Multiple platform build/check report for BioC 3.7 - CHECK report for easyRNASeq on merida2

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### Running command:
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###   /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_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/easyRNASeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.16.0’
* 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          96.683  1.967  99.981
easyRNASeq-package               66.356  1.657  69.768
easyRNASeq-synthetic-transcripts 56.134  1.493  58.645
* 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-3.7-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL easyRNASeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, 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
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 -- Tue Oct 16 21:16:29 2018 
*********************************************** 
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 
Warning messages:
1: In FUN(X[[i]], ...) : Bam file: ACACTG.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: ACACTG.bam Strandedness could not be determined using 18615 regions spanning 1300192 bp on either strand at a 90% cutoff; 73.67 percent appear to be stranded.
3: In FUN(X[[i]], ...) : Bam file: ACTAGC.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: ACTAGC.bam Strandedness could not be determined using 14772 regions spanning 1023473 bp on either strand at a 90% cutoff; 76.6 percent appear to be stranded.
5: In FUN(X[[i]], ...) : Bam file: ATGGCT.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: ATGGCT.bam Strandedness could not be determined using 18462 regions spanning 1280337 bp on either strand at a 90% cutoff; 74.26 percent appear to be stranded.
7: In FUN(X[[i]], ...) : Bam file: TTGCGA.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: TTGCGA.bam Strandedness could not be determined using 19659 regions spanning 1381886 bp on either strand at a 90% cutoff; 73.37 percent appear to be stranded.
9: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) :
  You provided an incorrect BAM parameter; 'paired' should be set to 'FALSE'.
10: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) :
  As of version 2.15.5, easyRNASeq assumes that, if the data is strand specific, the sequencing was done using a protocol such as the Illumina TruSeq, where the reverse strand is quantified - i.e. the strandProtocol argument of the BamParam class defaults to 'reverse'.
> 
> # cleanup
> file.remove(exFiles)
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> 
> proc.time()
   user  system elapsed 
 59.411   1.886  70.980

Example timings

name	user	system	elapsed
DESeq-methods	0.001	0.000	0.002
GenomicRanges-methods	0.524	0.019	0.555
IRanges-methods	0.003	0.000	0.003
Rsamtools-methods	0.657	0.050	2.953
ShortRead-methods	0.005	0.000	0.006
easyRNASeq-AnnotParam-accessors	0.021	0.013	0.384
easyRNASeq-AnnotParam-class	0.002	0.001	0.003
easyRNASeq-AnnotParam	0.017	0.005	0.291
easyRNASeq-BamFileList	0.125	0.032	0.378
easyRNASeq-BamParam-accessors	0.004	0.000	0.004
easyRNASeq-BamParam-class	0.003	0.000	0.003
easyRNASeq-BamParam	0.005	0.000	0.006
easyRNASeq-RnaSeqParam-accessors	0.007	0.000	0.008
easyRNASeq-RnaSeqParam-class	0.002	0.001	0.003
easyRNASeq-RnaSeqParam	0.009	0.001	0.009
easyRNASeq-accessors	0.002	0.000	0.002
easyRNASeq-annotation-methods	0.003	0.001	0.003
easyRNASeq-class	0.002	0.000	0.002
easyRNASeq-correction-methods	0.004	0.000	0.005
easyRNASeq-coverage-methods	0.003	0.000	0.003
easyRNASeq-easyRNASeq	0.005	0.001	0.006
easyRNASeq-island-methods	0.004	0.001	0.005
easyRNASeq-package	66.356	1.657	69.768
easyRNASeq-simpleRNASeq	96.683	1.967	99.981
easyRNASeq-summarization-methods	0.004	0.000	0.005
easyRNASeq-synthetic-transcripts	56.134	1.493	58.645
edgeR-methods	0.001	0.000	0.002
genomeIntervals-methods	1.568	0.181	1.977
parallel-methods	0.001	0.001	0.001

CHECK report for easyRNASeq on merida2

Summary

Command output

Installation output

Tests output

Example timings