Package: easyRNASeq

Version: 2.16.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:easyRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings easyRNASeq_2.16.0.tar.gz

StartedAt: 2018-10-17 01:43:46 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:58:03 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 857.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: easyRNASeq.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:easyRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings easyRNASeq_2.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/easyRNASeq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'easyRNASeq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/GenomicRanges-methods.Rd:20: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/GenomicRanges-methods.Rd:22: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/GenomicRanges-methods.Rd:93: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:14: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:37: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/easyRNASeq-annotation-methods.Rd:38: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/easyRNASeq-package.Rd:133: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/genomeIntervals-methods.Rd:39: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/parallel-methods.Rd:41: file link 'makePSOCKcluster' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/parallel-methods.Rd:42: file link 'stopCluster' in package 'parallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/easyRNASeq.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
easyRNASeq-simpleRNASeq          86.22   1.05   87.87
easyRNASeq-package               47.06   5.98   53.58
easyRNASeq-synthetic-transcripts 43.78   0.91   44.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
easyRNASeq-simpleRNASeq          74.58   0.57   75.41
easyRNASeq-package               49.14   0.99   51.31
easyRNASeq-synthetic-transcripts 41.48   0.57   42.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/easyRNASeq.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/easyRNASeq_2.16.0.tar.gz && rm -rf easyRNASeq.buildbin-libdir && mkdir easyRNASeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=easyRNASeq.buildbin-libdir easyRNASeq_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL easyRNASeq_2.16.0.zip && rm easyRNASeq_2.16.0.tar.gz easyRNASeq_2.16.0.zip
###
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100  121k  100  121k    0     0  2045k      0 --:--:-- --:--:-- --:--:-- 2285k

install for i386

* 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
  converting help for package 'easyRNASeq'
    finding HTML links ... done
    DESeq-methods                           html  
    finding level-2 HTML links ... done

    GenomicRanges-methods                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/GenomicRanges-methods.Rd:20: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/GenomicRanges-methods.Rd:22: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/GenomicRanges-methods.Rd:93: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
    IRanges-methods                         html  
    Rsamtools-methods                       html  
    ShortRead-methods                       html  
    basename-methods                        html  
    easyRNASeq-AnnotParam-accessors         html  
    easyRNASeq-AnnotParam-class             html  
    easyRNASeq-AnnotParam                   html  
    easyRNASeq-BamFileList                  html  
    easyRNASeq-BamParam-accessors           html  
    easyRNASeq-BamParam-class               html  
    easyRNASeq-BamParam                     html  
    easyRNASeq-RnaSeqParam-accessors        html  
    easyRNASeq-RnaSeqParam-class            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:14: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:37: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    easyRNASeq-RnaSeqParam                  html  
    easyRNASeq-accessors                    html  
    easyRNASeq-annotation-internal-methods
                                            html  
    easyRNASeq-annotation-methods           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/easyRNASeq-annotation-methods.Rd:38: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
    easyRNASeq-class                        html  
    easyRNASeq-correction-methods           html  
    easyRNASeq-coverage-methods             html  
    easyRNASeq-datasets                     html  
    easyRNASeq-defunct-annotation-methods   html  
    easyRNASeq-defunct                      html  
    easyRNASeq-easyRNASeq                   html  
    easyRNASeq-global-variables             html  
    easyRNASeq-internal-AnnotParam-methods
                                            html  
    easyRNASeq-internal-methods             html  
    easyRNASeq-island-methods               html  
    easyRNASeq-package                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/easyRNASeq-package.Rd:133: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
    easyRNASeq-simpleRNASeq                 html  
    easyRNASeq-summarization-internal-methods
                                            html  
    easyRNASeq-summarization-methods        html  
    easyRNASeq-synthetic-transcripts        html  
    edgeR-methods                           html  
    file.exists-methods                     html  
    genomeIntervals-methods                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/genomeIntervals-methods.Rd:39: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
    parallel-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/parallel-methods.Rd:41: file link 'makePSOCKcluster' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpEHYsYT/R.INSTALL1f9478f858c4/easyRNASeq/man/parallel-methods.Rd:42: file link 'stopCluster' in package 'parallel' does not exist and so has been treated as a topic
    print-methods                           html  
    show-methods                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'easyRNASeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'easyRNASeq' as easyRNASeq_2.16.0.zip
* DONE (easyRNASeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'easyRNASeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 -- Wed Oct 17 01:56:33 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 
  59.75    2.09   85.12 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 -- Wed Oct 17 01:57:56 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 
  55.79    1.73   82.34