Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:21 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the scDblFinder package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDblFinder.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1691/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scDblFinder 1.6.0 (landing page) Pierre-Luc Germain
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: scDblFinder |
Version: 1.6.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDblFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scDblFinder_1.6.0.tar.gz |
StartedAt: 2021-10-15 05:10:04 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 05:16:48 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 403.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: scDblFinder.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDblFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scDblFinder_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scDblFinder.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'scDblFinder/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scDblFinder' version '1.6.0' * 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 'scDblFinder' 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 'library' or 'require' call not declared from: 'mbkmeans' 'library' or 'require' call to 'mbkmeans' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. ':::' call which should be '::': 'mbkmeans:::mbkmeans' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE clusterStickiness: no visible binding for global variable 'sce' doubletPairwiseEnrichment: no visible binding for global variable 'sce' plotThresholds: no visible global function definition for 'aes' plotThresholds: no visible binding for global variable 'threshold' plotThresholds: no visible binding for global variable 'FNR' plotThresholds: no visible binding for global variable 'FDR' plotThresholds: no visible binding for global variable 'dev' plotThresholds: no visible binding for global variable 'cost' Undefined global functions or variables: FDR FNR aes cost dev sce threshold * checking Rd files ... WARNING checkRd: (7) cxds2.Rd:27: Tag \href is invalid in a \code block * 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 ... WARNING Documented arguments not in \usage in documentation object 'doubletThresholding': 'verbose' 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 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scDblFinder 8.75 0.31 9.06 doubletThresholding 7.86 0.41 8.27 clusterStickiness 5.77 0.15 5.92 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scDblFinder 7.64 0.29 7.93 doubletThresholding 7.00 0.15 7.15 clusterStickiness 6.09 0.13 6.21 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scDblFinder.Rcheck/00check.log' for details.
scDblFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/scDblFinder_1.6.0.tar.gz && rm -rf scDblFinder.buildbin-libdir && mkdir scDblFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scDblFinder.buildbin-libdir scDblFinder_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL scDblFinder_1.6.0.zip && rm scDblFinder_1.6.0.tar.gz scDblFinder_1.6.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 820k 0 5189 0 0 63065 0 0:00:13 --:--:-- 0:00:13 63280 100 820k 100 820k 0 0 1681k 0 --:--:-- --:--:-- --:--:-- 1681k install for i386 * installing *source* package 'scDblFinder' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'scDblFinder' finding HTML links ... done TFIDF html addDoublets html aggregateFeatures html clusterStickiness html computeDoubletDensity html finding level-2 HTML links ... done createDoublets html cxds2 html data html doubletPairwiseEnrichment html doubletThresholding html fastcluster html findDoubletClusters html getArtificialDoublets html getCellPairs html getExpectedDoublets html mockDoubletSCE html plotDoubletMap html plotThresholds html propHomotypic html recoverDoublets html scDblFinder html selFeatures html ** 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 install for x64 * installing *source* package 'scDblFinder' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'scDblFinder' as scDblFinder_1.6.0.zip * DONE (scDblFinder) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'scDblFinder' successfully unpacked and MD5 sums checked
scDblFinder.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) 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(scDblFinder) > test_check("scDblFinder") [ FAIL 0 | WARN 8 | SKIP 0 | PASS 85 ] > > proc.time() user system elapsed 37.09 1.82 38.92 |
scDblFinder.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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(scDblFinder) > test_check("scDblFinder") [ FAIL 0 | WARN 8 | SKIP 0 | PASS 85 ] > > proc.time() user system elapsed 40.65 1.25 41.89 |
scDblFinder.Rcheck/examples_i386/scDblFinder-Ex.timings
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scDblFinder.Rcheck/examples_x64/scDblFinder-Ex.timings
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