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 18/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ADImpute 1.15.0 (landing page) Ana Carolina Leote
| 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 ADImpute package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ADImpute.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: ADImpute |
Version: 1.15.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ADImpute.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ADImpute_1.15.0.tar.gz |
StartedAt: 2024-06-09 23:20:51 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 23:27:53 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 421.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ADImpute.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ADImpute.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ADImpute_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ADImpute.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 'ADImpute/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ADImpute' version '1.15.0' * 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 'ADImpute' 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 ... WARNING '::' or ':::' imports not declared from: 'SCRABBLE' 'scImpute' * 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 LazyData ... 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 Impute 0.87 0.48 13.64 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.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 See 'F:/biocbuild/bbs-3.20-bioc/meat/ADImpute.Rcheck/00check.log' for details.
ADImpute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ADImpute ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ADImpute' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (ADImpute)
ADImpute.Rcheck/tests/testthat.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. > library(testthat) > library(ADImpute) > > test_check("ADImpute") Calculating Spearman distance. Calculating Pearson distance. Clustering for k : 10 Clustering for k : 11 Clustering for k : 12 Clustering for k : 13 Clustering for k : 14 Clustering for k : 15 cls object have 12 number of clustering sets. Zero percentage : Before impute : 76 percent. After impute : 31 percent. 46 percent of zeros are imputed. Calculating Spearman distance. Calculating Pearson distance. Clustering for k : 10 Clustering for k : 11 Clustering for k : 12 Clustering for k : 13 Clustering for k : 14 Clustering for k : 15 cls object have 12 number of clustering sets. Zero percentage : Before impute : 84 percent. After impute : 59 percent. 25 percent of zeros are imputed. Calculating Spearman distance. Calculating Pearson distance. Clustering for k : 10 Clustering for k : 11 Clustering for k : 12 Clustering for k : 13 Clustering for k : 14 Clustering for k : 15 cls object have 12 number of clustering sets. Zero percentage : Before impute : 84 percent. After impute : 63 percent. 22 percent of zeros are imputed. Calculating Spearman distance. Calculating Pearson distance. Clustering for k : 10 Clustering for k : 11 Clustering for k : 12 Clustering for k : 13 Clustering for k : 14 Clustering for k : 15 cls object have 12 number of clustering sets. Zero percentage : Before impute : 76 percent. After impute : 42 percent. 34 percent of zeros are imputed. Calculating Spearman distance. Calculating Pearson distance. Clustering for k : 10 Clustering for k : 11 Clustering for k : 12 Clustering for k : 13 Clustering for k : 14 Clustering for k : 15 cls object have 12 number of clustering sets. Zero percentage : Before impute : 76 percent. After impute : 47 percent. 30 percent of zeros are imputed. [ FAIL 0 | WARN 8 | SKIP 0 | PASS 134 ] [ FAIL 0 | WARN 8 | SKIP 0 | PASS 134 ] > > proc.time() user system elapsed 53.31 9.98 261.17
ADImpute.Rcheck/ADImpute-Ex.timings
name | user | system | elapsed | |
EvaluateMethods | 2.14 | 0.63 | 2.78 | |
Impute | 0.87 | 0.48 | 13.64 | |
NormalizeRPM | 0 | 0 | 0 | |
NormalizeTPM | 1.26 | 0.13 | 1.39 | |
WriteCSV | 0.02 | 0.00 | 0.01 | |
WriteTXT | 0 | 0 | 0 | |