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CHECK report for easyRNASeq on merida2

This page was generated on 2019-03-21 15:13:25 -0400 (Thu, 21 Mar 2019).

Package 461/1676HostnameOS / ArchINSTALLBUILDCHECK
easyRNASeq 2.19.2
Nicolas Delhomme
Snapshot Date: 2019-03-20 17:01:06 -0400 (Wed, 20 Mar 2019)
URL: https://git.bioconductor.org/packages/easyRNASeq
Branch: master
Last Commit: f5bddc5
Last Changed Date: 2018-12-03 06:50:12 -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  WARNINGS UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ]

Summary

Package: easyRNASeq
Version: 2.19.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings easyRNASeq_2.19.2.tar.gz
StartedAt: 2019-03-21 00:33:28 -0400 (Thu, 21 Mar 2019)
EndedAt: 2019-03-21 00:42:54 -0400 (Thu, 21 Mar 2019)
EllapsedTime: 566.0 seconds
RetCode: 0
Status:  OK 
CheckDir: easyRNASeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings easyRNASeq_2.19.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/easyRNASeq.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.19.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/01-Introduction.Rmd’
   ‘inst/doc/02-AnnotParam.Rmd’
   ‘inst/doc/03-SyntheticTranscripts.Rmd’
   ‘inst/doc/04-BamParam.Rmd’
   ‘inst/doc/05-RnaSeqParam.Rmd’
   ‘inst/doc/06-simpleRNASeq.Rmd’
   ‘inst/doc/08-Session-Info.Rmd’
   ‘inst/doc/09-Acknowledgments.Rmd’
   ‘inst/doc/10-Foonotes.Rmd’
   ‘inst/doc/11-Images.Rmd’
   ‘inst/doc/12-Appendix.Rmd’
(Is a VignetteBuilder field missing?)
* 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 ‘easyRNASeq’ 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 ... OK
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
easyRNASeq-simpleRNASeq          93.993  1.951  97.601
easyRNASeq-package               68.095  1.391  71.052
easyRNASeq-synthetic-transcripts 59.851  0.997  62.115
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.



Installation output

easyRNASeq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL easyRNASeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘easyRNASeq’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘basename’ from package ‘base’ in package ‘easyRNASeq’
Creating a generic function for ‘file.exists’ from package ‘base’ in package ‘easyRNASeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (easyRNASeq)

Tests output

easyRNASeq.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.

> # get the example data and annotation files from GitHub using curl
> library(curl)
> exFiles <- c("gAnnot.rda",
+               "Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz",
+               "Dmel-mRNA-exon-r5.52.gff3.gz",
+               "ACACTG.bam","ACTAGC.bam","ATGGCT.bam","TTGCGA.bam",
+               "ACACTG.bam.bai","ACTAGC.bam.bai","ATGGCT.bam.bai","TTGCGA.bam.bai")
> 
> invisible(sapply(exFiles,function(f){
+      if(!file.exists(f)){
+          invisible(curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
+                                     "master/tutorial/easyRNASeq/",f),f))
+      }
+  }))
> 
> # run the tests
> BiocGenerics:::testPackage("easyRNASeq")
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 object is masked from 'package:easyRNASeq':

    basename

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
No validation performed at that stage
Validated a datasource of type biomaRt
No validation performed at that stage
Validated a datasource of type rda
Read 1000 records
Validated a datasource of type gtf
Read 999 records
Validated a datasource of type gff3


RUNIT TEST PROTOCOL -- Thu Mar 21 00:42:46 2019 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
easyRNASeq RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
There were 21 warnings (use warnings() to see them)
> 
> # cleanup
> file.remove(exFiles)
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> 
> proc.time()
   user  system elapsed 
 56.874   1.746  68.515 

Example timings

easyRNASeq.Rcheck/easyRNASeq-Ex.timings

nameusersystemelapsed
DESeq-methods0.0000.0000.001
GenomicRanges-methods0.3900.0140.410
IRanges-methods0.0010.0000.001
Rsamtools-methods0.6630.0411.791
ShortRead-methods0.0010.0000.001
easyRNASeq-AnnotParam-accessors0.0170.0100.329
easyRNASeq-AnnotParam-class0.0010.0010.001
easyRNASeq-AnnotParam0.0110.0050.243
easyRNASeq-BamFileList0.0810.0310.662
easyRNASeq-BamParam-accessors0.0020.0000.002
easyRNASeq-BamParam-class0.0010.0000.001
easyRNASeq-BamParam0.0030.0000.003
easyRNASeq-RnaSeqParam-accessors0.0040.0010.004
easyRNASeq-RnaSeqParam-class0.0000.0000.001
easyRNASeq-RnaSeqParam0.0060.0010.006
easyRNASeq-accessors0.0000.0010.000
easyRNASeq-annotation-methods000
easyRNASeq-class0.0010.0000.001
easyRNASeq-correction-methods0.0000.0000.001
easyRNASeq-coverage-methods0.0010.0000.001
easyRNASeq-easyRNASeq0.0000.0000.001
easyRNASeq-island-methods0.0000.0010.001
easyRNASeq-package68.095 1.39171.052
easyRNASeq-simpleRNASeq93.993 1.95197.601
easyRNASeq-summarization-methods0.0010.0000.001
easyRNASeq-synthetic-transcripts59.851 0.99762.115
edgeR-methods0.0000.0010.001
genomeIntervals-methods2.0550.0792.494
parallel-methods0.0000.0000.001