Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the AffiXcan package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AffiXcan.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 21/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AffiXcan 1.10.0 (landing page) Alessandro Lussana
| 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: AffiXcan |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AffiXcan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AffiXcan_1.10.0.tar.gz |
StartedAt: 2021-10-14 16:07:01 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:10:27 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 206.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AffiXcan.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AffiXcan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AffiXcan_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/AffiXcan.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 ‘AffiXcan/DESCRIPTION’ ... OK * this is package ‘AffiXcan’ version ‘1.10.0’ * 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 ... 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 ‘AffiXcan’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE computeBs: no visible binding for global variable ‘V1’ computeRSquared: no visible binding for global variable ‘exprMatrix’ Undefined global functions or variables: V1 exprMatrix * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AffiXcan-package 4.273 1.379 3.367 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/AffiXcan.Rcheck/00check.log’ for details.
AffiXcan.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AffiXcan ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘AffiXcan’ ... ** using staged installation ** R ** data ** 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 (AffiXcan)
AffiXcan.Rcheck/AffiXcan-Ex.timings
name | user | system | elapsed | |
AffiXcan-package | 4.273 | 1.379 | 3.367 | |
affiXcanBs | 0.002 | 0.001 | 0.002 | |
affiXcanGReX | 0.002 | 0.001 | 0.003 | |
affiXcanImpute | 3.132 | 1.642 | 2.228 | |
affiXcanPca | 0.001 | 0.000 | 0.001 | |
affiXcanPcs | 0.001 | 0.001 | 0.002 | |
affiXcanTrain | 0.001 | 0.000 | 0.002 | |
assoc2list | 0.000 | 0.000 | 0.001 | |
computeBs | 0.006 | 0.002 | 0.007 | |
computeCorrelation | 0.002 | 0.001 | 0.002 | |
computeExpr | 0.002 | 0.000 | 0.003 | |
computePca | 0.003 | 0.001 | 0.003 | |
computePcs | 0.002 | 0.001 | 0.002 | |
computeRSquared | 0.001 | 0.001 | 0.001 | |
exprMatrix | 0.018 | 0.004 | 0.023 | |
overlookRegions | 0 | 0 | 0 | |
regionAssoc | 0.007 | 0.004 | 0.010 | |
subsetKFold | 0.001 | 0.001 | 0.000 | |
trainingCovariates | 0.003 | 0.003 | 0.005 | |