Claudia Cava
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/SpidermiR |
| Branch: RELEASE_3_6 |
| Last Commit: 58ab31b |
| Last Changed Date: 2018-01-20 06:58:27 -0400 (Sat, 20 Jan 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:14:43 -0400 (Thu, 12 Apr 2018).
| Package 1330/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SpidermiR 1.8.2 Claudia Cava
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SpidermiR |
| Version: 1.8.2 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SpidermiR_1.8.2.tar.gz |
| StartedAt: 2018-04-12 03:05:06 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:09:33 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 266.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpidermiR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SpidermiR_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SpidermiR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.2’
* 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 ... 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SpidermiRdownload_miRNAvalidate 6.244 0.204 11.157
* 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 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/SpidermiR.Rcheck/00check.log’
for details.
SpidermiR.Rcheck/00install.out
* installing *source* package ‘SpidermiR’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, 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
11.264 0.176 12.497
SpidermiR.Rcheck/SpidermiR-Ex.timings
| name | user | system | elapsed | |
| Case_Study1_loading_1_network | 0.000 | 0.000 | 0.001 | |
| Case_Study1_loading_2_network | 0 | 0 | 0 | |
| Case_Study1_loading_3_network | 0.000 | 0.000 | 0.001 | |
| Case_Study1_loading_4_network | 0.004 | 0.000 | 0.000 | |
| Case_Study2_loading_1_network | 0 | 0 | 0 | |
| Case_Study2_loading_2_network | 0 | 0 | 0 | |
| Case_Study2_loading_3_network | 0.000 | 0.000 | 0.001 | |
| SpidermiRanalyze_Community_detection | 0.040 | 0.000 | 0.043 | |
| SpidermiRanalyze_Community_detection_bi | 0.760 | 0.000 | 0.759 | |
| SpidermiRanalyze_Community_detection_net | 0.008 | 0.000 | 0.006 | |
| SpidermiRanalyze_degree_centrality | 0.004 | 0.000 | 0.002 | |
| SpidermiRanalyze_direct_net | 0.028 | 0.000 | 0.027 | |
| SpidermiRanalyze_direct_subnetwork | 0.004 | 0.000 | 0.003 | |
| SpidermiRanalyze_mirna_gene_complnet | 2.748 | 0.064 | 4.850 | |
| SpidermiRanalyze_mirna_network | 2.608 | 0.008 | 4.633 | |
| SpidermiRanalyze_mirnanet_pharm | 0.000 | 0.000 | 0.002 | |
| SpidermiRanalyze_subnetwork_neigh | 0.020 | 0.000 | 0.018 | |
| SpidermiRdownload_miRNAextra_cir | 0.100 | 0.004 | 1.512 | |
| SpidermiRdownload_miRNAprediction | 3.636 | 0.176 | 3.815 | |
| SpidermiRdownload_miRNAvalidate | 6.244 | 0.204 | 11.157 | |
| SpidermiRdownload_net | 0.460 | 0.032 | 1.200 | |
| SpidermiRdownload_pharmacomir | 0.016 | 0.000 | 0.418 | |
| SpidermiRprepare_NET | 0.632 | 0.020 | 1.527 | |
| SpidermiRquery_disease | 0.044 | 0.000 | 0.617 | |
| SpidermiRquery_networks_type | 0.028 | 0.000 | 0.301 | |
| SpidermiRquery_spec_networks | 0.096 | 0.000 | 0.244 | |
| SpidermiRquery_species | 0.012 | 0.004 | 0.117 | |
| SpidermiRvisualize_3Dbarplot | 0.144 | 0.000 | 0.145 | |
| SpidermiRvisualize_BI | 0.212 | 0.004 | 0.236 | |
| SpidermiRvisualize_adj_matrix | 0.072 | 0.008 | 0.079 | |
| SpidermiRvisualize_degree_dist | 0.012 | 0.000 | 0.010 | |
| SpidermiRvisualize_direction | 0.224 | 0.004 | 0.307 | |
| SpidermiRvisualize_mirnanet | 0.084 | 0.000 | 0.083 | |
| SpidermiRvisualize_plot_target | 0.756 | 0.004 | 0.762 | |