Lorena Pantano
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/isomiRs |
| Branch: RELEASE_3_7 |
| Last Commit: 02c5527 |
| Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:28:47 -0400 (Wed, 17 Oct 2018).
| Package 758/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| isomiRs 1.8.0 Lorena Pantano
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: isomiRs |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings isomiRs_1.8.0.tar.gz |
| StartedAt: 2018-10-16 01:24:12 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:27:30 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 197.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: isomiRs.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings isomiRs_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/isomiRs.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isomiRs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘isomiRs’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘isomiRs’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
data 6.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘tidyr’
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.predict_correlate_mirna_targets: no visible binding for global
variable ‘mrna_de’
.predict_correlate_mirna_targets: no visible binding for global
variable ‘mirna_se’
.predict_correlate_mirna_targets: no visible binding for global
variable ‘mrna_se’
.run_enricher: no visible binding for global variable ‘sel_genes’
.run_enricher: no visible global function definition for ‘enrichGO’
.run_enricher: no visible binding for global variable ‘Count’
.viz_mirna_gene_enrichment: no visible binding for global variable ‘X1’
isoNetwork: no visible binding for global variable ‘Description’
isoNetwork: no visible binding for global variable ‘geneID’
isoPlotNet: no visible binding for global variable ‘ngene’
Undefined global functions or variables:
Count Description X1 enrichGO geneID mirna_se mrna_de mrna_se ngene
sel_genes
* 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 or elapsed time > 5s
user system elapsed
isoNetwork 7.46 0.02 7.482
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/isomiRs.Rcheck/00check.log’
for details.
isomiRs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL isomiRs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘isomiRs’ ... ** 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 * DONE (isomiRs)
isomiRs.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-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(isomiRs)
Loading required package: DiscriMiner
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
>
> test_check("isomiRs")
Dimmension of cor matrix: 20 20
Dimmension of cor matrix: 3 2
Dimmension of cor matrix: 3 2
Dimmension of cor matrix: 0 0
══ testthat results ═══════════════════════════════════════════════════════════
OK: 28 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
13.480 0.368 13.861
isomiRs.Rcheck/isomiRs-Ex.timings
| name | user | system | elapsed | |
| IsomirDataSeq | 0.780 | 0.028 | 0.878 | |
| IsomirDataSeqFromFiles | 0.380 | 0.000 | 0.377 | |
| counts | 0.760 | 0.040 | 0.799 | |
| design | 0.828 | 0.020 | 0.847 | |
| findTargets | 0.100 | 0.000 | 0.098 | |
| isoCounts | 1.112 | 0.008 | 1.120 | |
| isoDE | 1.812 | 0.032 | 1.845 | |
| isoNetwork | 7.460 | 0.020 | 7.482 | |
| isoNorm | 1.208 | 0.012 | 1.221 | |
| isoPLSDA | 1.644 | 0.000 | 1.645 | |
| isoPLSDAplot | 1.840 | 0.004 | 1.841 | |
| isoPlot | 0.708 | 0.012 | 0.721 | |
| isoPlotPosition | 1.172 | 0.036 | 1.207 | |
| isoSelect | 0.336 | 0.012 | 0.349 | |
| isoTop | 0.364 | 0.020 | 0.382 | |
| mirna2targetscan | 1.680 | 0.016 | 1.719 | |