Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-26 15:05:48 -0500 (Fri, 26 Nov 2021).

CHECK results for easyRNASeq on machv2

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? here 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 556/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
easyRNASeq 2.30.0  (landing page)
Nicolas Delhomme
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/easyRNASeq
git_branch: RELEASE_3_14
git_last_commit: deeb59e
git_last_commit_date: 2021-10-26 12:01:41 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: easyRNASeq
Version: 2.30.0
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_2.30.0.tar.gz
StartedAt: 2021-11-25 16:12:12 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 16:28:13 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 960.6 seconds
RetCode: 0
Status:   OK  
CheckDir: easyRNASeq.Rcheck
Warnings: 0

Command output

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###
### 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_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/easyRNASeq.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.30.0’
* 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          156.974  2.956 165.360
easyRNASeq-package               104.432  2.373 110.586
easyRNASeq-synthetic-transcripts  71.986  0.690  73.393
BiocFileCache-methods             31.539  1.148  47.008
easyRNASeq-BamFileList            21.680  0.584  26.205
Rsamtools-methods                 17.332  0.493  20.941
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.



Installation output

easyRNASeq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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, 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
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 Nov 25 16:28:01 2021 
*********************************************** 
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: 791e21676cf8_TTGCGA.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 791e21676cf8_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.
3: In FUN(X[[i]], ...) :
  Bam file: 791e430de552_ATGGCT.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 791e430de552_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: 791e470e0b83_ACACTG.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 791e470e0b83_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.
7: In FUN(X[[i]], ...) :
  Bam file: 791e6baf31f6_ACTAGC.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 791e6baf31f6_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.
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 
138.129   2.982 170.960 

Example timings

easyRNASeq.Rcheck/easyRNASeq-Ex.timings

nameusersystemelapsed
BiocFileCache-methods31.539 1.14847.008
GenomicRanges-methods0.6200.0220.643
IRanges-methods0.0000.0000.001
Rsamtools-methods17.332 0.49320.941
ShortRead-methods0.0010.0010.001
easyRNASeq-AnnotParam-accessors1.1800.0471.432
easyRNASeq-AnnotParam-class0.0020.0000.002
easyRNASeq-AnnotParam1.1870.0271.461
easyRNASeq-BamFileList21.680 0.58426.205
easyRNASeq-BamParam-accessors0.0020.0000.001
easyRNASeq-BamParam-class0.0010.0010.001
easyRNASeq-BamParam0.0020.0000.003
easyRNASeq-RnaSeqParam-accessors0.0030.0000.003
easyRNASeq-RnaSeqParam-class0.0000.0000.001
easyRNASeq-RnaSeqParam0.0030.0010.004
easyRNASeq-accessors0.0000.0010.000
easyRNASeq-annotation-methods0.0010.0000.001
easyRNASeq-class0.0010.0010.001
easyRNASeq-correction-methods0.0000.0010.001
easyRNASeq-coverage-methods000
easyRNASeq-easyRNASeq0.0010.0000.001
easyRNASeq-island-methods000
easyRNASeq-package104.432 2.373110.586
easyRNASeq-simpleRNASeq156.974 2.956165.360
easyRNASeq-summarization-methods0.0010.0010.001
easyRNASeq-synthetic-transcripts71.986 0.69073.393
edgeR-methods0.0010.0010.001
genomeIntervals-methods2.9331.1444.740
parallel-methods0.0000.0010.001