0.00 | 0.01 | |
processed | 0.02 | 0.00 | 0.02 | |
resStratification | 0 | 0 | 0 | |
runClustAll | 0.01 | 0.00 | 0.01 | |
showData | 0.35 | 0.03 | 0.46 | |
summary_clusters | 1.81 | 0.09 | 19.22 | |
validateStratification | 0.01 | 0.02 | 0.03 | |