Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-07 11:06:47 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for easyRNASeq on merida1


To the developers/maintainers of the easyRNASeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/easyRNASeq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 577/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
easyRNASeq 2.35.0  (landing page)
Nicolas Delhomme
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/easyRNASeq
git_branch: master
git_last_commit: 04012c4
git_last_commit_date: 2022-11-01 11:06:37 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: easyRNASeq
Version: 2.35.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings easyRNASeq_2.35.0.tar.gz
StartedAt: 2023-02-07 01:00:41 -0500 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 01:23:51 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 1389.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: easyRNASeq.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings easyRNASeq_2.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.35.0’
* 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 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          177.016  2.503 238.025
easyRNASeq-package               111.968  2.698 154.006
easyRNASeq-synthetic-transcripts  89.269  1.641 119.932
BiocFileCache-methods             19.720  1.710  34.729
easyRNASeq-BamFileList            10.146  0.762  16.277
Rsamtools-methods                  7.893  0.588  12.573
* 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: 12c013844684b_ATGGCT.bam is considered unstranded.
  4: In FUN(X[[i]], ...) :
    Bam file: 12c013844684b_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: 12c015e1fe5eb_TTGCGA.bam is considered unstranded.
  6: In FUN(X[[i]], ...) :
    Bam file: 12c015e1fe5eb_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: 12c019b163bf_ACACTG.bam is considered unstranded.
  8: In FUN(X[[i]], ...) :
    Bam file: 12c019b163bf_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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.


Installation output

easyRNASeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL easyRNASeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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)

Tests output

easyRNASeq.Rcheck/tests/runTests.Rout.fail


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
No methods found in package 'BiocGenerics' for request: 'clusterApply' when loading '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

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: 0.068 0.005 10.75
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 10001 milliseconds with 0 bytes received
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 -- Tue Feb  7 01:23:35 2023 
*********************************************** 
Number of test functions: 20 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
easyRNASeq RUnit Tests - 20 test functions, 1 error, 0 failures
ERROR in test_getAnnotation_BiomaRt: 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 10001 milliseconds with 0 bytes received

Test files with failing tests

   test_annotations.R 
     test_getAnnotation_BiomaRt 


Error in BiocGenerics:::testPackage("easyRNASeq") : 
  unit tests failed for package easyRNASeq
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
  Bam file: 12c0123889250_ACTAGC.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 12c0123889250_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: 12c013844684b_ATGGCT.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 12c013844684b_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: 12c015e1fe5eb_TTGCGA.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 12c015e1fe5eb_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: 12c019b163bf_ACACTG.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 12c019b163bf_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

Example timings

easyRNASeq.Rcheck/easyRNASeq-Ex.timings

nameusersystemelapsed
BiocFileCache-methods19.720 1.71034.729
GenomicRanges-methods0.6410.0240.857
IRanges-methods0.0010.0010.000
Rsamtools-methods 7.893 0.58812.573
ShortRead-methods0.0000.0010.002
easyRNASeq-AnnotParam-accessors0.6450.0440.955
easyRNASeq-AnnotParam-class0.0010.0000.004
easyRNASeq-AnnotParam0.5960.0370.901
easyRNASeq-BamFileList10.146 0.76216.277
easyRNASeq-BamParam-accessors0.0030.0000.003
easyRNASeq-BamParam-class0.0000.0000.001
easyRNASeq-BamParam0.0040.0010.004
easyRNASeq-RnaSeqParam-accessors0.0060.0010.008
easyRNASeq-RnaSeqParam-class0.0010.0000.005
easyRNASeq-RnaSeqParam0.0060.0000.007
easyRNASeq-accessors000
easyRNASeq-annotation-methods0.0000.0010.001
easyRNASeq-class0.0010.0000.001
easyRNASeq-correction-methods000
easyRNASeq-coverage-methods0.0000.0010.000
easyRNASeq-easyRNASeq0.0010.0010.001
easyRNASeq-island-methods0.0000.0000.001
easyRNASeq-package111.968 2.698154.006
easyRNASeq-simpleRNASeq177.016 2.503238.025
easyRNASeq-summarization-methods0.0000.0010.001
easyRNASeq-synthetic-transcripts 89.269 1.641119.932
edgeR-methods000
genomeIntervals-methods2.3800.4974.124
parallel-methods0.0000.0000.001