Stian Lågstad
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/chimeraviz |
| git_branch: RELEASE_3_17 |
| git_last_commit: 9ce5919 |
| git_last_commit_date: 2023-04-25 10:51:20 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 323/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chimeraviz 1.26.0 (landing page) Stian Lågstad
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the chimeraviz package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: chimeraviz |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chimeraviz_1.26.0.tar.gz |
| StartedAt: 2023-10-17 08:41:06 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 08:59:07 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 1080.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chimeraviz_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/chimeraviz.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘1.26.0’
* 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 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 35.874 0.701 63.349
plot_transcripts 24.065 0.453 37.575
plot_fusion_transcript 19.483 0.226 28.396
plot_fusion_transcripts_graph 12.579 0.176 19.602
plot_fusion_transcript_with_protein_domain 12.285 0.132 18.833
get_transcripts_ensembl_db 7.941 0.186 12.454
select_transcript 7.906 0.076 12.373
create_fusion_report 2.869 0.480 7.951
* 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-3.17-bioc-mac-arm64/meat/chimeraviz.Rcheck/00check.log’
for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
199.872 4.021 313.997
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| add_fusion_reads_alignment | 0.946 | 0.025 | 1.485 | |
| create_fusion_report | 2.869 | 0.480 | 7.951 | |
| decide_transcript_category | 0.250 | 0.008 | 0.391 | |
| down_shift | 0.075 | 0.001 | 0.121 | |
| downstream_partner_gene | 0.078 | 0.003 | 0.122 | |
| fetch_reads_from_fastq | 0 | 0 | 0 | |
| fusion_spanning_reads_count | 0.037 | 0.002 | 0.060 | |
| fusion_split_reads_count | 0.037 | 0.002 | 0.063 | |
| fusion_to_data_frame | 0.038 | 0.001 | 0.062 | |
| get_ensembl_ids | 0.702 | 0.052 | 1.169 | |
| get_fusion_by_chromosome | 0.038 | 0.001 | 0.058 | |
| get_fusion_by_gene_name | 0.038 | 0.002 | 0.060 | |
| get_fusion_by_id | 0.038 | 0.001 | 0.061 | |
| get_transcripts_ensembl_db | 7.941 | 0.186 | 12.454 | |
| import_aeron | 0.566 | 0.009 | 0.888 | |
| import_chimpipe | 0.107 | 0.002 | 0.172 | |
| import_defuse | 0.108 | 0.002 | 0.176 | |
| import_ericscript | 0.118 | 0.002 | 0.187 | |
| import_fusioncatcher | 0.109 | 0.002 | 0.171 | |
| import_fusionmap | 0.112 | 0.003 | 0.179 | |
| import_infusion | 0.113 | 0.003 | 0.179 | |
| import_jaffa | 0.110 | 0.003 | 0.176 | |
| import_oncofuse | 0.155 | 0.003 | 0.242 | |
| import_prada | 0.109 | 0.003 | 0.178 | |
| import_soapfuse | 0.107 | 0.002 | 0.166 | |
| import_squid | 0.105 | 0.002 | 0.170 | |
| import_starfusion | 0.107 | 0.003 | 0.169 | |
| partner_gene_ensembl_id | 0.074 | 0.002 | 0.120 | |
| partner_gene_junction_sequence | 0.045 | 0.001 | 0.071 | |
| plot_circle | 0.826 | 0.022 | 1.270 | |
| plot_fusion | 35.874 | 0.701 | 63.349 | |
| plot_fusion_reads | 2.150 | 0.030 | 3.278 | |
| plot_fusion_transcript | 19.483 | 0.226 | 28.396 | |
| plot_fusion_transcript_with_protein_domain | 12.285 | 0.132 | 18.833 | |
| plot_fusion_transcripts_graph | 12.579 | 0.176 | 19.602 | |
| plot_transcripts | 24.065 | 0.453 | 37.575 | |
| select_transcript | 7.906 | 0.076 | 12.373 | |
| split_on_utr_and_add_feature | 0.470 | 0.010 | 0.737 | |
| upstream_partner_gene | 0.078 | 0.003 | 0.123 | |
| write_fusion_reference | 0.045 | 0.002 | 0.076 | |