BioC 3.2: CHECK report for easyRNASeq on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings easyRNASeq_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/easyRNASeq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.6.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘easyRNASeq’ can be installed ... [26s/27s] 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.convertToUCSC’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [86s/94s]
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
    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'.
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.


R version 3.2.2 Patched (2015-10-08 r69496) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (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.

> BiocGenerics:::testPackage("easyRNASeq")
Loading required package: GenomicRanges
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, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unlist, unsplit

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Warning messages:
1: Getting the organism name is deprecated. Use an AnnotParam object instead and get its datasource. 
2: Getting the organism name is deprecated. Use an AnnotParam object instead and get its datasource. 
Timing stopped at: 0.017 0.002 5.459 
Error in dataset %in% listDatasets(useMart(biomart = "ensembl"))$dataset : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

No validation performed at that stage
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Timing stopped at: 0.012 0.001 1.627 
Error in dataset %in% listDatasets(useMart(biomart = "ensembl"))$dataset : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2



RUNIT TEST PROTOCOL -- Tue Nov 10 04:29:52 2015 
*********************************************** 
Number of test functions: 21 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
easyRNASeq RUnit Tests - 21 test functions, 2 errors, 0 failures
ERROR in test_getAnnotation_BiomaRt: Error in dataset %in% listDatasets(useMart(biomart = "ensembl"))$dataset : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

ERROR in test_internal_getAnnotation: Error in dataset %in% listDatasets(useMart(biomart = "ensembl"))$dataset : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2


Test files with failing tests

   test_annotations.R 
     test_getAnnotation_BiomaRt 
     test_internal_getAnnotation 


Error in BiocGenerics:::testPackage("easyRNASeq") : 
  unit tests failed for package easyRNASeq
In addition: 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'.
Execution halted

* installing *source* package ‘easyRNASeq’ ...
** R
** inst
** preparing 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’
Creating a generic function for ‘print’ from package ‘base’ in package ‘easyRNASeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (easyRNASeq)

name	user	system	elapsed
DESeq-methods	0.001	0.000	0.001
GenomicRanges-methods	0.709	0.016	0.725
IRanges-methods	0.001	0.000	0.001
Rsamtools-methods	0.063	0.007	0.195
ShortRead-methods	0.002	0.000	0.002
easyRNASeq-AnnotParam-accessors	0.003	0.000	0.004
easyRNASeq-AnnotParam-class	0.001	0.001	0.002
easyRNASeq-AnnotParam	0.002	0.000	0.002
easyRNASeq-BamFileList	0.179	0.010	0.213
easyRNASeq-BamParam-accessors	0.002	0.000	0.002
easyRNASeq-BamParam-class	0.001	0.000	0.001
easyRNASeq-BamParam	0.003	0.000	0.004
easyRNASeq-RnaSeqParam-accessors	0.006	0.000	0.006
easyRNASeq-RnaSeqParam-class	0.001	0.000	0.002
easyRNASeq-RnaSeqParam	0.008	0.000	0.008
easyRNASeq-accessors	0.004	0.001	0.004
easyRNASeq-annotation-methods	0.001	0.000	0.001
easyRNASeq-class	0.001	0.001	0.002
easyRNASeq-correction-methods	0.001	0.000	0.002
easyRNASeq-coverage-methods	0.001	0.000	0.001
easyRNASeq-easyRNASeq	0.002	0.000	0.002
easyRNASeq-island-methods	0.001	0.000	0.002
easyRNASeq-package	0.002	0.000	0.002
easyRNASeq-simpleRNASeq	0.001	0.000	0.002
easyRNASeq-summarization-methods	0.001	0.000	0.002
easyRNASeq-synthetic-transcripts	0.001	0.000	0.001
edgeR-methods	0.001	0.001	0.001
genomeIntervals-methods	0.000	0.000	0.001
parallel-methods	0.000	0.000	0.001

BioC 3.2: CHECK report for easyRNASeq on perceval

Summary

Command output