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This page was generated on 2023-03-24 11:05:26 -0400 (Fri, 24 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4546
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4307
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4299
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 nebbiolo1


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 1385/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NxtIRFcore 1.5.0  (landing page)
Alex Chit Hei Wong
Snapshot Date: 2023-03-23 14:00:15 -0400 (Thu, 23 Mar 2023)
git_url: https://git.bioconductor.org/packages/NxtIRFcore
git_branch: devel
git_last_commit: 4bdae9a
git_last_commit_date: 2022-11-01 11:26:02 -0400 (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    OK    OK  UNNEEDED, same version is already published

Summary

Package: NxtIRFcore
Version: 1.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings NxtIRFcore_1.5.0.tar.gz
StartedAt: 2023-03-23 22:18:27 -0400 (Thu, 23 Mar 2023)
EndedAt: 2023-03-23 22:27:39 -0400 (Thu, 23 Mar 2023)
EllapsedTime: 552.6 seconds
RetCode: 0
Status:   OK  
CheckDir: NxtIRFcore.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings NxtIRFcore_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘NxtIRFcore/DESCRIPTION’ ... OK
* this is package ‘NxtIRFcore’ version ‘1.5.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   4.2Mb
* 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 loading without being on the library search path ... 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 18.680  0.455  19.106
CollateData    16.347  0.479  16.867
* 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 ...
  ‘NxtIRF.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck/00check.log’
for details.



Installation output

NxtIRFcore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NxtIRFcore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘NxtIRFcore’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c BAM2blocks.cpp -o BAM2blocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c FastaReader.cpp -o FastaReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c FragmentBlocks.cpp -o FragmentBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c GZTools.cpp -o GZTools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c IRFinder.cpp -o IRFinder.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DRNXTIRF -fpic  -g -O2  -Wall -c covTools.cpp -o covTools.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/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 -fopenmp -DRNXTIRF -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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 Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
Mar 23 22:24:53 Reference generated without non-polyA reference
Mar 23 22:24:53 Reference generated without Mappability reference
Mar 23 22:24:53 Reference generated without Blacklist exclusion
Mar 23 22:24:53 Converting FASTA to local TwoBitFile...done
Mar 23 22:24:55 Connecting to genome TwoBitFile...done
Mar 23 22:24:55 Making local copy of GTF file...done
Mar 23 22:24:55 Reading source GTF file...done
Mar 23 22:24:55 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Mar 23 22:24:57 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Mar 23 22:25:01 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
Mar 23 22:25:08 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
done
Mar 23 22:25:11 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
Mar 23 22:25:12 Splice Annotations Filtered
Mar 23 22:25:12 Translating Alternate Splice Peptides...done
Mar 23 22:25:14 Splice Annotations finished

Reference build finished
Mar 23 22:25:14 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
/tmp/Rtmp0bwGs8/02H003.bam processed
/tmp/Rtmp0bwGs8/02H025.bam processed
/tmp/Rtmp0bwGs8/02H026.bam processed
/tmp/Rtmp0bwGs8/02H033.bam processed
/tmp/Rtmp0bwGs8/02H043.bam processed
/tmp/Rtmp0bwGs8/02H046.bam processed
Mar 23 22:25:16 Validating Experiment; checking COV files...
Mar 23 22:25:18 Using MulticoreParam 1 threads
Mar 23 22:25:18 Compiling Sample Stats
Mar 23 22:25:18 Compiling Junction List...merging...done
Mar 23 22:25:19 Compiling Intron Retention List...done
Mar 23 22:25:21 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done

Mar 23 22:25:23 Generating NxtIRF assays
Mar 23 22:25:24 Using MulticoreParam 1 threads

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Building Final SummarizedExperiment Object

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NxtIRF Collation Finished
Mar 23 22:25:29 Loading NxtSE object from file...done

Mar 23 22:25:29 Removing overlapping introns...
Mar 23 22:25:29 Iterating through IR events to determine introns of main isoforms
Mar 23 22:25:29 Iteration 1
Mar 23 22:25:29 Iteration 2
Mar 23 22:25:31 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
Processing BAM file /tmp/Rtmp0bwGs8/02H003.bam
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/tmp/Rtmp0bwGs8/02H003.bam processed
Mar 23 22:25:32 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 2 threads
Processing BAM file /tmp/Rtmp0bwGs8/02H003.bam
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Compiling data from threads
Performing final sort of fragment maps
Writing COV file
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/tmp/Rtmp0bwGs8/02H003.bam processed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
   user  system elapsed 
 54.499   2.915  57.279 

Example timings

NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings

nameusersystemelapsed
ASE-methods0.7840.0280.812
BuildReference18.680 0.45519.106
CollateData16.347 0.47916.867
CoordToGR0.0150.0000.016
Coverage0.9440.0040.935
Find_Samples0.0060.0000.006
IRFinder2.3300.1942.540
IsCOV0.0030.0040.009
MakeSE2.8970.0923.009
Mappability-methods0.0340.0030.039
NxtFilter-class0.0410.0030.046
NxtSE-class4.2590.3744.651
Plot_Coverage4.5070.3554.759
Run_NxtIRF_Filters0.5110.0190.530
STAR-methods0.0030.0000.004
example-NxtIRF-data0.0050.0040.009
make_plot_data0.0400.0040.044
theme_white0.1310.0120.143