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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:easyRNASeq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings easyRNASeq_2.31.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/easyRNASeq.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '2.31.0'
* 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 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 ... NOTE
Namespace in Imports field not imported from: 'locfit'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.parallelize: no visible global function definition for 'clusterApply'
Undefined global functions or variables:
  clusterApply
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
easyRNASeq-simpleRNASeq          69.92   2.73   76.54
easyRNASeq-package               45.87   2.41   52.61
easyRNASeq-synthetic-transcripts 32.82   1.07   35.00
BiocFileCache-methods             8.89   1.44   24.26
easyRNASeq-BamFileList            6.50   1.05   12.38
Rsamtools-methods                 4.74   0.98    9.30
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/easyRNASeq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL easyRNASeq
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'easyRNASeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for request: 'clusterApply' when loading 'easyRNASeq'
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
    BiocFileCache-methods                   html  
    finding level-2 HTML links ... done

    GenomicRanges-methods                   html  
    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  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-easyRNASeq/00new/easyRNASeq/help/bamParam.html
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-easyRNASeq/00new/easyRNASeq/help/annotParam.html
    easyRNASeq-RnaSeqParam-class            html  
    easyRNASeq-RnaSeqParam                  html  
    easyRNASeq-accessors                    html  
    easyRNASeq-annotation-internal-methods
                                            html  
    easyRNASeq-annotation-methods           html  
    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  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-easyRNASeq/00new/easyRNASeq/help/easyRNASeq-defunct.html
    easyRNASeq-global-variables             html  
    easyRNASeq-internal-AnnotParam-methods
                                            html  
    easyRNASeq-internal-methods             html  
    easyRNASeq-island-methods               html  
    easyRNASeq-package                      html  
    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  
    parallel-methods                        html  
    print-methods                           html  
    show-methods                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'BiocGenerics' for request: 'clusterApply' when loading 'easyRNASeq'
** testing if installed package can be loaded from final location
No methods found in package 'BiocGenerics' for request: 'clusterApply' when loading 'easyRNASeq'
** testing if installed package keeps a record of temporary installation path
* DONE (easyRNASeq)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'progeny' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'spicyR' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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
> library(easyRNASeq)
No methods found in package 'BiocGenerics' for request: 'clusterApply' when loading 'easyRNASeq'
> tutorialData()
[1] "C:/Users/BIOCBU~1/AppData/Local/easyRNASeq/easyRNASeq/Cache"
> 
> # 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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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 -- Thu Mar 17 19:08:26 2022 
*********************************************** 
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: 418010925600_ACTAGC.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 418010925600_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: 41803ca87526_ATGGCT.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 41803ca87526_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: 418064361051_TTGCGA.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 418064361051_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: 41806ca72fc8_ACACTG.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 41806ca72fc8_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) :
  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
> # removebfc(easyRNASeq:::.get_cache(),ask=FALSE)
> 
> proc.time()
   user  system elapsed 
  60.06    4.21   84.03