Multiple platform build/check report for BioC 3.12 - CHECK report for chimeraviz on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chimeraviz_1.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/chimeraviz.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘1.16.1’
* 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                                38.357  0.872  42.360
plot_transcripts                           25.718  0.463  26.216
plot_fusion_transcript                     20.277  0.094  20.398
plot_fusion_transcripts_graph              13.412  0.087  13.523
plot_fusion_transcript_with_protein_domain 12.804  0.070  12.895
get_transcripts_ensembl_db                  8.689  0.183   8.884
select_transcript                           8.579  0.020   8.606
* 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-3.12-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chimeraviz
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
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 
228.329   3.244 236.137

Example timings

name	user	system	elapsed
add_fusion_reads_alignment	1.585	0.025	1.612
create_fusion_report	3.333	0.169	3.615
decide_transcript_category	0.257	0.005	0.265
down_shift	0.077	0.002	0.078
downstream_partner_gene	0.098	0.004	0.101
fetch_reads_from_fastq	0.000	0.001	0.001
fusion_spanning_reads_count	0.051	0.005	0.055
fusion_split_reads_count	0.056	0.002	0.058
fusion_to_data_frame	0.050	0.004	0.055
get_ensembl_ids	0.466	0.023	0.490
get_fusion_by_chromosome	0.056	0.006	0.062
get_fusion_by_gene_name	0.061	0.008	0.068
get_fusion_by_id	0.055	0.006	0.061
get_transcripts_ensembl_db	8.689	0.183	8.884
import_aeron	0.752	0.003	0.757
import_chimpipe	0.132	0.001	0.133
import_defuse	0.127	0.001	0.128
import_ericscript	0.137	0.001	0.139
import_fusioncatcher	0.121	0.001	0.122
import_fusionmap	0.130	0.001	0.132
import_infusion	0.142	0.002	0.143
import_jaffa	0.134	0.001	0.135
import_oncofuse	0.140	0.001	0.141
import_prada	0.166	0.002	0.168
import_soapfuse	0.158	0.002	0.160
import_squid	0.116	0.001	0.117
import_starfusion	0.133	0.002	0.136
partner_gene_ensembl_id	0.097	0.002	0.098
partner_gene_junction_sequence	0.056	0.001	0.057
plot_circle	0.807	0.029	0.836
plot_fusion	38.357	0.872	42.360
plot_fusion_reads	2.137	0.021	2.162
plot_fusion_transcript	20.277	0.094	20.398
plot_fusion_transcript_with_protein_domain	12.804	0.070	12.895
plot_fusion_transcripts_graph	13.412	0.087	13.523
plot_transcripts	25.718	0.463	26.216
select_transcript	8.579	0.020	8.606
split_on_utr_and_add_feature	0.422	0.003	0.425
upstream_partner_gene	0.085	0.001	0.087
write_fusion_reference	0.101	0.001	0.102

CHECK report for chimeraviz on merida1

Summary

Command output

Installation output

Tests output

Example timings