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This page was generated on 2023-05-10 10:04:36 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 NanoMethViz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoMethViz.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1332/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoMethViz 2.7.0 (landing page) Shian Su
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: NanoMethViz |
| Version: 2.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings NanoMethViz_2.7.0.tar.gz |
| StartedAt: 2023-05-09 22:45:14 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 22:57:14 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 720.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NanoMethViz.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings NanoMethViz_2.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/NanoMethViz.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘2.7.0’
* 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 ‘NanoMethViz’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... OK
Not all R platforms support C++20
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
libs 2.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... NOTE
The following files look like leftovers:
‘NanoMethViz/ModBamResults-class.Rd’
Please remove them from your package.
* 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 C/C++/Fortran sources/headers ... 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
get_exons 53.936 2.678 56.845
get_exons_mus_musculus 18.034 0.500 18.535
get_exons_homo_sapiens 16.556 0.520 17.076
plot_agg_regions 7.559 0.076 7.635
NanoMethResult-class 5.262 0.480 5.747
cluster_regions 5.398 0.155 5.555
* 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 ...
‘DimensionalityReduction.Rmd’ using ‘UTF-8’... OK
‘ExonAnnotations.Rmd’ using ‘UTF-8’... OK
‘ImportingExportingData.Rmd’ using ‘UTF-8’... OK
‘Introduction.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++20 g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c modbam.cpp -o modbam.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++20 -shared -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o modbam.o utils.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-NanoMethViz/00new/NanoMethViz/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 (NanoMethViz)
NanoMethViz.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "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(NanoMethViz)
Loading required package: ggplot2
>
> test_check("NanoMethViz")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 97 ]
>
> proc.time()
user system elapsed
135.839 7.433 80.608
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 5.262 | 0.480 | 5.747 | |
| bsseq_to_edger | 0.881 | 0.072 | 0.902 | |
| bsseq_to_log_methy_ratio | 1.359 | 0.086 | 1.360 | |
| cluster_regions | 5.398 | 0.155 | 5.555 | |
| create_tabix_file | 0.162 | 0.024 | 0.187 | |
| exons_to_genes | 0.394 | 0.016 | 0.410 | |
| filter_methy | 2.525 | 0.192 | 2.716 | |
| get_example_exons_mus_musculus | 0.333 | 0.012 | 0.345 | |
| get_exons | 53.936 | 2.678 | 56.845 | |
| get_exons_homo_sapiens | 16.556 | 0.520 | 17.076 | |
| get_exons_mus_musculus | 18.034 | 0.500 | 18.535 | |
| load_example_nanomethresult | 0.382 | 0.008 | 0.390 | |
| methy | 0.000 | 0.003 | 0.003 | |
| methy_col_names | 0 | 0 | 0 | |
| methy_to_bsseq | 1.267 | 0.088 | 1.228 | |
| methy_to_edger | 1.413 | 0.054 | 1.314 | |
| plot_agg_genes | 2.735 | 0.056 | 2.791 | |
| plot_agg_regions | 7.559 | 0.076 | 7.635 | |
| plot_gene | 1.456 | 0.023 | 1.480 | |
| plot_gene_heatmap | 2.610 | 0.061 | 2.670 | |
| plot_grange | 1.528 | 0.008 | 1.535 | |
| plot_grange_heatmap | 2.280 | 0.032 | 2.312 | |
| plot_mds | 1.875 | 0.067 | 1.765 | |
| plot_pca | 1.947 | 0.085 | 1.805 | |
| plot_region | 1.220 | 0.007 | 1.227 | |
| plot_region_heatmap | 1.924 | 0.019 | 1.943 | |
| query_methy | 0.517 | 0.011 | 0.530 | |
| region_methy_stats | 1.437 | 0.004 | 1.441 | |