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This page was generated on 2018-10-17 08:56:11 -0400 (Wed, 17 Oct 2018).
Package 1409/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SpidermiR 1.10.0 Claudia Cava
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: SpidermiR |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SpidermiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SpidermiR_1.10.0.tar.gz |
StartedAt: 2018-10-17 00:13:01 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 00:19:14 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 372.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SpidermiR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SpidermiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SpidermiR_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SpidermiR.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpidermiR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpidermiR’ version ‘1.10.0’ * 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 ‘SpidermiR’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black") See ‘/Users/biocbuild/bbs-3.7-bioc/meat/SpidermiR.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 .SpidermiRvisualize_gene: possible error in simpleNetwork(NetworkData, linkColour = "gray", textColour = "black", zoom = TRUE): unused argument (textColour = "black") Case_Study1_loading_3_network: no visible global function definition for ‘SpidermiRanalyze_DEnetworkTCGA’ SpidermiRvisualize_plot_target: no visible binding for global variable ‘miRNAs’ SpidermiRvisualize_plot_target: no visible binding for global variable ‘mRNA_target’ Undefined global functions or variables: SpidermiRanalyze_DEnetworkTCGA mRNA_target miRNAs * 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 or elapsed time > 5s user system elapsed SpidermiRdownload_miRNAvalidate 9.874 0.627 15.706 SpidermiRdownload_miRNAprediction 6.517 1.818 12.730 SpidermiRanalyze_mirna_gene_complnet 3.991 0.342 6.322 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.7-bioc/meat/SpidermiR.Rcheck/00check.log’ for details.
SpidermiR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SpidermiR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘SpidermiR’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black") ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (SpidermiR)
SpidermiR.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(SpidermiR) Loading required package: miRNAtap Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid > > test_check("SpidermiR") [1] "Downloading: http://genemania.org/data/current/Saccharomyces_cerevisiae/Shared_protein_domains.INTERPRO.txt ... reference n. 1 of 2" [1] "Downloading: http://genemania.org/data/current/Saccharomyces_cerevisiae/Shared_protein_domains.PFAM.txt ... reference n. 2 of 2" ══ testthat results ═══════════════════════════════════════════════════════════ OK: 4 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 14.829 0.802 17.502
SpidermiR.Rcheck/SpidermiR-Ex.timings
name | user | system | elapsed | |
Case_Study1_loading_1_network | 0.001 | 0.000 | 0.001 | |
Case_Study1_loading_2_network | 0.001 | 0.000 | 0.001 | |
Case_Study1_loading_3_network | 0.001 | 0.000 | 0.001 | |
Case_Study1_loading_4_network | 0.002 | 0.000 | 0.002 | |
Case_Study2_loading_1_network | 0.002 | 0.000 | 0.001 | |
Case_Study2_loading_2_network | 0.001 | 0.000 | 0.001 | |
Case_Study2_loading_3_network | 0.002 | 0.000 | 0.001 | |
SpidermiRanalyze_Community_detection | 0.015 | 0.003 | 0.018 | |
SpidermiRanalyze_Community_detection_bi | 0.231 | 0.035 | 0.268 | |
SpidermiRanalyze_Community_detection_net | 0.008 | 0.002 | 0.010 | |
SpidermiRanalyze_degree_centrality | 0.002 | 0.000 | 0.003 | |
SpidermiRanalyze_direct_net | 0.004 | 0.001 | 0.004 | |
SpidermiRanalyze_direct_subnetwork | 0.004 | 0.001 | 0.005 | |
SpidermiRanalyze_mirna_gene_complnet | 3.991 | 0.342 | 6.322 | |
SpidermiRanalyze_mirna_network | 2.494 | 0.281 | 4.554 | |
SpidermiRanalyze_mirnanet_pharm | 0.003 | 0.000 | 0.004 | |
SpidermiRanalyze_subnetwork_neigh | 0.006 | 0.001 | 0.007 | |
SpidermiRdownload_miRNAextra_cir | 0.105 | 0.013 | 1.593 | |
SpidermiRdownload_miRNAprediction | 6.517 | 1.818 | 12.730 | |
SpidermiRdownload_miRNAvalidate | 9.874 | 0.627 | 15.706 | |
SpidermiRdownload_net | 0.307 | 0.031 | 1.217 | |
SpidermiRdownload_pharmacomir | 0.014 | 0.002 | 0.348 | |
SpidermiRprepare_NET | 0.640 | 0.055 | 2.820 | |
SpidermiRquery_disease | 0.039 | 0.003 | 0.630 | |
SpidermiRquery_networks_type | 0.021 | 0.002 | 0.336 | |
SpidermiRquery_spec_networks | 0.061 | 0.001 | 0.233 | |
SpidermiRquery_species | 0.013 | 0.000 | 0.126 | |
SpidermiRvisualize_3Dbarplot | 0.091 | 0.001 | 0.093 | |
SpidermiRvisualize_BI | 0.121 | 0.007 | 0.131 | |
SpidermiRvisualize_adj_matrix | 0.068 | 0.002 | 0.071 | |
SpidermiRvisualize_degree_dist | 0.011 | 0.001 | 0.014 | |
SpidermiRvisualize_direction | 0.033 | 0.008 | 0.042 | |
SpidermiRvisualize_mirnanet | 0.027 | 0.005 | 0.031 | |
SpidermiRvisualize_plot_target | 0.295 | 0.003 | 0.299 | |