Shian Su
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/NanoMethViz |
| git_branch: RELEASE_3_15 |
| git_last_commit: ccc98e8 |
| git_last_commit_date: 2022-04-26 12:10:18 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:21 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1296/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoMethViz 2.2.0 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | 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: 2.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoMethViz_2.2.0.tar.gz |
| StartedAt: 2022-10-19 05:20:06 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 05:32:32 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 745.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NanoMethViz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoMethViz_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘2.2.0’
* 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
* 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 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_homo_sapiens 25.590 1.320 26.966
get_exons_mus_musculus 23.882 1.083 25.049
plot_gene_heatmap 21.031 0.157 21.226
plot_region_heatmap 20.670 0.172 20.873
plot_agg_regions 12.637 0.121 12.771
NanoMethResult-class 7.052 0.816 7.880
plot_grange_heatmap 7.465 0.052 7.525
cluster_regions 6.590 0.217 6.816
plot_gene 4.953 0.069 5.037
* 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
‘/Users/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
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
[2022-10-19 05:31:06] creating intermediate files...
[2022-10-19 05:31:06] parsing chr11...
[2022-10-19 05:31:06] parsing chr12...
[2022-10-19 05:31:06] parsing chr18...
[2022-10-19 05:31:06] parsing chr5...
[2022-10-19 05:31:06] parsing chr7...
[2022-10-19 05:31:07] parsing chrX...
[2022-10-19 05:31:07] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6
[2022-10-19 05:31:07] creating bsseq object...
[2022-10-19 05:31:07] reading in parsed data...
[2022-10-19 05:31:07] constructing matrices...
[2022-10-19 05:31:07] done
[2022-10-19 05:31:09] creating intermediate files...
[2022-10-19 05:31:09] parsing chr11...
[2022-10-19 05:31:09] parsing chr12...
[2022-10-19 05:31:09] parsing chr18...
[2022-10-19 05:31:09] parsing chr5...
[2022-10-19 05:31:09] parsing chr7...
[2022-10-19 05:31:09] parsing chrX...
[2022-10-19 05:31:09] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6
[2022-10-19 05:31:09] creating bsseq object...
[2022-10-19 05:31:09] reading in parsed data...
[2022-10-19 05:31:10] constructing matrices...
[2022-10-19 05:31:10] done
[2022-10-19 05:31:10] creating intermediate files...
[2022-10-19 05:31:10] parsing chr11...
[2022-10-19 05:31:10] parsing chr12...
[2022-10-19 05:31:11] parsing chr18...
[2022-10-19 05:31:11] parsing chr5...
[2022-10-19 05:31:11] parsing chr7...
[2022-10-19 05:31:11] parsing chrX...
[2022-10-19 05:31:11] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6
[2022-10-19 05:31:11] creating bsseq object...
[2022-10-19 05:31:11] reading in parsed data...
[2022-10-19 05:31:11] constructing matrices...
[2022-10-19 05:31:12] done
[2022-10-19 05:31:12] creating intermediate files...
[2022-10-19 05:31:12] parsing chr11...
[2022-10-19 05:31:13] parsing chr12...
[2022-10-19 05:31:13] parsing chr18...
[2022-10-19 05:31:13] parsing chr5...
[2022-10-19 05:31:13] parsing chr7...
[2022-10-19 05:31:13] parsing chrX...
[2022-10-19 05:31:13] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6
[2022-10-19 05:31:13] creating bsseq object...
[2022-10-19 05:31:13] reading in parsed data...
[2022-10-19 05:31:13] constructing matrices...
[2022-10-19 05:31:14] done
processing /Library/Frameworks/R.framework/Versions/4.2/Resources/library/NanoMethViz/sample1_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
processing /Library/Frameworks/R.framework/Versions/4.2/Resources/library/NanoMethViz/sample2_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
[2022-10-19 05:32:20] sorting methylation table
[2022-10-19 05:32:20] compressing methylation table to tabix with index
[2022-10-19 05:32:20] creating intermediate files...
[2022-10-19 05:32:20] parsing chr1...
[2022-10-19 05:32:20] parsing chr2...
[2022-10-19 05:32:20] parsing chr3...
[2022-10-19 05:32:20] parsing chr4...
[2022-10-19 05:32:20] parsing chr5...
[2022-10-19 05:32:20] parsing chr6...
[2022-10-19 05:32:20] parsing chr7...
[2022-10-19 05:32:20] parsing chr8...
[2022-10-19 05:32:20] parsing chr9...
[2022-10-19 05:32:20] parsing chr10...
[2022-10-19 05:32:20] parsing chr11...
[2022-10-19 05:32:20] parsing chr12...
[2022-10-19 05:32:20] parsing chr13...
[2022-10-19 05:32:20] parsing chr14...
[2022-10-19 05:32:20] parsing chr15...
[2022-10-19 05:32:20] parsing chr16...
[2022-10-19 05:32:20] parsing chr17...
[2022-10-19 05:32:20] parsing chr18...
[2022-10-19 05:32:20] parsing chr19...
[2022-10-19 05:32:20] parsing chrM...
[2022-10-19 05:32:20] parsing chrX...
[2022-10-19 05:32:20] parsing chrY...
[2022-10-19 05:32:20] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 sample1_nanopolish.tsv sample2_nanopolish.tsv
[2022-10-19 05:32:20] creating bsseq object...
[2022-10-19 05:32:20] reading in parsed data...
[2022-10-19 05:32:20] constructing matrices...
[2022-10-19 05:32:21] done
processing /Library/Frameworks/R.framework/Versions/4.2/Resources/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-10-19 05:32:22] sorting methylation table
[2022-10-19 05:32:22] compressing methylation table to tabix with index
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 51 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 51 ]
>
> proc.time()
user system elapsed
107.857 2.676 110.146
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 7.052 | 0.816 | 7.880 | |
| bsseq_to_edger | 1.613 | 0.072 | 1.636 | |
| bsseq_to_log_methy_ratio | 3.736 | 0.099 | 3.767 | |
| cluster_regions | 6.590 | 0.217 | 6.816 | |
| create_tabix_file | 0.325 | 0.034 | 0.362 | |
| exons | 0.004 | 0.000 | 0.004 | |
| exons_to_genes | 0.975 | 0.025 | 1.001 | |
| filter_methy | 3.812 | 0.150 | 3.979 | |
| get_example_exons_mus_musculus | 0.898 | 0.025 | 0.926 | |
| get_exons_homo_sapiens | 25.590 | 1.320 | 26.966 | |
| get_exons_mus_musculus | 23.882 | 1.083 | 25.049 | |
| load_example_nanomethresult | 0.947 | 0.029 | 0.977 | |
| methy | 0.000 | 0.000 | 0.001 | |
| methy_col_names | 0.001 | 0.000 | 0.000 | |
| methy_to_bsseq | 2.470 | 0.088 | 2.489 | |
| methy_to_edger | 2.847 | 0.098 | 2.833 | |
| plot_agg_regions | 12.637 | 0.121 | 12.771 | |
| plot_gene | 4.953 | 0.069 | 5.037 | |
| plot_gene_heatmap | 21.031 | 0.157 | 21.226 | |
| plot_grange | 2.717 | 0.038 | 2.760 | |
| plot_grange_heatmap | 7.465 | 0.052 | 7.525 | |
| plot_mds | 3.334 | 0.090 | 3.291 | |
| plot_pca | 3.351 | 0.078 | 3.273 | |
| plot_region | 4.651 | 0.055 | 4.717 | |
| plot_region_heatmap | 20.670 | 0.172 | 20.873 | |
| query_methy | 1.193 | 0.025 | 1.219 | |
| region_methy_stats | 2.724 | 0.036 | 2.763 | |
| samples | 0.001 | 0.000 | 0.002 | |