Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:55:35 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE RITAN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1495/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
RITAN 1.12.0 Michael Zimmermann
| 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: RITAN |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RITAN.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RITAN_1.12.0.tar.gz |
StartedAt: 2020-10-17 04:49:30 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 04:51:12 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 102.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RITAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RITAN.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RITAN_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RITAN.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RITAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RITAN’ version ‘1.12.0’ * 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 ‘RITAN’ 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 Namespaces in Imports field not imported from: ‘BgeeDB’ ‘knitr’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE icon_test: no visible global function definition for ‘is’ network_overlap: no visible global function definition for ‘is’ network_overlap : map.input.to.STRING: no visible global function definition for ‘is’ plot.term_enrichment_by_subset: no visible global function definition for ‘is’ plot.term_enrichment_by_subset: no visible binding for global variable ‘Var2’ plot.term_enrichment_by_subset: no visible binding for global variable ‘Var1’ readSIF: no visible global function definition for ‘is’ term_enrichment_by_subset: no visible global function definition for ‘is’ writeGMT: no visible global function definition for ‘is’ Undefined global functions or variables: Var1 Var2 is Consider adding importFrom("methods", "is") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed summary.term_enrichment_by_subset 2.245 0.032 9.091 enrichment_symbols 2.193 0.065 5.683 * 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 ‘/home/biocbuild/bbs-3.11-bioc/meat/RITAN.Rcheck/00check.log’ for details.
RITAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RITAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘RITAN’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (RITAN)
RITAN.Rcheck/RITAN-Ex.timings
name | user | system | elapsed | |
as.graph | 0 | 0 | 0 | |
check_any_net_input | 1.859 | 0.092 | 2.041 | |
check_net_input | 0.084 | 0.000 | 0.084 | |
enrichment_symbols | 2.193 | 0.065 | 5.683 | |
geneset_overlap | 0.125 | 0.008 | 0.133 | |
icon_test | 0 | 0 | 0 | |
load_geneset_symbols | 0.009 | 0.000 | 0.008 | |
network_overlap | 0.016 | 0.000 | 0.015 | |
plot.term_enrichment | 1.512 | 0.024 | 4.812 | |
plot.term_enrichment_by_subset | 0.024 | 0.000 | 0.025 | |
readGMT | 0.000 | 0.000 | 0.001 | |
readSIF | 0.000 | 0.000 | 0.001 | |
resource_reduce | 2.939 | 0.012 | 2.950 | |
show_active_genesets_hist | 0.016 | 0.000 | 0.016 | |
summary.term_enrichment | 1.123 | 0.028 | 3.958 | |
summary.term_enrichment_by_subset | 2.245 | 0.032 | 9.091 | |
term_enrichment | 1.128 | 0.025 | 4.174 | |
term_enrichment_by_subset | 0.015 | 0.000 | 0.015 | |
vac1.day0vs31.de.genes | 0.001 | 0.000 | 0.000 | |
vac1.day0vs56.de.genes | 0 | 0 | 0 | |
vac2.day0vs31.de.genes | 0 | 0 | 0 | |
vac2.day0vs56.de.genes | 0 | 0 | 0 | |
writeGMT | 0 | 0 | 0 | |
write_simple_table | 0 | 0 | 0 | |