| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:41 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1356/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NxtIRFcore 1.5.0 (landing page) Alex Chit Hei Wong
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: NxtIRFcore |
| Version: 1.5.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NxtIRFcore.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings NxtIRFcore_1.5.0.tar.gz |
| StartedAt: 2022-12-29 01:54:45 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 02:00:45 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 359.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NxtIRFcore.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NxtIRFcore.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings NxtIRFcore_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/NxtIRFcore.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 whether package 'NxtIRFcore' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/NxtIRFcore/libs/x64/NxtIRFcore.dll':
Found '_assert', possibly from 'assert' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BuildReference 14.37 0.17 15.75
CollateData 12.89 0.60 14.31
Plot_Coverage 3.83 0.12 5.05
* 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/NxtIRFcore.Rcheck/00check.log'
for details.
NxtIRFcore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL NxtIRFcore ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'NxtIRFcore' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BAM2blocks.cpp -o BAM2blocks.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastaReader.cpp -o FastaReader.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FragmentBlocks.cpp -o FragmentBlocks.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GZTools.cpp -o GZTools.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRFinder.cpp -o IRFinder.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c covTools.cpp -o covTools.o g++ -shared -s -static-libgcc -o NxtIRFcore.dll tmp.def BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o IRFinder.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o covTools.o -fopenmp -DRNXTIRF -LF:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-NxtIRFcore/00new/NxtIRFcore/libs/x64 ** 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 ** 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
Dec 29 2:00:04 AM Reference generated without non-polyA reference
Dec 29 2:00:04 AM Reference generated without Mappability reference
Dec 29 2:00:04 AM Reference generated without Blacklist exclusion
Dec 29 2:00:04 AM Converting FASTA to local TwoBitFile...done
Dec 29 2:00:05 AM Connecting to genome TwoBitFile...done
Dec 29 2:00:05 AM Making local copy of GTF file...done
Dec 29 2:00:05 AM Reading source GTF file...done
Dec 29 2:00:06 AM Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Dec 29 2:00:07 AM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Dec 29 2:00:11 AM 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
Dec 29 2:00:16 AM Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
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|======================================================================| 100%
done
Dec 29 2:00:17 AM 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
Dec 29 2:00:18 AM Splice Annotations Filtered
Dec 29 2:00:18 AM Translating Alternate Splice Peptides...done
Dec 29 2:00:19 AM Splice Annotations finished
Reference build finished
Dec 29 2:00:19 AM Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\02H003.bam processed
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\02H025.bam processed
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\02H026.bam processed
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\02H033.bam processed
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\02H043.bam processed
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\02H046.bam processed
Dec 29 2:00:22 AM Validating Experiment; checking COV files...
Dec 29 2:00:22 AM Using SnowParam 1 threads
Dec 29 2:00:22 AM Compiling Sample Stats
Dec 29 2:00:23 AM Compiling Junction List...merging...done
Dec 29 2:00:23 AM Compiling Intron Retention List...done
Dec 29 2:00:24 AM Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done
Dec 29 2:00:26 AM Generating NxtIRF assays
Dec 29 2:00:27 AM Using SnowParam 1 threads
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Building Final SummarizedExperiment Object
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NxtIRF Collation Finished
Dec 29 2:00:31 AM Loading NxtSE object from file...done
Dec 29 2:00:31 AM Removing overlapping introns...
Dec 29 2:00:31 AM Iterating through IR events to determine introns of main isoforms
Dec 29 2:00:31 AM Iteration 1
Dec 29 2:00:31 AM Iteration 2
Dec 29 2:00:33 AM Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
Processing BAM file F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\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
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\02H003.bam processed
Dec 29 2:00:34 AM Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 2 threads
Processing BAM file F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\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
F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpWCeYpi\02H003.bam processed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
43.15 2.03 46.56
NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 0.50 | 0.11 | 0.70 | |
| BuildReference | 14.37 | 0.17 | 15.75 | |
| CollateData | 12.89 | 0.60 | 14.31 | |
| CoordToGR | 0.02 | 0.00 | 0.02 | |
| Coverage | 0.75 | 0.03 | 0.79 | |
| Find_Samples | 0 | 0 | 0 | |
| IRFinder | 2.32 | 0.05 | 2.36 | |
| IsCOV | 0.01 | 0.00 | 0.01 | |
| MakeSE | 2.49 | 0.39 | 2.88 | |
| Mappability-methods | 0.01 | 0.03 | 0.05 | |
| NxtFilter-class | 0.05 | 0.00 | 0.04 | |
| NxtSE-class | 3.64 | 0.72 | 4.36 | |
| Plot_Coverage | 3.83 | 0.12 | 5.05 | |
| Run_NxtIRF_Filters | 0.56 | 0.01 | 0.58 | |
| STAR-methods | 0 | 0 | 0 | |
| example-NxtIRF-data | 0.02 | 0.00 | 0.01 | |
| make_plot_data | 0.03 | 0.00 | 0.04 | |
| theme_white | 0.11 | 0.00 | 0.11 | |