Lorena Pantano
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/isomiRs |
| Branch: RELEASE_3_8 |
| Last Commit: 92e8540 |
| Last Changed Date: 2019-01-04 13:05:59 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:51:59 -0400 (Tue, 16 Apr 2019).
| Package 802/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| isomiRs 1.10.1 Lorena Pantano
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: isomiRs |
| Version: 1.10.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings isomiRs_1.10.1.tar.gz |
| StartedAt: 2019-04-16 00:54:45 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:58:52 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 246.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: isomiRs.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings isomiRs_1.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/isomiRs.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 ‘isomiRs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘isomiRs’ version ‘1.10.1’
* 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 ... 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
isoPlot: no visible binding for global variable ‘iso_sample’
isoPlotPosition: no visible binding for global variable ‘iso_sample’
mirna2targetscan: no visible binding for global variable
‘targetscan.Hs.egMIRNA’
mirna2targetscan: no visible binding for global variable
‘targetscan.Hs.egMIRBASE2FAMILY’
mirna2targetscan: no visible binding for global variable
‘targetscan.Hs.egTARGETS’
mirna2targetscan: no visible binding for global variable
‘targetscan.Hs.egTARGETSFULL’
mirna2targetscan: no visible binding for global variable
‘targetscan.Mm.egMIRNA’
mirna2targetscan: no visible binding for global variable
‘targetscan.Mm.egMIRBASE2FAMILY’
mirna2targetscan: no visible binding for global variable
‘targetscan.Mm.egTARGETS’
mirna2targetscan: no visible binding for global variable
‘targetscan.Mm.egTARGETSFULL’
Undefined global functions or variables:
iso_sample targetscan.Hs.egMIRBASE2FAMILY targetscan.Hs.egMIRNA
targetscan.Hs.egTARGETS targetscan.Hs.egTARGETSFULL
targetscan.Mm.egMIRBASE2FAMILY targetscan.Mm.egMIRNA
targetscan.Mm.egTARGETS targetscan.Mm.egTARGETSFULL
* 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 8.628 0.012 8.649
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/isomiRs.Rcheck/00check.log’
for details.
isomiRs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL isomiRs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
18.608 0.356 18.989
isomiRs.Rcheck/isomiRs-Ex.timings
| name | user | system | elapsed | |
| IsomirDataSeq | 0.392 | 0.008 | 0.425 | |
| IsomirDataSeqFromFiles | 0.404 | 0.004 | 0.407 | |
| counts | 0.128 | 0.024 | 0.151 | |
| design | 0.156 | 0.008 | 0.163 | |
| findTargets | 0.164 | 0.000 | 0.165 | |
| isoCounts | 0.996 | 0.008 | 1.006 | |
| isoDE | 4.292 | 0.008 | 4.305 | |
| isoNetwork | 8.628 | 0.012 | 8.649 | |
| isoNorm | 1.248 | 0.000 | 1.249 | |
| isoPLSDA | 1.488 | 0.028 | 1.518 | |
| isoPLSDAplot | 2.504 | 0.016 | 2.523 | |
| isoPlot | 0.776 | 0.008 | 0.787 | |
| isoPlotPosition | 0.568 | 0.000 | 0.565 | |
| isoSelect | 0.148 | 0.008 | 0.158 | |
| isoTop | 0.16 | 0.00 | 0.16 | |
| mirna2targetscan | 1.948 | 0.028 | 2.222 | |