| Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:37:19 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 1403/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Alex Chit Hei Wong
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the NxtIRFcore package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: NxtIRFcore |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2023-10-16 04:44:35 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 05:00:58 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 982.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: NxtIRFcore.Rcheck |
| Warnings: 1 |
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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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NxtIRFcore/DESCRIPTION’ ... OK
* this is package ‘NxtIRFcore’ version ‘1.6.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: Package 'NxtIRFcore' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 startup messages can be suppressed ... 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 28.282 0.841 40.144
CollateData 25.994 1.462 38.533
Plot_Coverage 9.368 0.194 12.318
NxtSE-class 7.649 0.698 10.884
IRFinder 5.790 1.158 5.471
MakeSE 5.340 0.886 8.106
* 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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck/00check.log’
for details.
NxtIRFcore.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NxtIRFcore
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘NxtIRFcore’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c FastaReader.cpp -o FastaReader.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c GZTools.cpp -o GZTools.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c IRFinder.cpp -o IRFinder.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
ReadBlockProcessor_CoverageBlocks.cpp:247:16: warning: variable 'len' set but not used [-Wunused-but-set-variable]
unsigned int len=0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DRNXTIRF -fPIC -falign-functions=64 -Wall -g -O2 -c covTools.cpp -o covTools.o
clang++ -arch x86_64 -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/opt/R/x86_64/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/4.3-x86_64/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
Warning: Package 'NxtIRFcore' is deprecated and will be removed from
Bioconductor version 3.18
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'NxtIRFcore' is deprecated and will be removed from
Bioconductor version 3.18
** testing if installed package keeps a record of temporary installation path
* DONE (NxtIRFcore)
NxtIRFcore.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
Warning message:
Package 'NxtIRFcore' is deprecated and will be removed from
Bioconductor version 3.18
>
> test_check("NxtIRFcore")
Oct 16 04:59:29 Reference generated without non-polyA reference
Oct 16 04:59:29 Reference generated without Mappability reference
Oct 16 04:59:29 Reference generated without Blacklist exclusion
Oct 16 04:59:29 Converting FASTA to local TwoBitFile...done
Oct 16 04:59:31 Connecting to genome TwoBitFile...done
Oct 16 04:59:31 Making local copy of GTF file...done
Oct 16 04:59:31 Reading source GTF file...done
Oct 16 04:59:32 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 16 04:59:37 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Oct 16 04:59:43 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 16 04:59:55 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
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|======================================================================| 100%
done
Oct 16 04:59:59 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 16 05:00:01 Splice Annotations Filtered
Oct 16 05:00:01 Translating Alternate Splice Peptides...done
Oct 16 05:00:05 Splice Annotations finished
Reference build finished
Oct 16 05:00:05 Running IRFinder
Oct 16 05:00:07 Using MulticoreParam 1 threads
Oct 16 05:00:08 IRFinder processed RtmpmI5TeY/02H003.bam
Oct 16 05:00:08 IRFinder processed RtmpmI5TeY/02H025.bam
Oct 16 05:00:09 IRFinder processed RtmpmI5TeY/02H026.bam
Oct 16 05:00:10 IRFinder processed RtmpmI5TeY/02H033.bam
Oct 16 05:00:11 IRFinder processed RtmpmI5TeY/02H043.bam
Oct 16 05:00:12 IRFinder processed RtmpmI5TeY/02H046.bam
Oct 16 05:00:12 Validating Experiment; checking COV files...
Oct 16 05:00:13 Using MulticoreParam 1 threads
Oct 16 05:00:13 Compiling Sample Stats
Oct 16 05:00:14 Compiling Junction List...merging...done
Oct 16 05:00:15 Compiling Intron Retention List...done
Oct 16 05:00:17 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done
Oct 16 05:00:21 Generating NxtIRF assays
Oct 16 05:00:23 Using MulticoreParam 1 threads
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Building Final SummarizedExperiment Object
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NxtIRF Collation Finished
Oct 16 05:00:32 Loading NxtSE object from file...done
Oct 16 05:00:33 Removing overlapping introns...
Oct 16 05:00:33 Iterating through IR events to determine introns of main isoforms
Oct 16 05:00:33 Iteration 1
Oct 16 05:00:34 Iteration 2
NxtIRF was compiled without OpenMP
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 16 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-OpenMP.R:1:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 16 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
87.268 3.706 114.761
NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 1.512 | 0.167 | 2.200 | |
| BuildReference | 28.282 | 0.841 | 40.144 | |
| CollateData | 25.994 | 1.462 | 38.533 | |
| CoordToGR | 0.036 | 0.002 | 0.056 | |
| Coverage | 2.086 | 0.056 | 2.846 | |
| Find_Samples | 0.011 | 0.005 | 0.022 | |
| IRFinder | 5.790 | 1.158 | 5.471 | |
| IsCOV | 0.016 | 0.038 | 0.056 | |
| MakeSE | 5.340 | 0.886 | 8.106 | |
| Mappability-methods | 0.063 | 0.019 | 0.101 | |
| NxtFilter-class | 0.104 | 0.006 | 0.145 | |
| NxtSE-class | 7.649 | 0.698 | 10.884 | |
| Plot_Coverage | 9.368 | 0.194 | 12.318 | |
| Run_NxtIRF_Filters | 1.269 | 0.017 | 1.602 | |
| STAR-methods | 0.006 | 0.011 | 0.027 | |
| example-NxtIRF-data | 0.015 | 0.006 | 0.024 | |
| make_plot_data | 0.079 | 0.003 | 0.102 | |
| theme_white | 0.279 | 0.004 | 0.333 | |