Lorena Pantano
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/isomiRs |
| Branch: master |
| Last Commit: 652a788 |
| Last Changed Date: 2018-12-03 12:53:08 -0400 (Mon, 03 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:15:58 -0400 (Tue, 09 Apr 2019).
| Package 826/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| isomiRs 1.11.1 Lorena Pantano
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: isomiRs |
| Version: 1.11.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings isomiRs_1.11.1.tar.gz |
| StartedAt: 2019-04-09 02:58:43 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:04:55 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 372.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: isomiRs.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings isomiRs_1.11.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/isomiRs.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.11.1’
* 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
.clean_noise: no visible binding for global variable ‘total’
.clean_noise: no visible binding for global variable ‘pct’
.clean_noise: no visible global function definition for ‘prop.test’
.clean_noise: no visible binding for global variable ‘prop’
.clean_noise: no visible binding for global variable ‘hits’
.clean_noise: no visible binding for global variable ‘p.value’
.clean_noise: no visible binding for global variable ‘fdr’
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:
fdr hits iso_sample p.value pct prop prop.test
targetscan.Hs.egMIRBASE2FAMILY targetscan.Hs.egMIRNA
targetscan.Hs.egTARGETS targetscan.Hs.egTARGETSFULL
targetscan.Mm.egMIRBASE2FAMILY targetscan.Mm.egMIRNA
targetscan.Mm.egTARGETS targetscan.Mm.egTARGETSFULL total
Consider adding
importFrom("stats", "prop.test")
to your NAMESPACE file.
* 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 12.197 0.280 12.477
isoDE 5.770 0.098 5.869
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/isomiRs.Rcheck/00check.log’
for details.
isomiRs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL isomiRs ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘isomiRs’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang Registered S3 method overwritten by 'GGally': method from +.gg ggplot2 ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (isomiRs)
isomiRs.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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(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, 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, rowsum
>
> 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
25.642 2.189 27.793
isomiRs.Rcheck/isomiRs-Ex.timings
| name | user | system | elapsed | |
| IsomirDataSeq | 0.520 | 0.044 | 0.567 | |
| IsomirDataSeqFromFiles | 0.567 | 0.022 | 0.590 | |
| counts | 0.141 | 0.032 | 0.172 | |
| design | 0.254 | 0.039 | 0.293 | |
| findTargets | 0.182 | 0.004 | 0.185 | |
| isoCounts | 1.097 | 0.067 | 1.165 | |
| isoDE | 5.770 | 0.098 | 5.869 | |
| isoNetwork | 12.197 | 0.280 | 12.477 | |
| isoNorm | 1.556 | 0.069 | 1.625 | |
| isoPLSDA | 2.454 | 0.338 | 2.792 | |
| isoPLSDAplot | 2.801 | 0.295 | 3.096 | |
| isoPlot | 1.015 | 0.069 | 1.085 | |
| isoPlotPosition | 0.864 | 0.031 | 0.895 | |
| isoSelect | 0.145 | 0.035 | 0.179 | |
| isoTop | 0.289 | 0.047 | 0.337 | |
| mirna2targetscan | 2.861 | 0.189 | 3.076 | |