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This page was generated on 2021-09-18 12:06:36 -0400 (Sat, 18 Sep 2021).

CHECK results for diffUTR on merida1

To the developers/maintainers of the diffUTR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffUTR.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 496/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffUTR 1.1.1  (landing page)
Pierre-Luc Germain
Snapshot Date: 2021-09-17 14:50:09 -0400 (Fri, 17 Sep 2021)
git_url: https://git.bioconductor.org/packages/diffUTR
git_branch: master
git_last_commit: dc72a02
git_last_commit_date: 2021-07-28 02:58:58 -0400 (Wed, 28 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: diffUTR
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffUTR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffUTR_1.1.1.tar.gz
StartedAt: 2021-09-18 02:17:19 -0400 (Sat, 18 Sep 2021)
EndedAt: 2021-09-18 02:23:37 -0400 (Sat, 18 Sep 2021)
EllapsedTime: 377.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: diffUTR.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffUTR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffUTR_1.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/diffUTR.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffUTR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘diffUTR’ version ‘1.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘diffUTR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
deuBinPlot: no visible binding for global variable 'x_start'
deuBinPlot: no visible binding for global variable 'x_end'
deuBinPlot: no visible binding for global variable 'y_start'
deuBinPlot: no visible binding for global variable 'y_end'
plotTopGenes: no visible binding for global variable 'sizeScore'
plotTopGenes: no visible binding for global variable 'q.value'
plotTopGenes: no visible binding for global variable 'density.ratio'
plotTopGenes: no visible binding for global variable 'geneMeanDensity'
plotTopGenes: no visible binding for global variable 'w.abs.coef'
plotTopGenes: no visible binding for global variable 'tmp'
plotTopGenes: no visible binding for global variable 'name'
Undefined global functions or variables:
  density.ratio geneMeanDensity name q.value sizeScore tmp w.abs.coef
  x_end x_start y_end y_start
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘diffUTR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: countFeatures
> ### Title: countFeatures
> ### Aliases: countFeatures
> 
> ### ** Examples
> 
> data("example_gene_annotation", package="diffUTR")
> bins <- prepareBins(example_gene_annotation)
Preparing annotation
Merging and disjoining bins
> bam_files <- list.files(system.file("extdata", package="diffUTR"),
+                         pattern="bam$", full=TRUE)
> se <- countFeatures(bam_files, bins, verbose=FALSE)

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.7.3

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           example1.bam                                     ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : /tmp/RtmpCCg9nd                                  ||
||                 Threads : 1                                                ||
||                   Level : feature level                                    ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid78601 ...         ||
||    Features : 3220                                                         ||
||    Meta-features : 3220                                                    ||
||    Chromosomes/contigs : 20                                                ||
||                                                                            ||
|| Process BAM file example1.bam...                                           ||
||    Single-end reads are included.                                          ||
||    Total alignments : 1000                                                 ||
||    Successfully assigned alignments : 0 (0.0%)                             ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

Error in file.remove(fout_annot) : object 'fout_annot' not found
Calls: countFeatures -> <Anonymous> -> file.remove
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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/diffUTR.Rcheck/00check.log’
for details.


Installation output

diffUTR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL diffUTR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘diffUTR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (diffUTR)

Tests output


Example timings

diffUTR.Rcheck/diffUTR-Ex.timings

nameusersystemelapsed
DEUwrappers2.9640.0584.565
addNormalizedAssays0.1690.0190.341