Multiple platform build/check report for BioC 3.18 - CHECK results for chimeraviz on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"	4692
palomino4	Windows Server 2022 Datacenter	x64	4.3.2 (2023-10-31 ucrt) -- "Eye Holes"	4445
lconway	macOS 12.7.1 Monterey	x86_64	4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"	4466
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*

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### Running command:
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###   /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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/chimeraviz.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘1.28.0’
* 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                                36.400  1.145  41.796
plot_transcripts                           21.496  0.550  22.336
plot_fusion_transcript                     17.443  0.211  17.761
plot_fusion_transcripts_graph              10.759  0.175  11.009
plot_fusion_transcript_with_protein_domain 10.801  0.131  11.006
select_transcript                           7.618  0.103   7.859
get_transcripts_ensembl_db                  7.061  0.140   7.256
* 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-3.18-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chimeraviz
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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)

Tests output


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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 
193.769   5.543 203.566

Example timings

name	user	system	elapsed
add_fusion_reads_alignment	1.963	0.050	2.033
create_fusion_report	3.175	0.254	3.752
decide_transcript_category	0.244	0.009	0.256
down_shift	0.073	0.001	0.075
downstream_partner_gene	0.077	0.002	0.080
fetch_reads_from_fastq	0.001	0.000	0.000
fusion_spanning_reads_count	0.036	0.002	0.038
fusion_split_reads_count	0.038	0.004	0.042
fusion_to_data_frame	0.041	0.004	0.047
get_ensembl_ids	0.753	0.058	0.821
get_fusion_by_chromosome	0.041	0.005	0.048
get_fusion_by_gene_name	0.039	0.004	0.044
get_fusion_by_id	0.036	0.005	0.041
get_transcripts_ensembl_db	7.061	0.140	7.256
import_aeron	0.434	0.005	0.443
import_chimpipe	0.107	0.003	0.112
import_defuse	0.094	0.002	0.097
import_ericscript	0.104	0.003	0.108
import_fusioncatcher	0.099	0.002	0.101
import_fusionmap	0.096	0.002	0.100
import_infusion	0.111	0.002	0.114
import_jaffa	0.105	0.002	0.109
import_oncofuse	0.154	0.003	0.160
import_prada	0.085	0.002	0.088
import_soapfuse	0.096	0.002	0.098
import_squid	0.104	0.002	0.107
import_starfusion	0.087	0.002	0.089
partner_gene_ensembl_id	0.074	0.002	0.077
partner_gene_junction_sequence	0.040	0.001	0.042
plot_circle	0.665	0.040	0.689
plot_fusion	36.400	1.145	41.796
plot_fusion_reads	2.357	0.048	2.419
plot_fusion_transcript	17.443	0.211	17.761
plot_fusion_transcript_with_protein_domain	10.801	0.131	11.006
plot_fusion_transcripts_graph	10.759	0.175	11.009
plot_transcripts	21.496	0.550	22.336
select_transcript	7.618	0.103	7.859
split_on_utr_and_add_feature	0.464	0.010	0.482
upstream_partner_gene	0.083	0.003	0.087
write_fusion_reference	0.050	0.002	0.053

CHECK results for chimeraviz on lconway

Summary

Command output

Installation output

Tests output

Example timings