Multiple platform build/check report for BioC 3.11 - CHECK report for easyRNASeq on celaya2

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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_2.23.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/easyRNASeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.23.2’
* 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/07-cleanUp.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 (user + system) or elapsed time > 5s
                                    user system elapsed
easyRNASeq-simpleRNASeq          129.386  4.495 141.472
easyRNASeq-package               103.100  3.981 109.981
easyRNASeq-synthetic-transcripts  72.071  1.935  74.356
easyRNASeq-BamFileList            17.462  0.577  19.666
Rsamtools-methods                 14.903  0.765  16.949
BiocFileCache-methods             11.027  0.543  23.852
genomeIntervals-methods            4.035  0.973   6.070
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  4: In FUN(X[[i]], ...) :
    Bam file: 104dd6195ce2c_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.
  5: In FUN(X[[i]], ...) :
    Bam file: 104dd745b1c95_TTGCGA.bam is considered unstranded.
  6: In FUN(X[[i]], ...) :
    Bam file: 104dd745b1c95_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.
  7: In FUN(X[[i]], ...) :
    Bam file: 104dd7d0e7b6d_ACACTG.bam is considered unstranded.
  8: In FUN(X[[i]], ...) :
    Bam file: 104dd7d0e7b6d_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.
  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'.
  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-3.11-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/4.0/Resources/library’
* installing *source* package ‘easyRNASeq’ ...
** using staged installation
** 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 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 (easyRNASeq)

Tests output


R Under development (unstable) (2019-12-14 r77572) -- "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.

> # get the example data
> library(easyRNASeq)
> tutorialData()
[1] "/Users/biocbuild/Library/Caches/easyRNASeq"
> 
> # set the env.var
> #TUTORIAL.DATA <- get("TUTORIAL.DATA",envir=as.environment("package:easyRNASeq"))
> 
> # 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, 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, 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
Timing stopped at: 0.002 0 0.003
Error : RangedData objects are defunct. Please migrate your code to use GRanges
  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
Timing stopped at: 0.001 0 0
Error : RangedData objects are defunct. Please migrate your code to use GRanges
  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData


RUNIT TEST PROTOCOL -- Thu Jan 16 04:18:23 2020 
*********************************************** 
Number of test functions: 20 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
easyRNASeq RUnit Tests - 20 test functions, 2 errors, 0 failures
ERROR in test_AnnotParamObject: Error : RangedData objects are defunct. Please migrate your code to use GRanges
  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
ERROR in test_GRangesColnames: Error : RangedData objects are defunct. Please migrate your code to use GRanges
  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData

Test files with failing tests

   test_classes.R 
     test_AnnotParamObject 

   test_extensions.R 
     test_GRangesColnames 


Error in BiocGenerics:::testPackage("easyRNASeq") : 
  unit tests failed for package easyRNASeq
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
  Bam file: 104dd102a00d7_ACTAGC.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 104dd102a00d7_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.
3: In FUN(X[[i]], ...) :
  Bam file: 104dd6195ce2c_ATGGCT.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 104dd6195ce2c_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.
5: In FUN(X[[i]], ...) :
  Bam file: 104dd745b1c95_TTGCGA.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 104dd745b1c95_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.
7: In FUN(X[[i]], ...) :
  Bam file: 104dd7d0e7b6d_ACACTG.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 104dd7d0e7b6d_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.
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'.
Execution halted

Example timings

name	user	system	elapsed
BiocFileCache-methods	11.027	0.543	23.852
DESeq-methods	0.000	0.001	0.001
GenomicRanges-methods	0.844	0.030	0.874
IRanges-methods	0.001	0.000	0.001
Rsamtools-methods	14.903	0.765	16.949
ShortRead-methods	0.001	0.002	0.003
easyRNASeq-AnnotParam-accessors	0.976	0.052	1.117
easyRNASeq-AnnotParam-class	0.001	0.000	0.002
easyRNASeq-AnnotParam	0.932	0.030	1.045
easyRNASeq-BamFileList	17.462	0.577	19.666
easyRNASeq-BamParam-accessors	0.003	0.000	0.003
easyRNASeq-BamParam-class	0.001	0.000	0.001
easyRNASeq-BamParam	0.005	0.001	0.005
easyRNASeq-RnaSeqParam-accessors	0.005	0.001	0.006
easyRNASeq-RnaSeqParam-class	0.001	0.001	0.001
easyRNASeq-RnaSeqParam	0.008	0.002	0.009
easyRNASeq-accessors	0.000	0.000	0.001
easyRNASeq-annotation-methods	0.001	0.000	0.001
easyRNASeq-class	0.001	0.000	0.002
easyRNASeq-correction-methods	0.001	0.001	0.001
easyRNASeq-coverage-methods	0.000	0.001	0.001
easyRNASeq-easyRNASeq	0.001	0.001	0.001
easyRNASeq-island-methods	0.001	0.001	0.000
easyRNASeq-package	103.100	3.981	109.981
easyRNASeq-simpleRNASeq	129.386	4.495	141.472
easyRNASeq-summarization-methods	0.001	0.000	0.001
easyRNASeq-synthetic-transcripts	72.071	1.935	74.356
edgeR-methods	0.000	0.000	0.001
genomeIntervals-methods	4.035	0.973	6.070
parallel-methods	0.000	0.000	0.001

CHECK report for easyRNASeq on celaya2

Summary

Command output

Installation output

Tests output

Example timings