Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:05:45 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for chimeraviz on palomino3


To the developers/maintainers of the chimeraviz package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 305/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.22.0  (landing page)
Stian Lågstad
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/chimeraviz
git_branch: RELEASE_3_15
git_last_commit: 6426ef0
git_last_commit_date: 2022-04-26 11:37:53 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: chimeraviz
Version: 1.22.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chimeraviz.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings chimeraviz_1.22.0.tar.gz
StartedAt: 2022-06-23 23:40:04 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:50:57 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 652.9 seconds
RetCode: 0
Status:   OK  
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chimeraviz.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings chimeraviz_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/chimeraviz.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.22.0'
* 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 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                                34.67   0.73   37.00
plot_transcripts                           20.41   0.53   20.95
plot_fusion_transcript                     18.37   0.20   18.58
plot_fusion_transcript_with_protein_domain 11.46   0.11   11.56
plot_fusion_transcripts_graph              10.32   0.12   10.45
select_transcript                           7.39   0.05    7.44
get_transcripts_ensembl_db                  7.05   0.14    7.19
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/chimeraviz.Rcheck/00check.log'
for details.



Installation output

chimeraviz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL chimeraviz
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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 2 | PASS 219 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 219 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 184.79    4.59  191.37 

Example timings

chimeraviz.Rcheck/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment1.700.031.74
create_fusion_report1.440.783.97
decide_transcript_category0.300.010.31
down_shift0.090.000.10
downstream_partner_gene0.080.020.09
fetch_reads_from_fastq000
fusion_spanning_reads_count0.050.000.05
fusion_split_reads_count0.030.020.05
fusion_to_data_frame0.060.000.06
get_ensembl_ids1.690.031.72
get_fusion_by_chromosome0.030.000.03
get_fusion_by_gene_name0.030.000.03
get_fusion_by_id0.030.000.03
get_transcripts_ensembl_db7.050.147.19
import_aeron0.670.000.73
import_chimpipe0.130.000.12
import_defuse0.140.000.14
import_ericscript0.120.000.13
import_fusioncatcher0.140.000.14
import_fusionmap0.080.000.08
import_infusion0.080.020.09
import_jaffa0.080.000.08
import_oncofuse0.090.000.09
import_prada0.110.000.11
import_soapfuse0.130.000.13
import_squid0.080.000.08
import_starfusion0.080.000.08
partner_gene_ensembl_id0.050.010.06
partner_gene_junction_sequence0.030.020.05
plot_circle0.620.391.14
plot_fusion34.67 0.7337.00
plot_fusion_reads2.350.102.45
plot_fusion_transcript18.37 0.2018.58
plot_fusion_transcript_with_protein_domain11.46 0.1111.56
plot_fusion_transcripts_graph10.32 0.1210.45
plot_transcripts20.41 0.5320.95
select_transcript7.390.057.44
split_on_utr_and_add_feature0.340.030.38
upstream_partner_gene0.070.000.06
write_fusion_reference0.030.000.03