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This page was generated on 2022-01-18 11:07:52 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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

CHECK results for NanoMethViz on riesling1


To the developers/maintainers of the NanoMethViz package:
- Please 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 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.

raw results

Package 1258/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoMethViz 2.1.2  (landing page)
Shian Su
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/NanoMethViz
git_branch: master
git_last_commit: 32400e1
git_last_commit_date: 2021-12-07 01:06:18 -0500 (Tue, 07 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'S4Vectors' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NanoMethViz
Version: 2.1.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoMethViz.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings NanoMethViz_2.1.2.tar.gz
StartedAt: 2022-01-17 19:35:09 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 19:40:39 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 329.6 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoMethViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoMethViz.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings NanoMethViz_2.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.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 'NanoMethViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NanoMethViz' version '2.1.2'
* 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 'NanoMethViz' 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 ... NOTE
'library' or 'require' calls in package code:
  'Homo.sapiens' 'Mus.musculus'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/libs/x64/NanoMethViz.dll':
  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
get_exons_homo_sapiens 13.61   1.28   14.89
get_exons_mus_musculus 12.08   1.05   13.16
NanoMethResult-class    5.26   1.48    6.75
plot_agg_regions        4.92   0.30    5.22
plot_region_heatmap     4.50   0.18    5.06
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck/00check.log'
for details.



Installation output

NanoMethViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL NanoMethViz
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'NanoMethViz' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -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/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o NanoMethViz.dll tmp.def RcppExports.o convert_methy_to_dss.o utils.o -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-NanoMethViz/00new/NanoMethViz/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NanoMethViz'
    finding HTML links ... done
    NanoMethResult-class                    html  
    NanoMethViz-package                     html  
    bsseq_to_edger                          html  
    bsseq_to_log_methy_ratio                html  
    convert_methy_format                    html  
    create_tabix_file                       html  
    exons-set                               html  
    exons                                   html  
    exons_to_genes                          html  
    get_example_exons_mus_musculus          html  
    get_exons_homo_sapiens                  html  
    get_exons_mus_musculus                  html  
    load_example_nanomethresult             html  
    methy-set                               html  
    methy                                   html  
    methy_col_names                         html  
    methy_to_bsseq                          html  
    plot_agg_regions                        html  
    plot_gene                               html  
    plot_gene_heatmap                       html  
    plot_grange                             html  
    plot_grange_heatmap                     html  
    plot_mds                                html  
    plot_pca                                html  
    plot_region                             html  
    plot_region_heatmap                     html  
    query_exons                             html  
    query_methy                             html  
    raw_methy_to_tabix                      html  
    samples-set                             html  
    samples                                 html  
    sort_methy_file                         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 (NanoMethViz)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'recount' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'UMI4Cats' is missing or broken
 done

Tests output

NanoMethViz.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(NanoMethViz)
Loading required package: ggplot2
> 
> test_check("NanoMethViz")
Loading required package: Mus.musculus
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:NanoMethViz':

    samples

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges

Attaching package: 'GenomicFeatures'

The following object is masked from 'package:NanoMethViz':

    exons

Loading required package: GO.db

Loading required package: org.Mm.eg.db

Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
[2022-01-17 19:40:09] creating intermediate files...
[2022-01-17 19:40:09] parsing chr11...
[2022-01-17 19:40:09] parsing chr12...
[2022-01-17 19:40:09] parsing chr18...
[2022-01-17 19:40:09] parsing chr5...
[2022-01-17 19:40:09] parsing chr7...
[2022-01-17 19:40:09] parsing chrX...
[2022-01-17 19:40:09] samples found: B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_cast B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-17 19:40:09] creating bsseq object...
[2022-01-17 19:40:09] reading in parsed data...
[2022-01-17 19:40:10] constructing matrices...
[2022-01-17 19:40:10] done
[2022-01-17 19:40:10] creating intermediate files...
[2022-01-17 19:40:10] parsing chr11...
[2022-01-17 19:40:10] parsing chr12...
[2022-01-17 19:40:10] parsing chr18...
[2022-01-17 19:40:10] parsing chr5...
[2022-01-17 19:40:10] parsing chr7...
[2022-01-17 19:40:10] parsing chrX...
[2022-01-17 19:40:10] samples found: B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_cast B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-17 19:40:10] creating bsseq object...
[2022-01-17 19:40:10] reading in parsed data...
[2022-01-17 19:40:10] constructing matrices...
[2022-01-17 19:40:11] done
[2022-01-17 19:40:11] creating intermediate files...
[2022-01-17 19:40:11] parsing chr11...
[2022-01-17 19:40:11] parsing chr12...
[2022-01-17 19:40:11] parsing chr18...
[2022-01-17 19:40:11] parsing chr5...
[2022-01-17 19:40:11] parsing chr7...
[2022-01-17 19:40:11] parsing chrX...
[2022-01-17 19:40:11] samples found: B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_cast B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-17 19:40:11] creating bsseq object...
[2022-01-17 19:40:11] reading in parsed data...
[2022-01-17 19:40:11] constructing matrices...
[2022-01-17 19:40:12] done
[2022-01-17 19:40:26] creating methylation table
processing D:/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/sample1_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
processing D:/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/sample2_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
[2022-01-17 19:40:26] sorting methylation table
[2022-01-17 19:40:26] compressing methylation table to tabix with index
[2022-01-17 19:40:26] creating intermediate files...
[2022-01-17 19:40:26] parsing chr1...
[2022-01-17 19:40:26] parsing chr10...
[2022-01-17 19:40:26] parsing chr11...
[2022-01-17 19:40:26] parsing chr12...
[2022-01-17 19:40:26] parsing chr13...
[2022-01-17 19:40:26] parsing chr14...
[2022-01-17 19:40:26] parsing chr15...
[2022-01-17 19:40:26] parsing chr16...
[2022-01-17 19:40:26] parsing chr17...
[2022-01-17 19:40:26] parsing chr18...
[2022-01-17 19:40:26] parsing chr19...
[2022-01-17 19:40:26] parsing chr2...
[2022-01-17 19:40:26] parsing chr3...
[2022-01-17 19:40:26] parsing chr4...
[2022-01-17 19:40:26] parsing chr5...
[2022-01-17 19:40:26] parsing chr6...
[2022-01-17 19:40:26] parsing chr7...
[2022-01-17 19:40:26] parsing chr8...
[2022-01-17 19:40:26] parsing chr9...
[2022-01-17 19:40:26] parsing chrM...
[2022-01-17 19:40:26] parsing chrX...
[2022-01-17 19:40:26] parsing chrY...
[2022-01-17 19:40:26] samples found: B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_cast B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast sample1_nanopolish.tsv sample2_nanopolish.tsv 
[2022-01-17 19:40:26] creating bsseq object...
[2022-01-17 19:40:26] reading in parsed data...
[2022-01-17 19:40:26] constructing matrices...
[2022-01-17 19:40:27] done
[2022-01-17 19:40:27] creating methylation table
processing D:/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-01-17 19:40:27] sorting methylation table
[2022-01-17 19:40:27] compressing methylation table to tabix with index
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
  29.75    2.92   31.75 

Example timings

NanoMethViz.Rcheck/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class5.261.486.75
bsseq_to_edger1.230.251.21
bsseq_to_log_methy_ratio1.740.331.73
create_tabix_file0.720.270.66
exons000
exons_to_genes0.590.030.62
get_example_exons_mus_musculus0.430.030.47
get_exons_homo_sapiens13.61 1.2814.89
get_exons_mus_musculus12.08 1.0513.16
load_example_nanomethresult0.360.040.41
methy000
methy_col_names000
methy_to_bsseq1.680.331.56
plot_agg_regions4.920.305.22
plot_gene2.710.192.89
plot_gene_heatmap4.560.124.70
plot_grange1.310.081.39
plot_grange_heatmap2.360.022.38
plot_mds2.030.092.07
plot_pca2.190.192.04
plot_region2.260.042.31
plot_region_heatmap4.500.185.06
query_methy0.50.00.5
samples000