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 13:20:35 -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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings NanoMethViz_2.2.0.tar.gz |
| StartedAt: 2022-10-18 20:48:41 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 20:55:10 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 389.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NanoMethViz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings NanoMethViz_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 15.895 0.908 16.804
get_exons_mus_musculus 13.407 0.319 13.727
plot_gene_heatmap 8.997 0.095 9.092
plot_region_heatmap 8.866 0.091 8.958
plot_agg_regions 5.272 0.040 5.311
* 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
‘/home/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/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++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o utils.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/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-pc-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")
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
[2022-10-18 20:54:30] creating intermediate files...
[2022-10-18 20:54:30] parsing chr11...
[2022-10-18 20:54:30] parsing chr12...
[2022-10-18 20:54:30] parsing chr18...
[2022-10-18 20:54:30] parsing chr5...
[2022-10-18 20:54:30] parsing chr7...
[2022-10-18 20:54:30] parsing chrX...
[2022-10-18 20:54:30] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
[2022-10-18 20:54:30] creating bsseq object...
[2022-10-18 20:54:30] reading in parsed data...
[2022-10-18 20:54:31] constructing matrices...
[2022-10-18 20:54:32] done
[2022-10-18 20:54:32] creating intermediate files...
[2022-10-18 20:54:32] parsing chr11...
[2022-10-18 20:54:32] parsing chr12...
[2022-10-18 20:54:32] parsing chr18...
[2022-10-18 20:54:32] parsing chr5...
[2022-10-18 20:54:33] parsing chr7...
[2022-10-18 20:54:33] parsing chrX...
[2022-10-18 20:54:33] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
[2022-10-18 20:54:33] creating bsseq object...
[2022-10-18 20:54:33] reading in parsed data...
[2022-10-18 20:54:33] constructing matrices...
[2022-10-18 20:54:33] done
[2022-10-18 20:54:33] creating intermediate files...
[2022-10-18 20:54:33] parsing chr11...
[2022-10-18 20:54:33] parsing chr12...
[2022-10-18 20:54:33] parsing chr18...
[2022-10-18 20:54:33] parsing chr5...
[2022-10-18 20:54:33] parsing chr7...
[2022-10-18 20:54:33] parsing chrX...
[2022-10-18 20:54:33] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
[2022-10-18 20:54:33] creating bsseq object...
[2022-10-18 20:54:33] reading in parsed data...
[2022-10-18 20:54:33] constructing matrices...
[2022-10-18 20:54:34] done
[2022-10-18 20:54:34] creating intermediate files...
[2022-10-18 20:54:34] parsing chr11...
[2022-10-18 20:54:34] parsing chr12...
[2022-10-18 20:54:34] parsing chr18...
[2022-10-18 20:54:34] parsing chr5...
[2022-10-18 20:54:34] parsing chr7...
[2022-10-18 20:54:34] parsing chrX...
[2022-10-18 20:54:34] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
[2022-10-18 20:54:34] creating bsseq object...
[2022-10-18 20:54:34] reading in parsed data...
[2022-10-18 20:54:35] constructing matrices...
[2022-10-18 20:54:35] done
processing /home/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/sample1_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
processing /home/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/sample2_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
[2022-10-18 20:55:06] sorting methylation table
[2022-10-18 20:55:06] compressing methylation table to tabix with index
[2022-10-18 20:55:06] creating intermediate files...
[2022-10-18 20:55:06] parsing chr1...
[2022-10-18 20:55:06] parsing chr2...
[2022-10-18 20:55:06] parsing chr3...
[2022-10-18 20:55:06] parsing chr4...
[2022-10-18 20:55:06] parsing chr5...
[2022-10-18 20:55:06] parsing chr6...
[2022-10-18 20:55:06] parsing chr7...
[2022-10-18 20:55:06] parsing chr8...
[2022-10-18 20:55:06] parsing chr9...
[2022-10-18 20:55:06] parsing chr10...
[2022-10-18 20:55:06] parsing chr11...
[2022-10-18 20:55:06] parsing chr12...
[2022-10-18 20:55:06] parsing chr13...
[2022-10-18 20:55:06] parsing chr14...
[2022-10-18 20:55:06] parsing chr15...
[2022-10-18 20:55:06] parsing chr16...
[2022-10-18 20:55:06] parsing chr17...
[2022-10-18 20:55:06] parsing chr18...
[2022-10-18 20:55:06] parsing chr19...
[2022-10-18 20:55:06] parsing chrM...
[2022-10-18 20:55:06] parsing chrX...
[2022-10-18 20:55:06] parsing chrY...
[2022-10-18 20:55:06] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6 sample1_nanopolish.tsv sample2_nanopolish.tsv
[2022-10-18 20:55:06] creating bsseq object...
[2022-10-18 20:55:06] reading in parsed data...
[2022-10-18 20:55:06] constructing matrices...
[2022-10-18 20:55:07] done
processing /home/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-10-18 20:55:07] sorting methylation table
[2022-10-18 20:55:07] 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
52.152 2.217 53.546
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 3.481 | 0.304 | 3.787 | |
| bsseq_to_edger | 0.758 | 0.097 | 0.810 | |
| bsseq_to_log_methy_ratio | 2.426 | 0.145 | 2.464 | |
| cluster_regions | 3.208 | 0.155 | 3.363 | |
| create_tabix_file | 0.186 | 0.013 | 0.197 | |
| exons | 0.002 | 0.000 | 0.002 | |
| exons_to_genes | 0.549 | 0.008 | 0.557 | |
| filter_methy | 2.623 | 0.036 | 2.645 | |
| get_example_exons_mus_musculus | 0.484 | 0.012 | 0.495 | |
| get_exons_homo_sapiens | 15.895 | 0.908 | 16.804 | |
| get_exons_mus_musculus | 13.407 | 0.319 | 13.727 | |
| load_example_nanomethresult | 0.478 | 0.012 | 0.489 | |
| methy | 0.000 | 0.001 | 0.001 | |
| methy_col_names | 0 | 0 | 0 | |
| methy_to_bsseq | 1.379 | 0.098 | 1.350 | |
| methy_to_edger | 2.669 | 0.231 | 2.699 | |
| plot_agg_regions | 5.272 | 0.040 | 5.311 | |
| plot_gene | 2.253 | 0.060 | 2.312 | |
| plot_gene_heatmap | 8.997 | 0.095 | 9.092 | |
| plot_grange | 1.345 | 0.024 | 1.369 | |
| plot_grange_heatmap | 3.393 | 0.080 | 3.473 | |
| plot_mds | 1.789 | 0.113 | 1.691 | |
| plot_pca | 2.071 | 0.103 | 1.811 | |
| plot_region | 2.146 | 0.044 | 2.189 | |
| plot_region_heatmap | 8.866 | 0.091 | 8.958 | |
| query_methy | 0.677 | 0.016 | 0.693 | |
| region_methy_stats | 1.502 | 0.028 | 1.529 | |
| samples | 0.000 | 0.001 | 0.001 | |