| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:23 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 302/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chimeraviz 1.25.0 (landing page) Stian Lågstad
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: chimeraviz |
| Version: 1.25.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chimeraviz.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings chimeraviz_1.25.0.tar.gz |
| StartedAt: 2022-12-28 22:25:21 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 22:33:23 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 481.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chimeraviz.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings chimeraviz_1.25.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/chimeraviz.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'chimeraviz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimeraviz' version '1.25.0'
* 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 22.83 0.47 24.33
plot_transcripts 14.09 0.36 14.52
plot_fusion_transcript 11.75 0.16 11.91
plot_fusion_transcript_with_protein_domain 7.29 0.06 7.35
plot_fusion_transcripts_graph 6.92 0.06 6.98
* 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/chimeraviz.Rcheck/00check.log'
for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'chimeraviz' ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chimeraviz)
chimeraviz.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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, aperm, 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
128.34 4.25 134.37
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| add_fusion_reads_alignment | 1.28 | 0.04 | 1.31 | |
| create_fusion_report | 1.13 | 0.87 | 3.13 | |
| decide_transcript_category | 0.17 | 0.00 | 0.17 | |
| down_shift | 0.04 | 0.00 | 0.04 | |
| downstream_partner_gene | 0.04 | 0.02 | 0.05 | |
| fetch_reads_from_fastq | 0 | 0 | 0 | |
| fusion_spanning_reads_count | 0.03 | 0.00 | 0.03 | |
| fusion_split_reads_count | 0.03 | 0.00 | 0.03 | |
| fusion_to_data_frame | 0.04 | 0.00 | 0.03 | |
| get_ensembl_ids | 1.07 | 0.00 | 1.09 | |
| get_fusion_by_chromosome | 0.02 | 0.01 | 0.04 | |
| get_fusion_by_gene_name | 0.03 | 0.00 | 0.03 | |
| get_fusion_by_id | 0.02 | 0.00 | 0.01 | |
| get_transcripts_ensembl_db | 4.61 | 0.11 | 4.72 | |
| import_aeron | 0.32 | 0.00 | 0.33 | |
| import_chimpipe | 0.07 | 0.02 | 0.08 | |
| import_defuse | 0.06 | 0.00 | 0.06 | |
| import_ericscript | 0.09 | 0.00 | 0.09 | |
| import_fusioncatcher | 0.08 | 0.00 | 0.08 | |
| import_fusionmap | 0.06 | 0.00 | 0.06 | |
| import_infusion | 0.07 | 0.00 | 0.07 | |
| import_jaffa | 0.06 | 0.01 | 0.08 | |
| import_oncofuse | 0.06 | 0.00 | 0.06 | |
| import_prada | 0.08 | 0.00 | 0.08 | |
| import_soapfuse | 0.06 | 0.00 | 0.06 | |
| import_squid | 0.06 | 0.00 | 0.06 | |
| import_starfusion | 0.07 | 0.00 | 0.06 | |
| partner_gene_ensembl_id | 0.04 | 0.00 | 0.05 | |
| partner_gene_junction_sequence | 0.03 | 0.00 | 0.03 | |
| plot_circle | 0.47 | 0.36 | 0.84 | |
| plot_fusion | 22.83 | 0.47 | 24.33 | |
| plot_fusion_reads | 1.58 | 0.06 | 1.67 | |
| plot_fusion_transcript | 11.75 | 0.16 | 11.91 | |
| plot_fusion_transcript_with_protein_domain | 7.29 | 0.06 | 7.35 | |
| plot_fusion_transcripts_graph | 6.92 | 0.06 | 6.98 | |
| plot_transcripts | 14.09 | 0.36 | 14.52 | |
| select_transcript | 4.70 | 0.08 | 4.78 | |
| split_on_utr_and_add_feature | 0.30 | 0.01 | 0.31 | |
| upstream_partner_gene | 0.08 | 0.00 | 0.08 | |
| write_fusion_reference | 0.05 | 0.00 | 0.05 | |