| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:12 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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. |
| Package 1371/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NxtIRFcore 1.4.0 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: NxtIRFcore |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings NxtIRFcore_1.4.0.tar.gz |
| StartedAt: 2023-04-10 22:24:56 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 22:33:45 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 529.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NxtIRFcore.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings NxtIRFcore_1.4.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/NxtIRFcore.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘NxtIRFcore/DESCRIPTION’ ... OK
* this is package ‘NxtIRFcore’ version ‘1.4.0’
* 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
* checking installed package size ... NOTE
installed size is 12.8Mb
sub-directories of 1Mb or more:
R 1.6Mb
libs 10.4Mb
* 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 20.288 0.604 20.846
CollateData 14.591 0.529 15.153
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/NxtIRFcore.Rcheck/00check.log’
for details.
NxtIRFcore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL NxtIRFcore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘NxtIRFcore’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-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-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-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)
NxtIRFcore.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
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")
Apr 10 22:31:10 Reference generated without non-polyA reference
Apr 10 22:31:10 Reference generated without Mappability reference
Apr 10 22:31:10 Reference generated without Blacklist exclusion
Apr 10 22:31:10 Converting FASTA to local TwoBitFile...done
Apr 10 22:31:11 Connecting to genome TwoBitFile...done
Apr 10 22:31:11 Making local copy of GTF file...done
Apr 10 22:31:11 Reading source GTF file...done
Apr 10 22:31:11 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 10 22:31:14 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Apr 10 22:31:17 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
Apr 10 22:31:23 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Apr 10 22:31:25 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
Apr 10 22:31:26 Splice Annotations Filtered
Apr 10 22:31:26 Translating Alternate Splice Peptides...done
Apr 10 22:31:27 Splice Annotations finished
Reference build finished
Apr 10 22:31:27 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
/tmp/RtmpQvTPjb/02H003.bam processed
/tmp/RtmpQvTPjb/02H025.bam processed
/tmp/RtmpQvTPjb/02H026.bam processed
/tmp/RtmpQvTPjb/02H033.bam processed
/tmp/RtmpQvTPjb/02H043.bam processed
/tmp/RtmpQvTPjb/02H046.bam processed
Apr 10 22:31:30 Validating Experiment; checking COV files...
Apr 10 22:31:30 Using MulticoreParam 1 threads
Apr 10 22:31:30 Compiling Sample Stats
Apr 10 22:31:30 Compiling Junction List...merging...done
Apr 10 22:31:31 Compiling Intron Retention List...done
Apr 10 22:31:32 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done
Apr 10 22:31:34 Generating NxtIRF assays
Apr 10 22:31:34 Using MulticoreParam 1 threads
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Building Final SummarizedExperiment Object
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NxtIRF Collation Finished
Apr 10 22:31:38 Loading NxtSE object from file...done
Apr 10 22:31:38 Removing overlapping introns...
Apr 10 22:31:38 Iterating through IR events to determine introns of main isoforms
Apr 10 22:31:38 Iteration 1
Apr 10 22:31:38 Iteration 2
Apr 10 22:31:39 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
Processing BAM file /tmp/RtmpQvTPjb/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/RtmpQvTPjb/02H003.bam processed
Apr 10 22:31:40 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 2 threads
Processing BAM file /tmp/RtmpQvTPjb/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/RtmpQvTPjb/02H003.bam processed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
45.138 1.729 46.642
NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 0.591 | 0.076 | 0.667 | |
| BuildReference | 20.288 | 0.604 | 20.846 | |
| CollateData | 14.591 | 0.529 | 15.153 | |
| CoordToGR | 0.016 | 0.000 | 0.016 | |
| Coverage | 0.957 | 0.060 | 1.003 | |
| Find_Samples | 0.004 | 0.000 | 0.005 | |
| IRFinder | 2.270 | 0.189 | 2.477 | |
| IsCOV | 0.003 | 0.004 | 0.009 | |
| MakeSE | 1.817 | 0.126 | 1.958 | |
| Mappability-methods | 0.033 | 0.000 | 0.033 | |
| NxtFilter-class | 0.086 | 0.000 | 0.086 | |
| NxtSE-class | 2.925 | 0.117 | 3.061 | |
| Plot_Coverage | 3.999 | 0.085 | 3.980 | |
| Run_NxtIRF_Filters | 0.517 | 0.000 | 0.517 | |
| STAR-methods | 0.004 | 0.000 | 0.003 | |
| example-NxtIRF-data | 0.005 | 0.003 | 0.009 | |
| make_plot_data | 0.037 | 0.001 | 0.038 | |
| theme_white | 0.152 | 0.000 | 0.152 | |