Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:37:27 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 328/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.28.0  (landing page)
Stian Lågstad
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/chimeraviz
git_branch: RELEASE_3_18
git_last_commit: 2a2ebf3
git_last_commit_date: 2023-10-24 10:54:26 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for chimeraviz on merida1


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.
- 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.

raw results


Summary

Package: chimeraviz
Version: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2024-03-26 00:27:12 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 00:48:57 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 1305.0 seconds
RetCode: 0
Status:   OK  
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/chimeraviz.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 12.7.1
* 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                                57.158  1.278  62.865
plot_transcripts                           39.600  0.669  43.583
plot_fusion_transcript                     32.779  0.183  34.243
plot_fusion_transcripts_graph              21.037  0.165  22.140
plot_fusion_transcript_with_protein_domain 20.572  0.105  21.507
get_transcripts_ensembl_db                 13.736  0.287  15.120
select_transcript                          12.992  0.069  14.405
* 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

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-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

chimeraviz.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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")
2024-03-26 00:42:43.416 R[52353:1893924040] XType: com.apple.fonts is not accessible.
2024-03-26 00:42:43.417 R[52353:1893924040] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 224 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
329.055   8.067 402.636 

Example timings

chimeraviz.Rcheck/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment2.3440.0732.508
create_fusion_report4.5280.2395.000
decide_transcript_category0.4140.0090.434
down_shift0.1030.0020.107
downstream_partner_gene0.1400.0030.147
fetch_reads_from_fastq0.0000.0010.001
fusion_spanning_reads_count0.0690.0020.078
fusion_split_reads_count0.0700.0020.072
fusion_to_data_frame0.0700.0030.073
get_ensembl_ids1.3410.0871.489
get_fusion_by_chromosome0.0760.0100.090
get_fusion_by_gene_name0.0790.0100.096
get_fusion_by_id0.0840.0130.099
get_transcripts_ensembl_db13.736 0.28715.120
import_aeron1.0670.0081.115
import_chimpipe0.1950.0030.210
import_defuse0.1990.0030.208
import_ericscript0.2050.0020.213
import_fusioncatcher0.2030.0030.216
import_fusionmap0.2000.0030.210
import_infusion0.2020.0020.216
import_jaffa0.2030.0020.216
import_oncofuse0.2000.0030.210
import_prada0.2020.0030.219
import_soapfuse0.2010.0030.215
import_squid0.1980.0030.213
import_starfusion0.2540.0060.270
partner_gene_ensembl_id0.1390.0030.148
partner_gene_junction_sequence0.0780.0020.086
plot_circle1.1800.0301.262
plot_fusion57.158 1.27862.865
plot_fusion_reads3.2090.0333.365
plot_fusion_transcript32.779 0.18334.243
plot_fusion_transcript_with_protein_domain20.572 0.10521.507
plot_fusion_transcripts_graph21.037 0.16522.140
plot_transcripts39.600 0.66943.583
select_transcript12.992 0.06914.405
split_on_utr_and_add_feature0.8030.0090.943
upstream_partner_gene0.1380.0030.174
write_fusion_reference0.0830.0030.100