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This page was generated on 2024-03-28 11:36:47 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1382/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoMethViz 2.99.4  (landing page)
Shian Su
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/NanoMethViz
git_branch: devel
git_last_commit: 34cc5aa
git_last_commit_date: 2024-01-17 23:12:00 -0400 (Wed, 17 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

CHECK results for NanoMethViz on nebbiolo1


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.
- 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.

raw results


Summary

Package: NanoMethViz
Version: 2.99.4
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NanoMethViz_2.99.4.tar.gz
StartedAt: 2024-03-28 00:41:46 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 00:51:52 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 605.9 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoMethViz.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NanoMethViz_2.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘2.99.4’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
  Not all R platforms support C++20
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
plot_violin: no visible binding for global variable ‘methy_data’
Undefined global functions or variables:
  methy_data
* 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              41.698  2.200  43.933
get_exons_homo_sapiens 12.288  0.184  12.474
get_exons_mus_musculus 11.607  0.240  11.848
plot_gene_heatmap       6.948  0.088   7.036
plot_grange_heatmap     5.052  0.064   5.116
plot_agg_regions        5.048  0.064   5.112
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.


Installation output

NanoMethViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL NanoMethViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘NanoMethViz’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++20
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c count_cg.cpp -o count_cg.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c modbam.cpp -o modbam.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o modbam.o utils.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/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)

Tests output

NanoMethViz.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 572 ]
> 
> proc.time()
   user  system elapsed 
179.341  15.134 133.665 

Example timings

NanoMethViz.Rcheck/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class3.8090.2764.086
bsseq_to_edger0.580.020.60
bsseq_to_log_methy_ratio1.0440.0201.064
cluster_regions3.8340.1323.966
create_tabix_file0.1880.0040.193
exons_to_genes0.3430.0200.363
filter_methy1.8730.0561.911
get_example_exons_mus_musculus0.2200.0000.221
get_exons41.698 2.20043.933
get_exons_homo_sapiens12.288 0.18412.474
get_exons_mus_musculus11.607 0.24011.848
load_example_nanomethresult0.2340.0000.234
methy0.0020.0000.003
methy_col_names000
methy_to_bsseq0.8800.0080.887
methy_to_edger1.1790.0241.203
modbam_to_tabix0.4260.4970.722
plot_agg_genes1.6690.0001.668
plot_agg_regions5.0480.0645.112
plot_gene1.9200.0681.988
plot_gene_heatmap6.9480.0887.036
plot_grange1.9590.0241.983
plot_grange_heatmap5.0520.0645.116
plot_mds1.3750.0201.395
plot_pca1.4370.0201.457
plot_region1.6280.0281.656
plot_region_heatmap4.7500.0644.815
plot_violin2.1950.0322.227
query_methy0.3410.0040.346
region_methy_stats0.880.060.94