Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:58:31 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE gaia PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 651/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
gaia 2.32.0 S. Morganella
| malbec2 | Linux (Ubuntu 18.04.4 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: gaia |
Version: 2.32.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gaia.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gaia_2.32.0.tar.gz |
StartedAt: 2020-10-17 01:18:19 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 01:19:06 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 46.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gaia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gaia.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gaia_2.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/gaia.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gaia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gaia’ version ‘2.32.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘gaia’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 generate_approx_null_hypothesis: no visible global function definition for ‘rbinom’ qvalue: no visible global function definition for ‘smooth.spline’ qvalue: no visible global function definition for ‘predict’ runGAIA: no visible global function definition for ‘write.table’ write_significant_regions: no visible global function definition for ‘write.table’ Undefined global functions or variables: predict rbinom smooth.spline write.table Consider adding importFrom("stats", "predict", "rbinom", "smooth.spline") importFrom("utils", "write.table") to your NAMESPACE file. * 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 runGAIA 8.605 0.076 8.709 gaia-package 6.210 0.106 6.322 * 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-3.11-bioc/meat/gaia.Rcheck/00check.log’ for details.
gaia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gaia ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘gaia’ ... ** 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 (gaia)
gaia.Rcheck/gaia-Ex.timings
name | user | system | elapsed | |
crc | 0.027 | 0.006 | 0.033 | |
crc_markers | 0.106 | 0.006 | 0.112 | |
gaia-package | 6.210 | 0.106 | 6.322 | |
load_cnv | 0.236 | 0.007 | 0.244 | |
load_markers | 0.014 | 0.003 | 0.016 | |
runGAIA | 8.605 | 0.076 | 8.709 | |
synthCNV_Matrix | 0.002 | 0.001 | 0.002 | |
synthMarkers_Matrix | 0.002 | 0.001 | 0.003 | |