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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings easyRNASeq_2.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.35.0’
* 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 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 ... 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          90.232  0.703 109.339
easyRNASeq-package               57.962  0.904  77.700
easyRNASeq-synthetic-transcripts 39.371  0.119  43.708
BiocFileCache-methods            13.055  0.808  78.737
easyRNASeq-BamFileList            8.818  0.338  23.240
Rsamtools-methods                 6.834  0.289  22.196
* 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:
  3: In FUN(X[[i]], ...) :
    Bam file: 2baec1607f22_TTGCGA.bam is considered unstranded.
  4: In FUN(X[[i]], ...) :
    Bam file: 2baec1607f22_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.
  5: In FUN(X[[i]], ...) :
    Bam file: 2baec164bab29e_ATGGCT.bam is considered unstranded.
  6: In FUN(X[[i]], ...) :
    Bam file: 2baec164bab29e_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: 2baec175d93bd9_ACACTG.bam is considered unstranded.
  8: In FUN(X[[i]], ...) :
    Bam file: 2baec175d93bd9_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'.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘simpleRNASeq.Rmd’ using ‘UTF-8’... OK
  ‘easyRNASeq.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘simpleRNASeq.Rmd’ using rmarkdown
Killed
--- re-building ‘easyRNASeq.Rnw’ using Sweave
--- finished re-building ‘easyRNASeq.Rnw’

/home/biocbuild/bbs-3.17-bioc/R/bin/R CMD Sweave easyRNASeq.Rnw
Output file:  easyRNASeq.tex
/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "tools::texi2pdf('easyRNASeq.tex')"
/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "rmarkdown::render('simpleRNASeq.Rmd')"


processing file: simpleRNASeq.Rmd


processing file: ./Chapters/01-Introduction.Rmd


processing file: ./Chapters/02-AnnotParam.Rmd


processing file: ./Chapters/03-SyntheticTranscripts.Rmd
Killed
make: *** [Makefile:14: html] Error 137
Error in tools::buildVignettes(dir = "/home/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck/vign_test/easyRNASeq",  : 
  running 'make' failed
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL easyRNASeq
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* installing to library ‘/home/biocbuild/bbs-3.17-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
** 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)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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] "/home/biocbuild/.cache/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

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, aperm, 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
Loading required package: GenomeInfoDb
Timing stopped at: 0.157 0.033 20.53
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www.ensembl.org:443] Operation timed out after 10001 milliseconds with 0 bytes received
No validation performed at that stage
Timing stopped at: 0.054 0.007 10.89
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 0 bytes received


RUNIT TEST PROTOCOL -- Tue Feb  7 00:50:35 2023 
*********************************************** 
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_getAnnotation_BiomaRt: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www.ensembl.org:443] Operation timed out after 10001 milliseconds with 0 bytes received
ERROR in test_internal_getAnnotation: Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 0 bytes received

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: 2baec124f7afe7_ACTAGC.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 2baec124f7afe7_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: 2baec1607f22_TTGCGA.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 2baec1607f22_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.
5: In FUN(X[[i]], ...) :
  Bam file: 2baec164bab29e_ATGGCT.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 2baec164bab29e_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: 2baec175d93bd9_ACACTG.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 2baec175d93bd9_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'.
Execution halted