| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:28 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 318/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chimeraviz 1.27.0 (landing page) Stian Lågstad
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: chimeraviz |
| Version: 1.27.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings chimeraviz_1.27.0.tar.gz |
| StartedAt: 2023-06-05 19:16:48 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 19:34:11 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 1042.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings chimeraviz_1.27.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/chimeraviz.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘1.27.0’
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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 42.296 1.481 51.450
plot_transcripts 26.017 0.531 26.588
plot_fusion_transcript 21.137 0.267 21.436
plot_fusion_transcripts_graph 13.584 0.136 13.743
plot_fusion_transcript_with_protein_domain 13.124 0.064 13.207
get_transcripts_ensembl_db 8.571 0.315 8.904
select_transcript 8.197 0.032 8.242
* 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 ...
‘chimeraviz-vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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 0 | PASS 224 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
217.138 5.029 228.691
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| add_fusion_reads_alignment | 0.943 | 0.005 | 0.950 | |
| create_fusion_report | 3.286 | 0.088 | 3.388 | |
| decide_transcript_category | 0.309 | 0.000 | 0.311 | |
| down_shift | 0.071 | 0.000 | 0.071 | |
| downstream_partner_gene | 0.087 | 0.000 | 0.087 | |
| fetch_reads_from_fastq | 0.001 | 0.000 | 0.000 | |
| fusion_spanning_reads_count | 0.043 | 0.000 | 0.042 | |
| fusion_split_reads_count | 0.042 | 0.000 | 0.043 | |
| fusion_to_data_frame | 0.040 | 0.004 | 0.044 | |
| get_ensembl_ids | 0.605 | 0.016 | 0.622 | |
| get_fusion_by_chromosome | 0.045 | 0.000 | 0.045 | |
| get_fusion_by_gene_name | 0.044 | 0.000 | 0.044 | |
| get_fusion_by_id | 0.047 | 0.000 | 0.047 | |
| get_transcripts_ensembl_db | 8.571 | 0.315 | 8.904 | |
| import_aeron | 0.640 | 0.052 | 0.697 | |
| import_chimpipe | 0.169 | 0.020 | 0.190 | |
| import_defuse | 0.123 | 0.012 | 0.136 | |
| import_ericscript | 0.124 | 0.012 | 0.136 | |
| import_fusioncatcher | 0.123 | 0.008 | 0.132 | |
| import_fusionmap | 0.132 | 0.000 | 0.134 | |
| import_infusion | 0.134 | 0.000 | 0.135 | |
| import_jaffa | 0.125 | 0.003 | 0.130 | |
| import_oncofuse | 0.127 | 0.004 | 0.132 | |
| import_prada | 0.131 | 0.000 | 0.132 | |
| import_soapfuse | 0.128 | 0.000 | 0.129 | |
| import_squid | 0.123 | 0.000 | 0.124 | |
| import_starfusion | 0.164 | 0.044 | 0.208 | |
| partner_gene_ensembl_id | 0.087 | 0.004 | 0.092 | |
| partner_gene_junction_sequence | 0.049 | 0.004 | 0.053 | |
| plot_circle | 0.741 | 0.020 | 0.757 | |
| plot_fusion | 42.296 | 1.481 | 51.450 | |
| plot_fusion_reads | 2.700 | 0.072 | 2.775 | |
| plot_fusion_transcript | 21.137 | 0.267 | 21.436 | |
| plot_fusion_transcript_with_protein_domain | 13.124 | 0.064 | 13.207 | |
| plot_fusion_transcripts_graph | 13.584 | 0.136 | 13.743 | |
| plot_transcripts | 26.017 | 0.531 | 26.588 | |
| select_transcript | 8.197 | 0.032 | 8.242 | |
| split_on_utr_and_add_feature | 0.589 | 0.016 | 0.606 | |
| upstream_partner_gene | 0.088 | 0.004 | 0.092 | |
| write_fusion_reference | 0.052 | 0.004 | 0.056 | |