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This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the Clonality package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Clonality.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 324/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Clonality 1.40.0 (landing page) Irina Ostrovnaya
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Clonality |
Version: 1.40.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Clonality.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Clonality_1.40.0.tar.gz |
StartedAt: 2021-10-14 21:10:24 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:14:25 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 241.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Clonality.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Clonality.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Clonality_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Clonality.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 'Clonality/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Clonality' version '1.40.0' * 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 'Clonality' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Fortran("fndcpt", ..., PACKAGE = "DNAcopy") See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE get.mutation.frequencies: no visible binding for global variable 'freqdata' Undefined global functions or variables: freqdata * 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 installed files from 'inst/doc' ... 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 clonality.analysis 49.48 0.19 49.67 LRtesting3or4tumors 24.35 0.00 24.34 ECMtesting 8.54 0.00 8.53 LOHclonality 7.82 0.02 7.84 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed clonality.analysis 43.07 0.19 43.25 LRtesting3or4tumors 18.39 0.00 18.39 ECMtesting 7.75 0.00 7.75 LOHclonality 7.56 0.00 7.57 * 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 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Clonality.Rcheck/00check.log' for details.
Clonality.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Clonality_1.40.0.tar.gz && rm -rf Clonality.buildbin-libdir && mkdir Clonality.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Clonality.buildbin-libdir Clonality_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Clonality_1.40.0.zip && rm Clonality_1.40.0.tar.gz Clonality_1.40.0.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 79 2434k 79 1944k 0 0 4328k 0 --:--:-- --:--:-- --:--:-- 4330k 100 2434k 100 2434k 0 0 4949k 0 --:--:-- --:--:-- --:--:-- 4947k install for i386 * installing *source* package 'Clonality' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Clonality' finding HTML links ... done Clonality-internal html Clonality-package html ECMtesting html LOHclonality html LRtesting3or4tumors html SNVtest html SNVtest2 html ave.adj.probes html chromosomePlots html clonEM html clonality.analysis html create.mutation.matrix html freqdata html genomewidePlots html get.mutation.frequencies html grid.lik html histogramPlot html lcis html model.lik html mutation.proba html mutation.rem html print.mutation.proba html print.mutation.rem html splitChromosomes html xidens html ** building package indices ** installing vignettes 'Clonality.Rnw' ** 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 'Clonality' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'Clonality' as Clonality_1.40.0.zip * DONE (Clonality) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'Clonality' successfully unpacked and MD5 sums checked
Clonality.Rcheck/examples_i386/Clonality-Ex.timings
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Clonality.Rcheck/examples_x64/Clonality-Ex.timings
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