Alex Chit Hei Wong
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/NxtIRFcore |
| git_branch: master |
| git_last_commit: f125c63 |
| git_last_commit_date: 2022-01-10 20:13:33 -0400 (Mon, 10 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:11 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1319/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NxtIRFcore 1.1.1 (landing page) Alex Chit Hei Wong
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | 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: 1.1.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NxtIRFcore.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings NxtIRFcore_1.1.1.tar.gz |
| StartedAt: 2022-03-17 19:45:33 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:51:18 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 345.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NxtIRFcore.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NxtIRFcore.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings NxtIRFcore_1.1.1.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/NxtIRFcore.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NxtIRFcore/DESCRIPTION' ... OK
* this is package 'NxtIRFcore' version '1.1.1'
* 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 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/NxtIRFcore/libs/x64/NxtIRFcore.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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. 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 11.08 0.14 13.06
CollateData 9.91 0.63 11.47
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/NxtIRFcore.Rcheck/00check.log'
for details.
NxtIRFcore.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL NxtIRFcore
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'NxtIRFcore' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c BAM2blocks.cpp -o BAM2blocks.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FastaReader.cpp -o FastaReader.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FragmentBlocks.cpp -o FragmentBlocks.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GZTools.cpp -o GZTools.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IRFinder.cpp -o IRFinder.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c covTools.cpp -o covTools.o
C:/rtools40/mingw64/bin/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 -LD:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-NxtIRFcore/00new/NxtIRFcore/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'NxtIRFcore'
finding HTML links ... done
ASE-methods html
BuildReference html
CollateData html
CoordToGR html
Coverage html
Find_Samples html
IRFinder html
IsCOV html
MakeSE html
Mappability-methods html
NxtFilter-class html
NxtIRFcore-package html
NxtSE-class html
finding level-2 HTML links ... done
Plot_Coverage html
Run_NxtIRF_Filters html
STAR-methods html
example-NxtIRF-data html
make_plot_data html
theme_white html
** 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)
Making 'packages.html' ... done
NxtIRFcore.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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")
Mar 17 7:50:26 PM Reference generated without non-polyA reference
Mar 17 7:50:26 PM Reference generated without Mappability reference
Mar 17 7:50:26 PM Reference generated without Blacklist exclusion
Mar 17 7:50:26 PM Converting FASTA to local TwoBitFile...done
Mar 17 7:50:27 PM Connecting to genome TwoBitFile...done
Mar 17 7:50:27 PM Making local copy of GTF file...done
Mar 17 7:50:28 PM Reading source GTF file...done
Mar 17 7:50:28 PM Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Mar 17 7:50:30 PM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Mar 17 7:50:33 PM 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
Mar 17 7:50:40 PM Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
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|======================================================================| 100%
done
Mar 17 7:50:41 PM 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
Mar 17 7:50:42 PM Splice Annotations Filtered
Mar 17 7:50:42 PM Translating Alternate Splice Peptides...done
Mar 17 7:50:43 PM Splice Annotations finished
Reference build finished
Mar 17 7:50:43 PM Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\02H003.bam processed
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\02H025.bam processed
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\02H026.bam processed
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\02H033.bam processed
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\02H043.bam processed
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\02H046.bam processed
Mar 17 7:50:46 PM Validating Experiment; checking COV files...
Mar 17 7:50:46 PM Using SnowParam 1 threads
Mar 17 7:50:46 PM Compiling Sample Stats
Mar 17 7:50:46 PM Compiling Junction List...merging...done
Mar 17 7:50:47 PM Compiling Intron Retention List...done
Mar 17 7:50:48 PM Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done
Mar 17 7:50:50 PM Generating NxtIRF assays
Mar 17 7:50:50 PM Using SnowParam 1 threads
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Building Final SummarizedExperiment Object
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NxtIRF Collation Finished
Mar 17 7:50:56 PM Loading NxtSE object from file...done
Mar 17 7:50:56 PM Removing overlapping introns...
Mar 17 7:50:57 PM Iterating through IR events to determine introns of main isoforms
Mar 17 7:50:57 PM Iteration 1
Mar 17 7:50:57 PM Iteration 2
Mar 17 7:50:59 PM Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
Processing BAM file D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\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
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\02H003.bam processed
Mar 17 7:51:00 PM Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 2 threads
Processing BAM file D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\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
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxa5kB\02H003.bam processed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
41.89 3.17 52.96
NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 1.08 | 0.09 | 1.17 | |
| BuildReference | 11.08 | 0.14 | 13.06 | |
| CollateData | 9.91 | 0.63 | 11.47 | |
| CoordToGR | 0.00 | 0.01 | 0.51 | |
| Coverage | 1.17 | 0.02 | 2.21 | |
| Find_Samples | 0.00 | 0.00 | 1.09 | |
| IRFinder | 2.67 | 0.56 | 3.61 | |
| IsCOV | 0 | 0 | 0 | |
| MakeSE | 1.75 | 0.20 | 4.00 | |
| Mappability-methods | 0.05 | 0.00 | 0.09 | |
| NxtFilter-class | 0.06 | 0.00 | 0.19 | |
| NxtSE-class | 3.11 | 0.53 | 4.00 | |
| Plot_Coverage | 3.47 | 0.07 | 3.55 | |
| Run_NxtIRF_Filters | 0.47 | 0.00 | 0.47 | |
| STAR-methods | 0 | 0 | 0 | |
| example-NxtIRF-data | 0.02 | 0.00 | 0.01 | |
| make_plot_data | 0.01 | 0.00 | 0.02 | |
| theme_white | 0.09 | 0.00 | 0.09 | |