| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:18 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
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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 1360/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NxtIRFcore 1.5.0 (landing page) Alex Chit Hei Wong
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: NxtIRFcore |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings NxtIRFcore_1.5.0.tar.gz |
| StartedAt: 2023-02-07 10:04:05 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 10:13:18 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 552.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: NxtIRFcore.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NxtIRFcore.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings NxtIRFcore_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘NxtIRFcore’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 10.3Mb
sub-directories of 1Mb or more:
R 1.6Mb
libs 7.8Mb
* 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 21.307 0.172 23.601
CollateData 19.432 0.360 21.485
Plot_Coverage 5.889 0.052 6.918
NxtSE-class 5.478 0.188 6.025
* 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 ...
‘NxtIRF.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘NxtIRF.Rmd’ using rmarkdown
Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/NxtIRFcore.Rcheck/00check.log’
for details.
NxtIRFcore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NxtIRFcore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘NxtIRFcore’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c BAM2blocks.cpp -o BAM2blocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c FastaReader.cpp -o FastaReader.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c FragmentBlocks.cpp -o FragmentBlocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c GZTools.cpp -o GZTools.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c IRFinder.cpp -o IRFinder.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DRNXTIRF -fPIC -g -O2 -Wall -c covTools.cpp -o covTools.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/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 -fopenmp -DRNXTIRF -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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")
Feb 07 10:11:43 Reference generated without non-polyA reference
Feb 07 10:11:43 Reference generated without Mappability reference
Feb 07 10:11:43 Reference generated without Blacklist exclusion
Feb 07 10:11:43 Converting FASTA to local TwoBitFile...done
Feb 07 10:11:44 Connecting to genome TwoBitFile...done
Feb 07 10:11:44 Making local copy of GTF file...done
Feb 07 10:11:44 Reading source GTF file...done
Feb 07 10:11:45 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Feb 07 10:11:47 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon islands
done
Feb 07 10:11:52 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
Feb 07 10:12:01 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
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|
|======================================================================| 100%
done
Feb 07 10:12:03 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
Feb 07 10:12:05 Splice Annotations Filtered
Feb 07 10:12:05 Translating Alternate Splice Peptides...done
Feb 07 10:12:07 Splice Annotations finished
Reference build finished
Feb 07 10:12:07 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
/tmp/RtmpaNRDiR/02H003.bam processed
/tmp/RtmpaNRDiR/02H025.bam processed
/tmp/RtmpaNRDiR/02H026.bam processed
/tmp/RtmpaNRDiR/02H033.bam processed
/tmp/RtmpaNRDiR/02H043.bam processed
/tmp/RtmpaNRDiR/02H046.bam processed
Feb 07 10:12:11 Validating Experiment; checking COV files...
Feb 07 10:12:12 Using MulticoreParam 1 threads
Feb 07 10:12:12 Compiling Sample Stats
Feb 07 10:12:12 Compiling Junction List...merging...done
Feb 07 10:12:14 Compiling Intron Retention List...done
Feb 07 10:12:15 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...saving annotations
...compiling rowEvents
done
Feb 07 10:12:17 Generating NxtIRF assays
Feb 07 10:12:19 Using MulticoreParam 1 threads
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Building Final SummarizedExperiment Object
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NxtIRF Collation Finished
Feb 07 10:12:24 Loading NxtSE object from file...done
Feb 07 10:12:24 Removing overlapping introns...
Feb 07 10:12:25 Iterating through IR events to determine introns of main isoforms
Feb 07 10:12:25 Iteration 1
Feb 07 10:12:25 Iteration 2
Feb 07 10:12:27 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 1 threads
Processing BAM file /tmp/RtmpaNRDiR/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
/tmp/RtmpaNRDiR/02H003.bam processed
Feb 07 10:12:28 Running IRFinder
Reading reference file
Running IRFinder with OpenMP using 2 threads
Processing BAM file /tmp/RtmpaNRDiR/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
/tmp/RtmpaNRDiR/02H003.bam processed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
63.531 1.773 70.885
NxtIRFcore.Rcheck/NxtIRFcore-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 0.977 | 0.048 | 1.238 | |
| BuildReference | 21.307 | 0.172 | 23.601 | |
| CollateData | 19.432 | 0.360 | 21.485 | |
| CoordToGR | 0.018 | 0.004 | 0.051 | |
| Coverage | 1.252 | 0.012 | 1.574 | |
| Find_Samples | 0.006 | 0.000 | 0.007 | |
| IRFinder | 2.915 | 0.173 | 3.269 | |
| IsCOV | 0.004 | 0.005 | 0.013 | |
| MakeSE | 3.720 | 0.081 | 4.062 | |
| Mappability-methods | 0.039 | 0.004 | 0.048 | |
| NxtFilter-class | 0.055 | 0.008 | 0.063 | |
| NxtSE-class | 5.478 | 0.188 | 6.025 | |
| Plot_Coverage | 5.889 | 0.052 | 6.918 | |
| Run_NxtIRF_Filters | 0.754 | 0.008 | 0.819 | |
| STAR-methods | 0.002 | 0.002 | 0.007 | |
| example-NxtIRF-data | 0.009 | 0.000 | 0.010 | |
| make_plot_data | 0.049 | 0.000 | 0.049 | |
| theme_white | 0.187 | 0.000 | 0.187 | |