Stian Lågstad
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/chimeraviz |
| git_branch: master |
| git_last_commit: ea91012 |
| git_last_commit_date: 2021-10-26 12:31:52 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:10 -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 chimeraviz package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chimeraviz.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 295/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chimeraviz 1.21.0 (landing page) Stian Lågstad
| 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: chimeraviz |
| Version: 1.21.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chimeraviz.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings chimeraviz_1.21.0.tar.gz |
| StartedAt: 2022-03-17 18:42:33 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:50:48 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 494.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chimeraviz.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings chimeraviz_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/chimeraviz.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 'chimeraviz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimeraviz' version '1.21.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biostrings', 'GenomicRanges', 'IRanges', 'Gviz', 'S4Vectors',
'ensembldb', 'AnnotationFilter', 'data.table'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'chimeraviz' 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
Namespace in Imports field not imported from: 'magick'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_fusion_transcript_with_protein_domain: no visible binding for
global variable 'protein_domain_location'
Undefined global functions or variables:
protein_domain_location
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_fusion 30.77 1.31 34.42
plot_transcripts 16.67 0.83 17.50
plot_fusion_transcript 13.36 0.15 13.52
plot_fusion_transcripts_graph 9.81 0.02 9.83
plot_fusion_transcript_with_protein_domain 8.08 0.05 8.12
* 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/chimeraviz.Rcheck/00check.log'
for details.
chimeraviz.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL chimeraviz
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'chimeraviz' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'chimeraviz'
finding HTML links ... done
Fusion-class html
PartnerGene-class html
add_fusion_reads_alignment html
chimeraviz-internals-fusions_to_gene_label_data
html
chimeraviz-internals-fusions_to_link_data
html
chimeraviz-internals-scaleListToInterval
html
chimeraviz html
create_fusion_report html
decide_transcript_category html
down_shift html
downstream_partner_gene html
fetch_reads_from_fastq html
fusion_spanning_reads_count html
fusion_split_reads_count html
fusion_to_data_frame html
get_ensembl_ids html
get_fusion_by_chromosome html
get_fusion_by_gene_name html
get_fusion_by_id html
get_transcripts_ensembl_db html
import_aeron html
import_chimpipe html
import_defuse html
import_ericscript html
import_function_non_ucsc html
import_fusioncatcher html
import_fusionmap html
import_infusion html
import_jaffa html
import_oncofuse html
import_prada html
import_soapfuse html
import_squid html
import_starfusion html
partner_gene_ensembl_id html
partner_gene_junction_sequence html
plot_circle html
plot_fusion html
plot_fusion_reads html
plot_fusion_transcript html
plot_fusion_transcript_with_protein_domain
html
plot_fusion_transcripts_graph html
plot_transcripts html
raw_Homo_sapiens.GRCh37.74 html
raw_chimpipe html
raw_cytobandhg19 html
raw_cytobandhg38 html
raw_defuse html
raw_ericscript html
raw_fusion5267proteindomains html
raw_fusion5267reads html
raw_fusion5267readsBedGraph html
raw_fusioncatcher html
raw_fusionmap html
raw_infusion html
raw_jaffa html
raw_oncofuse html
raw_prada html
raw_soapfuse html
raw_starfusion html
select_transcript html
show-Fusion-method html
show-PartnerGene-method html
split_on_utr_and_add_feature html
upstream_partner_gene html
write_fusion_reference 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 (chimeraviz)
Making 'packages.html' ... done
chimeraviz.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(chimeraviz)
Loading required package: Biostrings
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: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: GenomicRanges
Loading required package: Gviz
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:Biostrings':
pattern
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.
Loading required package: AnnotationFilter
Attaching package: 'AnnotationFilter'
The following object is masked from 'package:Gviz':
feature
The following object is masked from 'package:testthat':
not
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
>
> test_check("chimeraviz")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 219 ]
== Skipped tests ===============================================================
* On Windows (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 219 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
118.98 5.98 128.25
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| add_fusion_reads_alignment | 1.50 | 0.01 | 1.52 | |
| create_fusion_report | 1.31 | 0.77 | 3.03 | |
| decide_transcript_category | 0.23 | 0.00 | 0.23 | |
| down_shift | 0.06 | 0.01 | 0.08 | |
| downstream_partner_gene | 0.05 | 0.00 | 0.04 | |
| fetch_reads_from_fastq | 0 | 0 | 0 | |
| fusion_spanning_reads_count | 0.03 | 0.02 | 0.05 | |
| fusion_split_reads_count | 0.88 | 0.00 | 0.88 | |
| fusion_to_data_frame | 0.01 | 0.00 | 0.01 | |
| get_ensembl_ids | 0.28 | 0.00 | 0.28 | |
| get_fusion_by_chromosome | 0.03 | 0.00 | 0.03 | |
| get_fusion_by_gene_name | 0.02 | 0.00 | 0.02 | |
| get_fusion_by_id | 0.03 | 0.00 | 0.03 | |
| get_transcripts_ensembl_db | 4.28 | 0.08 | 4.36 | |
| import_aeron | 0.33 | 0.01 | 0.34 | |
| import_chimpipe | 0.11 | 0.00 | 0.11 | |
| import_defuse | 0.09 | 0.00 | 0.10 | |
| import_ericscript | 0.11 | 0.00 | 0.11 | |
| import_fusioncatcher | 0.10 | 0.00 | 0.09 | |
| import_fusionmap | 0.09 | 0.00 | 0.09 | |
| import_infusion | 0.08 | 0.00 | 0.08 | |
| import_jaffa | 0.06 | 0.00 | 0.07 | |
| import_oncofuse | 0.06 | 0.00 | 0.06 | |
| import_prada | 0.08 | 0.00 | 0.08 | |
| import_soapfuse | 0.08 | 0.00 | 0.08 | |
| import_squid | 0.08 | 0.00 | 0.08 | |
| import_starfusion | 0.09 | 0.00 | 0.09 | |
| partner_gene_ensembl_id | 0.05 | 0.00 | 0.04 | |
| partner_gene_junction_sequence | 0.03 | 0.00 | 0.04 | |
| plot_circle | 0.39 | 0.36 | 0.76 | |
| plot_fusion | 30.77 | 1.31 | 34.42 | |
| plot_fusion_reads | 1.98 | 0.10 | 2.08 | |
| plot_fusion_transcript | 13.36 | 0.15 | 13.52 | |
| plot_fusion_transcript_with_protein_domain | 8.08 | 0.05 | 8.12 | |
| plot_fusion_transcripts_graph | 9.81 | 0.02 | 9.83 | |
| plot_transcripts | 16.67 | 0.83 | 17.50 | |
| select_transcript | 4.91 | 0.00 | 4.91 | |
| split_on_utr_and_add_feature | 0.26 | 0.00 | 0.26 | |
| upstream_partner_gene | 0.05 | 0.00 | 0.05 | |
| write_fusion_reference | 0.02 | 0.01 | 0.03 | |