Claudia Cava
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/SpidermiR |
| Branch: RELEASE_3_7 |
| Last Commit: ed23c45 |
| Last Changed Date: 2018-04-30 10:35:40 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
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 |
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### Running command:
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### /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
###
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* 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 | |