Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the DriverNet package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DriverNet.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 533/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DriverNet 1.32.0 (landing page) Jiarui Ding
| 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: DriverNet |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DriverNet_1.32.0.tar.gz |
StartedAt: 2021-10-14 18:36:07 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:37:43 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 95.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DriverNet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DriverNet_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/DriverNet.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DriverNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DriverNet’ version ‘1.32.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DriverNet’ 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 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 ... NOTE Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .computeDriversHelper: no visible global function definition for ‘new’ getPatientOutlierMatrix: no visible binding for global variable ‘sd’ getPatientOutlierMatrix: no visible global function definition for ‘dnorm’ resultSummary: no visible global function definition for ‘write.table’ Undefined global functions or variables: dnorm new sd write.table Consider adding importFrom("methods", "new") importFrom("stats", "dnorm", "sd") importFrom("utils", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DriverNet-package 29.174 0.957 30.165 computeDrivers 17.678 0.545 18.245 computeRandomizedResult 11.183 0.046 11.240 * 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/DriverNet.Rcheck/00check.log’ for details.
DriverNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DriverNet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘DriverNet’ ... ** using staged installation ** R ** data ** 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 (DriverNet)
DriverNet.Rcheck/DriverNet-Ex.timings
name | user | system | elapsed | |
DriverNet-package | 29.174 | 0.957 | 30.165 | |
DriverNetResult-class | 0.015 | 0.003 | 0.018 | |
actualEvents | 0.080 | 0.111 | 0.191 | |
computeDrivers | 17.678 | 0.545 | 18.245 | |
computeRandomizedResult | 11.183 | 0.046 | 11.240 | |
drivers | 0.071 | 0.102 | 0.173 | |
getPatientOutlierMatrix | 0.230 | 0.012 | 0.242 | |
preprocessMatrices | 0.235 | 0.008 | 0.244 | |
resultSummary | 0.283 | 0.019 | 0.302 | |
sampleDriversList | 0.022 | 0.003 | 0.024 | |
sampleGeneNames | 0.031 | 0.001 | 0.033 | |
sampleInfluenceGraph | 0.196 | 0.003 | 0.199 | |
samplePatientExpressionMatrix | 0.109 | 0.002 | 0.112 | |
samplePatientMutationMatrix | 0.017 | 0.003 | 0.021 | |
samplePatientOutlierMatrix | 0.014 | 0.002 | 0.016 | |
sampleRandomDriversResult | 0.002 | 0.003 | 0.005 | |
totalEvents | 0.013 | 0.002 | 0.015 | |