| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:27 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 1312/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NxtIRFcore 1.0.0 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: NxtIRFcore |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2022-04-12 16:14:01 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:23:10 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 548.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NxtIRFcore.Rcheck |
| Warnings: 0 |
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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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/NxtIRFcore.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.0.0’
* 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 ... 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 22.524 0.370 22.932
CollateData 21.692 0.762 22.487
Plot_Coverage 7.564 0.151 7.757
NxtSE-class 4.892 0.419 5.317
IRFinder 4.009 1.237 2.853
* 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-3.14-bioc/meat/NxtIRFcore.Rcheck/00check.log’
for details.
NxtIRFcore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NxtIRFcore ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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)
NxtIRFcore.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
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")
Apr 12 16:22:18 Reference generated without non-polyA reference
Apr 12 16:22:18 Reference generated without Mappability reference
Apr 12 16:22:18 Reference generated without Blacklist exclusion
Apr 12 16:22:18 Converting FASTA to local TwoBitFile...done
Apr 12 16:22:19 Connecting to genome TwoBitFile...done
Apr 12 16:22:19 Making local copy of GTF file...done
Apr 12 16:22:20 Reading source GTF file...done
Apr 12 16:22:20 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 12 16:22:24 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Apr 12 16:22:28 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 12 16:22:37 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
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|======================================================================| 100%
done
Apr 12 16:22:39 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 12 16:22:40 Splice Annotations Filtered
Apr 12 16:22:40 Translating Alternate Splice Peptides...done
Apr 12 16:22:41 Splice Annotations finished
Reference build finished
Apr 12 16:22:41 Running IRFinder
Apr 12 16:22:41 Using MulticoreParam 1 threads
Apr 12 16:22:42 IRFinder processed RtmpxPKHZs/02H003.bam
Apr 12 16:22:42 IRFinder processed RtmpxPKHZs/02H025.bam
Apr 12 16:22:43 IRFinder processed RtmpxPKHZs/02H026.bam
Apr 12 16:22:44 IRFinder processed RtmpxPKHZs/02H033.bam
Apr 12 16:22:44 IRFinder processed RtmpxPKHZs/02H043.bam
Apr 12 16:22:45 IRFinder processed RtmpxPKHZs/02H046.bam
Apr 12 16:22:45 Validating Experiment; checking COV files...
Apr 12 16:22:45 Using MulticoreParam 1 threads
Apr 12 16:22:45 Compiling Sample Stats
Apr 12 16:22:45 Compiling Junction List...merging...done
Apr 12 16:22:46 Compiling Intron Retention List...done
Apr 12 16:22:47 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done
Apr 12 16:22:50 Generating NxtIRF assays
Apr 12 16:22:50 Using MulticoreParam 1 threads
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Building Final SummarizedExperiment Object
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NxtIRF Collation Finished
Apr 12 16:22:56 Loading NxtSE object from file...done
Apr 12 16:22:57 Removing overlapping introns...
Apr 12 16:22:57 Iterating through IR events to determine introns of main isoforms
Apr 12 16:22:57 Iteration 1
Apr 12 16:22:57 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
68.439 2.151 70.773
NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 1.287 | 0.085 | 1.375 | |
| BuildReference | 22.524 | 0.370 | 22.932 | |
| CollateData | 21.692 | 0.762 | 22.487 | |
| CoordToGR | 0.041 | 0.002 | 0.042 | |
| Coverage | 1.783 | 0.059 | 1.846 | |
| Find_Samples | 0.007 | 0.003 | 0.009 | |
| IRFinder | 4.009 | 1.237 | 2.853 | |
| IsCOV | 0.016 | 0.013 | 0.030 | |
| MakeSE | 2.648 | 0.371 | 3.022 | |
| Mappability-methods | 0.061 | 0.014 | 0.075 | |
| NxtFilter-class | 0.098 | 0.013 | 0.111 | |
| NxtSE-class | 4.892 | 0.419 | 5.317 | |
| Plot_Coverage | 7.564 | 0.151 | 7.757 | |
| Run_NxtIRF_Filters | 0.255 | 0.006 | 0.261 | |
| STAR-methods | 0.005 | 0.005 | 0.008 | |
| example-NxtIRF-data | 0.013 | 0.003 | 0.016 | |
| make_plot_data | 0.108 | 0.001 | 0.109 | |
| theme_white | 0.170 | 0.003 | 0.173 | |