Shian Su
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/NanoMethViz |
| git_branch: master |
| git_last_commit: c071f38 |
| git_last_commit_date: 2022-03-16 08:32:39 -0400 (Wed, 16 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:09 -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 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. |
| Package 1270/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoMethViz 2.1.5 (landing page) Shian Su
| 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: NanoMethViz |
| Version: 2.1.5 |
| 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_2.1.5.tar.gz |
| StartedAt: 2022-03-17 19:43:00 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:49:19 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 379.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NanoMethViz.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:NanoMethViz.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings NanoMethViz_2.1.5.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 '2.1.5'
* 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 ... NOTE
cluster_regions: no visible binding for global variable 'pos'
cluster_regions: no visible global function definition for 'quantile'
cluster_regions: no visible global function definition for 'hist'
cluster_regions: no visible global function definition for 'approxfun'
cluster_regions : sample_methy_grid: no visible global function
definition for 'approxfun'
cluster_regions: no visible global function definition for 'prcomp'
cluster_regions: no visible global function definition for 'kmeans'
plot_agg_regions: no visible global function definition for 'sd'
Undefined global functions or variables:
approxfun hist kmeans pos prcomp quantile sd
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "approxfun", "kmeans", "prcomp", "quantile", "sd")
to your NAMESPACE file.
* 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_mus_musculus 16.11 1.91 18.11
get_exons_homo_sapiens 14.28 1.64 15.96
plot_gene_heatmap 10.39 0.11 10.50
plot_region_heatmap 8.27 0.08 8.35
plot_agg_regions 5.61 0.07 5.67
plot_grange_heatmap 5.28 0.33 5.61
NanoMethResult-class 4.03 1.34 5.40
* 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: 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck/00check.log'
for details.
NanoMethViz.Rcheck/00install.out
##############################################################################
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###
### 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
cluster_regions html
convert_methy_format html
create_tabix_file html
exons-set html
exons html
exons_to_genes html
filter_methy 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
methy_to_edger 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
region_methy_stats 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' ... done
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
[2022-03-17 19:48:29] creating intermediate files...
[2022-03-17 19:48:29] parsing chr11...
[2022-03-17 19:48:29] parsing chr12...
[2022-03-17 19:48:29] parsing chr18...
[2022-03-17 19:48:29] parsing chr5...
[2022-03-17 19:48:29] parsing chr7...
[2022-03-17 19:48:29] parsing chrX...
[2022-03-17 19:48:29] 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
[2022-03-17 19:48:29] creating bsseq object...
[2022-03-17 19:48:29] reading in parsed data...
[2022-03-17 19:48:30] constructing matrices...
[2022-03-17 19:48:30] done
[2022-03-17 19:48:31] creating intermediate files...
[2022-03-17 19:48:31] parsing chr11...
[2022-03-17 19:48:31] parsing chr12...
[2022-03-17 19:48:31] parsing chr18...
[2022-03-17 19:48:31] parsing chr5...
[2022-03-17 19:48:31] parsing chr7...
[2022-03-17 19:48:31] parsing chrX...
[2022-03-17 19:48:31] 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
[2022-03-17 19:48:31] creating bsseq object...
[2022-03-17 19:48:31] reading in parsed data...
[2022-03-17 19:48:31] constructing matrices...
[2022-03-17 19:48:32] done
[2022-03-17 19:48:32] creating intermediate files...
[2022-03-17 19:48:32] parsing chr11...
[2022-03-17 19:48:32] parsing chr12...
[2022-03-17 19:48:32] parsing chr18...
[2022-03-17 19:48:32] parsing chr5...
[2022-03-17 19:48:32] parsing chr7...
[2022-03-17 19:48:32] parsing chrX...
[2022-03-17 19:48:32] 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
[2022-03-17 19:48:32] creating bsseq object...
[2022-03-17 19:48:32] reading in parsed data...
[2022-03-17 19:48:32] constructing matrices...
[2022-03-17 19:48:33] done
[2022-03-17 19:48:33] creating intermediate files...
[2022-03-17 19:48:33] parsing chr11...
[2022-03-17 19:48:33] parsing chr12...
[2022-03-17 19:48:33] parsing chr18...
[2022-03-17 19:48:33] parsing chr5...
[2022-03-17 19:48:33] parsing chr7...
[2022-03-17 19:48:33] parsing chrX...
[2022-03-17 19:48:33] 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
[2022-03-17 19:48:33] creating bsseq object...
[2022-03-17 19:48:33] reading in parsed data...
[2022-03-17 19:48:34] constructing matrices...
[2022-03-17 19:48:35] done
[2022-03-17 19:49:08] 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...
[2022-03-17 19:49:08] sorting methylation table
[2022-03-17 19:49:09] compressing methylation table to tabix with index
[2022-03-17 19:49:09] creating intermediate files...
[2022-03-17 19:49:09] parsing chr1...
[2022-03-17 19:49:09] parsing chr10...
[2022-03-17 19:49:09] parsing chr11...
[2022-03-17 19:49:09] parsing chr12...
[2022-03-17 19:49:09] parsing chr13...
[2022-03-17 19:49:09] parsing chr14...
[2022-03-17 19:49:09] parsing chr15...
[2022-03-17 19:49:09] parsing chr16...
[2022-03-17 19:49:09] parsing chr17...
[2022-03-17 19:49:09] parsing chr18...
[2022-03-17 19:49:09] parsing chr19...
[2022-03-17 19:49:09] parsing chr2...
[2022-03-17 19:49:09] parsing chr3...
[2022-03-17 19:49:09] parsing chr4...
[2022-03-17 19:49:09] parsing chr5...
[2022-03-17 19:49:09] parsing chr6...
[2022-03-17 19:49:09] parsing chr7...
[2022-03-17 19:49:09] parsing chr8...
[2022-03-17 19:49:09] parsing chr9...
[2022-03-17 19:49:09] parsing chrM...
[2022-03-17 19:49:09] parsing chrX...
[2022-03-17 19:49:09] parsing chrY...
[2022-03-17 19:49:09] 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 sample1_nanopolish.tsv sample2_nanopolish.tsv
[2022-03-17 19:49:09] creating bsseq object...
[2022-03-17 19:49:09] reading in parsed data...
[2022-03-17 19:49:09] constructing matrices...
[2022-03-17 19:49:10] done
[2022-03-17 19:49:10] creating methylation table
processing D:/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-03-17 19:49:10] sorting methylation table
[2022-03-17 19:49:10] compressing methylation table to tabix with index
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 51 ]
>
> proc.time()
user system elapsed
54.71 3.78 56.73
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 4.03 | 1.34 | 5.40 | |
| bsseq_to_edger | 1.36 | 0.28 | 1.37 | |
| bsseq_to_log_methy_ratio | 1.97 | 0.22 | 2.11 | |
| cluster_regions | 3.24 | 0.36 | 3.60 | |
| create_tabix_file | 0.51 | 0.27 | 0.56 | |
| exons | 0 | 0 | 0 | |
| exons_to_genes | 0.47 | 0.01 | 0.48 | |
| filter_methy | 1.97 | 0.24 | 2.28 | |
| get_example_exons_mus_musculus | 0.41 | 0.01 | 0.43 | |
| get_exons_homo_sapiens | 14.28 | 1.64 | 15.96 | |
| get_exons_mus_musculus | 16.11 | 1.91 | 18.11 | |
| load_example_nanomethresult | 0.72 | 0.09 | 0.88 | |
| methy | 0 | 0 | 0 | |
| methy_col_names | 0 | 0 | 0 | |
| methy_to_bsseq | 1.99 | 0.25 | 2.18 | |
| plot_agg_regions | 5.61 | 0.07 | 5.67 | |
| plot_gene | 3.25 | 0.12 | 3.38 | |
| plot_gene_heatmap | 10.39 | 0.11 | 10.50 | |
| plot_grange | 1.63 | 0.00 | 1.62 | |
| plot_grange_heatmap | 5.28 | 0.33 | 5.61 | |
| plot_mds | 1.68 | 0.27 | 1.65 | |
| plot_pca | 1.87 | 0.30 | 1.82 | |
| plot_region | 1.73 | 0.04 | 1.78 | |
| plot_region_heatmap | 8.27 | 0.08 | 8.35 | |
| query_methy | 0.54 | 0.02 | 0.57 | |
| region_methy_stats | 1.07 | 0.04 | 1.11 | |
| samples | 0 | 0 | 0 | |