| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:23 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 1346/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NxtIRFcore 1.2.1 (landing page) Alex Chit Hei Wong
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 2022-10-19 05:34:57 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 05:45:29 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 631.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NxtIRFcore.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* 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 25.238 0.469 25.762
CollateData 20.343 0.658 21.049
Plot_Coverage 8.174 0.133 8.321
IRFinder 4.323 1.404 3.120
NxtSE-class 5.048 0.440 5.495
* 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.
NxtIRFcore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NxtIRFcore ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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)
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")
Oct 19 05:44:33 Reference generated without non-polyA reference
Oct 19 05:44:33 Reference generated without Mappability reference
Oct 19 05:44:33 Reference generated without Blacklist exclusion
Oct 19 05:44:33 Converting FASTA to local TwoBitFile...done
Oct 19 05:44:34 Connecting to genome TwoBitFile...done
Oct 19 05:44:34 Making local copy of GTF file...done
Oct 19 05:44:34 Reading source GTF file...done
Oct 19 05:44:35 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 19 05:44:38 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Oct 19 05:44:43 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
Oct 19 05:44:52 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Oct 19 05:44:54 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
Oct 19 05:44:56 Splice Annotations Filtered
Oct 19 05:44:56 Translating Alternate Splice Peptides...done
Oct 19 05:44:58 Splice Annotations finished
Reference build finished
Oct 19 05:44:58 Running IRFinder
Oct 19 05:44:58 Using MulticoreParam 1 threads
Oct 19 05:44:59 IRFinder processed RtmpF56cJ4/02H003.bam
Oct 19 05:45:00 IRFinder processed RtmpF56cJ4/02H025.bam
Oct 19 05:45:01 IRFinder processed RtmpF56cJ4/02H026.bam
Oct 19 05:45:01 IRFinder processed RtmpF56cJ4/02H033.bam
Oct 19 05:45:02 IRFinder processed RtmpF56cJ4/02H043.bam
Oct 19 05:45:03 IRFinder processed RtmpF56cJ4/02H046.bam
Oct 19 05:45:03 Validating Experiment; checking COV files...
Oct 19 05:45:03 Using MulticoreParam 1 threads
Oct 19 05:45:03 Compiling Sample Stats
Oct 19 05:45:03 Compiling Junction List...merging...done
Oct 19 05:45:04 Compiling Intron Retention List...done
Oct 19 05:45:05 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done
Oct 19 05:45:08 Generating NxtIRF assays
Oct 19 05:45:08 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Building Final SummarizedExperiment Object
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
NxtIRF Collation Finished
Oct 19 05:45:15 Loading NxtSE object from file...done
Oct 19 05:45:15 Removing overlapping introns...
Oct 19 05:45:15 Iterating through IR events to determine introns of main isoforms
Oct 19 05:45:16 Iteration 1
Oct 19 05:45:16 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
71.729 2.178 74.022
NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 1.325 | 0.061 | 1.389 | |
| BuildReference | 25.238 | 0.469 | 25.762 | |
| CollateData | 20.343 | 0.658 | 21.049 | |
| CoordToGR | 0.030 | 0.001 | 0.031 | |
| Coverage | 1.797 | 0.036 | 1.838 | |
| Find_Samples | 0.009 | 0.003 | 0.013 | |
| IRFinder | 4.323 | 1.404 | 3.120 | |
| IsCOV | 0.013 | 0.018 | 0.032 | |
| MakeSE | 2.622 | 0.377 | 3.003 | |
| Mappability-methods | 0.058 | 0.011 | 0.068 | |
| NxtFilter-class | 0.103 | 0.012 | 0.114 | |
| NxtSE-class | 5.048 | 0.440 | 5.495 | |
| Plot_Coverage | 8.174 | 0.133 | 8.321 | |
| Run_NxtIRF_Filters | 1.040 | 0.009 | 1.051 | |
| STAR-methods | 0.005 | 0.004 | 0.009 | |
| example-NxtIRF-data | 0.012 | 0.003 | 0.015 | |
| make_plot_data | 0.064 | 0.002 | 0.066 | |
| theme_white | 0.225 | 0.002 | 0.227 | |