Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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

Package 616/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
easyRNASeq 2.43.0  (landing page)
Nicolas Delhomme
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/easyRNASeq
git_branch: devel
git_last_commit: d32c68e
git_last_commit_date: 2024-10-29 09:39:50 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for easyRNASeq on kunpeng2

To the developers/maintainers of the easyRNASeq package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: easyRNASeq
Version: 2.43.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings easyRNASeq_2.43.0.tar.gz
StartedAt: 2024-12-24 06:21:07 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 06:35:28 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 860.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: easyRNASeq.Rcheck
Warnings: 6

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings easyRNASeq_2.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.43.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck/00install.out’ for details.
* 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 code 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
Warning: program compiled against libxml 212 using older 211

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... NOTE
checkRd: (-1) easyRNASeq-AnnotParam.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-AnnotParam.Rd:44-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-RnaSeqParam-class.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-RnaSeqParam-class.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-annotation-methods.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-annotation-methods.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-correction-methods.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-correction-methods.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-datasets.Rd:11-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-internal-AnnotParam-methods.Rd:25: Lost braces
    25 | These are \code{\linkS4class{AnnotParam}}{AnnotParam} class internal methods:
       |                                          ^
checkRd: (-1) easyRNASeq-package.Rd:109-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-package.Rd:113-121: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BiocFileCache-methods.Rd: BiocFileCache-class
  GenomicRanges-methods.Rd: GRangesList-class, GAlignments-class,
    DataFrame-class
  IRanges-methods.Rd: IRangesList-class
  Rsamtools-methods.Rd: BamFile-class
  ShortRead-methods.Rd: AlignedRead-class, SRFilter-class
  basename-methods.Rd: BamFile-class
  easyRNASeq-annotation-internal-methods.Rd:
    Genome_intervals_stranded-class
  easyRNASeq-class.Rd: GRangesList-class, RleList-class
  easyRNASeq-coverage-methods.Rd: Rle-class
  easyRNASeq-easyRNASeq.Rd: GRangesList-class
  easyRNASeq-simpleRNASeq.Rd: BamFile-class
  edgeR-methods.Rd: DGEList-class
  file.exists-methods.Rd: BamFile-class
  genomeIntervals-methods.Rd: Genome_intervals-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'easyRNASeq-annotation-internal-methods.Rd':
  ‘annotation.type’ ‘fields’ ‘filename’ ‘format’ ‘gAnnot’ ‘nbCore’

Objects in \usage without \alias in Rd file 'easyRNASeq-coverage-methods.Rd':
  ‘\S4method{fetchCoverage}{RNAseq}’

Documented arguments not in \usage in Rd file 'easyRNASeq-internal-AnnotParam-methods.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'easyRNASeq-internal-methods.Rd':
  ‘arg’ ‘chr.names’ ‘fun’ ‘organism’ ‘type’ ‘value’ ‘x’ ‘...’

Documented arguments not in \usage in Rd file 'easyRNASeq-summarization-internal-methods.Rd':
  ‘chr.map’ ‘chr.sel’ ‘cList’ ‘count’ ‘filename’ ‘filter’ ‘format’
  ‘gapped’ ‘min.cov’ ‘min.length’ ‘max.gap’ ‘plot’ ‘rnaSeq’
  ‘summarization’ ‘silent’ ‘subType’ ‘type’ ‘validity.check’ ‘values’
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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          88.762  0.903 107.763
easyRNASeq-package               60.536  1.012  75.612
easyRNASeq-synthetic-transcripts 41.844  0.227  44.484
BiocFileCache-methods            15.809  0.830  67.348
easyRNASeq-BamFileList           11.265  0.391  22.041
Rsamtools-methods                 8.951  0.266  17.374
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.


Installation output

easyRNASeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL easyRNASeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘easyRNASeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
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
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (easyRNASeq)

Tests output

easyRNASeq.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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)
Warning: program compiled against libxml 212 using older 211
> 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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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 -- Tue Dec 24 06:35:22 2024 
*********************************************** 
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: 410b44d62000e_ATGGCT.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 410b44d62000e_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.
3: In FUN(X[[i]], ...) :
  Bam file: 410b453c98b25_ACTAGC.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 410b453c98b25_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.
5: In FUN(X[[i]], ...) :
  Bam file: 410b46d917320_TTGCGA.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 410b46d917320_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: 410b476b3401a_ACACTG.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 410b476b3401a_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 
 95.210   6.083 158.237 

Example timings

easyRNASeq.Rcheck/easyRNASeq-Ex.timings

nameusersystemelapsed
BiocFileCache-methods15.809 0.83067.348
GenomicRanges-methods0.4560.0120.469
IRanges-methods0.0010.0000.000
Rsamtools-methods 8.951 0.26617.374
ShortRead-methods000
easyRNASeq-AnnotParam-accessors0.4620.0250.773
easyRNASeq-AnnotParam-class0.0010.0000.001
easyRNASeq-AnnotParam0.4550.0200.787
easyRNASeq-BamFileList11.265 0.39122.041
easyRNASeq-BamParam-accessors0.0010.0010.001
easyRNASeq-BamParam-class000
easyRNASeq-BamParam0.0020.0000.002
easyRNASeq-RnaSeqParam-accessors0.0030.0000.003
easyRNASeq-RnaSeqParam-class0.0010.0000.001
easyRNASeq-RnaSeqParam0.0040.0000.004
easyRNASeq-accessors0.0010.0000.001
easyRNASeq-annotation-methods000
easyRNASeq-class000
easyRNASeq-correction-methods000
easyRNASeq-coverage-methods000
easyRNASeq-easyRNASeq000
easyRNASeq-island-methods0.0010.0000.000
easyRNASeq-package60.536 1.01275.612
easyRNASeq-simpleRNASeq 88.762 0.903107.763
easyRNASeq-summarization-methods000
easyRNASeq-synthetic-transcripts41.844 0.22744.484
edgeR-methods000
genomeIntervals-methods1.6760.0603.134
parallel-methods0.0010.0000.000