Michael Zimmermann
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RITAN |
| Branch: RELEASE_3_8 |
| Last Commit: 581a092 |
| Last Changed Date: 2018-10-30 11:42:05 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:47 -0400 (Tue, 16 Apr 2019).
| Package 1316/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RITAN 1.6.0 Michael Zimmermann
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: RITAN |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RITAN.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RITAN_1.6.0.tar.gz |
| StartedAt: 2019-04-16 02:39:08 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:40:40 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 92.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RITAN.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RITAN.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RITAN_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RITAN.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.6.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘gplots::plotCI’ by ‘plotrix::plotCI’ when loading ‘RITAN’
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘RITAN’
Warning: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘RITAN’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘RITAN’
See ‘/home/biocbuild/bbs-3.8-bioc/meat/RITAN.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘sqldf’
A package should be listed in only one of these fields.
* 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
check_any_net_input: no visible binding for global variable
‘network_list’
enrichment_symbols: no visible binding for global variable
‘active_genesets’
icon_dual_between: no visible global function definition for ‘ss2’
icon_dual_between: no visible binding for global variable ‘all_symbols’
icon_dual_between: no visible binding for global variable ‘all_net’
icon_single_within: no visible global function definition for ‘ss2’
icon_single_within: no visible binding for global variable
‘all_symbols’
icon_single_within: no visible binding for global variable ‘all_net’
load_geneset_symbols: no visible binding for global variable
‘geneset_list’
load_geneset_symbols: no visible binding for global variable ‘f’
load_geneset_symbols: no visible binding for global variable
‘active_genesets’
network_overlap : <anonymous>: no visible binding for global variable
‘network_list’
network_overlap: no visible binding for global variable ‘network_list’
network_overlap : select_edges: no visible binding for global variable
‘network_list’
plot.term_enrichment_by_subset: no visible binding for global variable
‘Var2’
plot.term_enrichment_by_subset: no visible binding for global variable
‘Var1’
show_active_genesets_hist: no visible binding for global variable
‘active_genesets’
term_enrichment : process_source: no visible binding for global
variable ‘active_genesets’
Undefined global functions or variables:
Var1 Var2 active_genesets all_net all_symbols f geneset_list
network_list ss2
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'resource_reduce':
‘mutual_overlap’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 or elapsed time > 5s
user system elapsed
enrichment_symbols 2.240 0.084 5.477
summary.term_enrichment_by_subset 1.748 0.036 6.888
* 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 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/RITAN.Rcheck/00check.log’
for details.
RITAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RITAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘RITAN’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘gplots::plotCI’ by ‘plotrix::plotCI’ when loading ‘RITAN’ Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘RITAN’ Warning: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘RITAN’ Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘RITAN’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import ‘gplots::plotCI’ by ‘plotrix::plotCI’ when loading ‘RITAN’ Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘RITAN’ Warning: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘RITAN’ Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘RITAN’ * DONE (RITAN)
RITAN.Rcheck/RITAN-Ex.timings
| name | user | system | elapsed | |
| as.graph | 0.000 | 0.000 | 0.001 | |
| check_any_net_input | 1.564 | 0.056 | 1.682 | |
| check_net_input | 0.044 | 0.004 | 0.050 | |
| enrichment_symbols | 2.240 | 0.084 | 5.477 | |
| geneset_overlap | 0.180 | 0.004 | 0.183 | |
| icon_test | 0 | 0 | 0 | |
| load_geneset_symbols | 0.012 | 0.000 | 0.010 | |
| network_overlap | 0.024 | 0.000 | 0.023 | |
| plot.term_enrichment | 1.472 | 0.004 | 4.002 | |
| plot.term_enrichment_by_subset | 0.024 | 0.000 | 0.022 | |
| readGMT | 0 | 0 | 0 | |
| readSIF | 0 | 0 | 0 | |
| resource_reduce | 3.052 | 0.008 | 3.062 | |
| show_active_genesets_hist | 0.016 | 0.000 | 0.015 | |
| summary.term_enrichment | 0.800 | 0.032 | 3.215 | |
| summary.term_enrichment_by_subset | 1.748 | 0.036 | 6.888 | |
| term_enrichment | 0.952 | 0.004 | 3.913 | |
| term_enrichment_by_subset | 0.064 | 0.004 | 0.068 | |
| vac1.day0vs31.de.genes | 0 | 0 | 0 | |
| vac1.day0vs56.de.genes | 0 | 0 | 0 | |
| vac2.day0vs31.de.genes | 0 | 0 | 0 | |
| vac2.day0vs56.de.genes | 0 | 0 | 0 | |
| writeGMT | 0.000 | 0.000 | 0.001 | |
| write_simple_table | 0 | 0 | 0 | |