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This page was generated on 2021-10-15 15:05:37 -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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Clonality.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Clonality_1.40.0.tar.gz |
StartedAt: 2021-10-14 09:16:59 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:18:53 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 114.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Clonality.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Clonality.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Clonality_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Clonality.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * 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 for sufficient/correct file permissions ... 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 * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed clonality.analysis 40.669 0.268 40.942 LRtesting3or4tumors 20.248 0.008 20.257 ECMtesting 6.362 0.005 6.366 LOHclonality 6.190 0.004 6.194 * 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/Clonality.Rcheck/00check.log’ for details.
Clonality.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Clonality ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘Clonality’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (Clonality)
Clonality.Rcheck/Clonality-Ex.timings
name | user | system | elapsed | |
ECMtesting | 6.362 | 0.005 | 6.366 | |
LOHclonality | 6.190 | 0.004 | 6.194 | |
LRtesting3or4tumors | 20.248 | 0.008 | 20.257 | |
SNVtest | 2.590 | 0.100 | 2.691 | |
SNVtest2 | 0.48 | 0.00 | 0.48 | |
ave.adj.probes | 1.506 | 0.004 | 1.510 | |
chromosomePlots | 0 | 0 | 0 | |
clonality.analysis | 40.669 | 0.268 | 40.942 | |
create.mutation.matrix | 1.187 | 0.020 | 1.207 | |
genomewidePlots | 0 | 0 | 0 | |
get.mutation.frequencies | 1.215 | 0.024 | 1.239 | |
histogramPlot | 0 | 0 | 0 | |
mutation.proba | 1.121 | 0.016 | 1.137 | |
mutation.rem | 1.576 | 0.020 | 1.596 | |
splitChromosomes | 0.005 | 0.000 | 0.005 | |