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CHECK report for isomiRs on celaya2

This page was generated on 2019-04-09 13:15:58 -0400 (Tue, 09 Apr 2019).

Package 826/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isomiRs 1.11.1
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

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

Command output

##############################################################################
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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.



Installation output

isomiRs.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

isomiRs.Rcheck/isomiRs-Ex.timings

nameusersystemelapsed
IsomirDataSeq0.5200.0440.567
IsomirDataSeqFromFiles0.5670.0220.590
counts0.1410.0320.172
design0.2540.0390.293
findTargets0.1820.0040.185
isoCounts1.0970.0671.165
isoDE5.7700.0985.869
isoNetwork12.197 0.28012.477
isoNorm1.5560.0691.625
isoPLSDA2.4540.3382.792
isoPLSDAplot2.8010.2953.096
isoPlot1.0150.0691.085
isoPlotPosition0.8640.0310.895
isoSelect0.1450.0350.179
isoTop0.2890.0470.337
mirna2targetscan2.8610.1893.076