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This page was generated on 2022-08-12 13:23:22 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 NxtIRFcore on merida1


To the developers/maintainers of the NxtIRFcore package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NxtIRFcore.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 1346/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NxtIRFcore 1.2.1  (landing page)
Alex Chit Hei Wong
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/NxtIRFcore
git_branch: RELEASE_3_15
git_last_commit: b13e810
git_last_commit_date: 2022-06-22 07:29:58 -0400 (Wed, 22 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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    OK    OK  UNNEEDED, same version is already published

Summary

Package: NxtIRFcore
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NxtIRFcore_1.2.1.tar.gz
StartedAt: 2022-08-12 05:32:42 -0400 (Fri, 12 Aug 2022)
EndedAt: 2022-08-12 05:43:30 -0400 (Fri, 12 Aug 2022)
EllapsedTime: 647.7 seconds
RetCode: 0
Status:   OK  
CheckDir: NxtIRFcore.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NxtIRFcore_1.2.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/NxtIRFcore.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NxtIRFcore/DESCRIPTION’ ... OK
* this is package ‘NxtIRFcore’ version ‘1.2.1’
* 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 ‘NxtIRFcore’ 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 ... OK
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
BuildReference 25.889  0.387  26.390
CollateData    21.341  0.739  22.174
Plot_Coverage   8.307  0.137   8.471
IRFinder        4.435  1.530   3.355
NxtSE-class     5.161  0.448   5.629
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/NxtIRFcore.Rcheck/00check.log’
for details.



Installation output

NxtIRFcore.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘NxtIRFcore’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c FastaReader.cpp -o FastaReader.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c GZTools.cpp -o GZTools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c IRFinder.cpp -o IRFinder.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include   -DRNXTIRF -fPIC  -Wall -g -O2  -c covTools.cpp -o covTools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o NxtIRFcore.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o IRFinder.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o covTools.o -DRNXTIRF -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-NxtIRFcore/00new/NxtIRFcore/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NxtIRFcore)

Tests output

NxtIRFcore.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.

> library(testthat)
> library(NxtIRFcore)
Loading required package: NxtIRFdata
> 
> test_check("NxtIRFcore")
Aug 12 05:42:31 Reference generated without non-polyA reference
Aug 12 05:42:31 Reference generated without Mappability reference
Aug 12 05:42:31 Reference generated without Blacklist exclusion
Aug 12 05:42:31 Converting FASTA to local TwoBitFile...done
Aug 12 05:42:32 Connecting to genome TwoBitFile...done
Aug 12 05:42:32 Making local copy of GTF file...done
Aug 12 05:42:32 Reading source GTF file...done
Aug 12 05:42:33 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Aug 12 05:42:36 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Aug 12 05:42:41 Generating IRFinder reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
IRFinder reference generation completed
Aug 12 05:42:50 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

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done
Aug 12 05:42:53 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Aug 12 05:42:55 Splice Annotations Filtered
Aug 12 05:42:55 Translating Alternate Splice Peptides...done
Aug 12 05:42:57 Splice Annotations finished

Reference build finished
Aug 12 05:42:57 Running IRFinder
Aug 12 05:42:57 Using MulticoreParam 1 threads
Aug 12 05:42:58 IRFinder processed RtmpuTnKQm/02H003.bam
Aug 12 05:42:59 IRFinder processed RtmpuTnKQm/02H025.bam
Aug 12 05:43:00 IRFinder processed RtmpuTnKQm/02H026.bam
Aug 12 05:43:01 IRFinder processed RtmpuTnKQm/02H033.bam
Aug 12 05:43:01 IRFinder processed RtmpuTnKQm/02H043.bam
Aug 12 05:43:02 IRFinder processed RtmpuTnKQm/02H046.bam
Aug 12 05:43:02 Validating Experiment; checking COV files...
Aug 12 05:43:02 Using MulticoreParam 1 threads
Aug 12 05:43:02 Compiling Sample Stats
Aug 12 05:43:02 Compiling Junction List...merging...done
Aug 12 05:43:03 Compiling Intron Retention List...done
Aug 12 05:43:05 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done

Aug 12 05:43:08 Generating NxtIRF assays
Aug 12 05:43:08 Using MulticoreParam 1 threads

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Building Final SummarizedExperiment Object

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NxtIRF Collation Finished
Aug 12 05:43:14 Loading NxtSE object from file...done

Aug 12 05:43:15 Removing overlapping introns...
Aug 12 05:43:15 Iterating through IR events to determine introns of main isoforms
Aug 12 05:43:15 Iteration 1
Aug 12 05:43:15 Iteration 2
NxtIRF was compiled without OpenMP
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 16 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 16 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
   user  system elapsed 
 74.724   2.327  77.353 

Example timings

NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings

nameusersystemelapsed
ASE-methods1.4190.1011.525
BuildReference25.889 0.38726.390
CollateData21.341 0.73922.174
CoordToGR0.0300.0010.032
Coverage1.9050.0601.989
Find_Samples0.0100.0040.014
IRFinder4.4351.5303.355
IsCOV0.0130.0210.036
MakeSE2.8710.4073.297
Mappability-methods0.0710.0140.086
NxtFilter-class0.1260.0160.142
NxtSE-class5.1610.4485.629
Plot_Coverage8.3070.1378.471
Run_NxtIRF_Filters1.1320.0081.143
STAR-methods0.0050.0040.009
example-NxtIRF-data0.0140.0040.018
make_plot_data0.0780.0010.079
theme_white0.2310.0020.234