Back to Multiple platform build/check report for BioC 3.15
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-19 11:11:11 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 merida1


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? here 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 294/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.21.0  (landing page)
Stian Lågstad
Snapshot Date: 2022-01-18 13:55:18 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/chimeraviz
git_branch: master
git_last_commit: ea91012
git_last_commit_date: 2021-10-26 12:31:52 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biostrings' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: chimeraviz
Version: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2022-01-18 23:06:55 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 23:23:23 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 988.4 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/chimeraviz.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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                                51.030  0.979  53.210
plot_transcripts                           35.181  0.551  35.799
plot_fusion_transcript                     27.425  0.103  27.579
plot_fusion_transcript_with_protein_domain 17.938  0.069  18.032
plot_fusion_transcripts_graph              17.828  0.093  17.950
get_transcripts_ensembl_db                 11.713  0.195  11.925
select_transcript                          10.818  0.024  10.857
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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

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
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 
289.498   3.929 298.382 

Example timings

chimeraviz.Rcheck/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment1.0880.0281.118
create_fusion_report4.0170.2584.569
decide_transcript_category0.3860.0050.409
down_shift0.1030.0010.104
downstream_partner_gene0.1240.0010.125
fetch_reads_from_fastq000
fusion_spanning_reads_count0.0620.0000.063
fusion_split_reads_count0.0620.0010.063
fusion_to_data_frame0.0650.0010.065
get_ensembl_ids0.8210.0130.835
get_fusion_by_chromosome0.0580.0010.059
get_fusion_by_gene_name0.0600.0010.061
get_fusion_by_id0.0640.0010.065
get_transcripts_ensembl_db11.713 0.19511.925
import_aeron0.9760.0040.981
import_chimpipe0.1700.0010.171
import_defuse0.1710.0000.171
import_ericscript0.1840.0010.185
import_fusioncatcher0.1750.0010.176
import_fusionmap0.1780.0000.179
import_infusion0.1710.0010.172
import_jaffa0.1770.0010.177
import_oncofuse0.1570.0010.159
import_prada0.1760.0010.178
import_soapfuse0.1770.0010.178
import_squid0.1500.0010.151
import_starfusion0.1790.0010.180
partner_gene_ensembl_id0.1610.0040.164
partner_gene_junction_sequence0.0680.0010.069
plot_circle1.0790.0311.112
plot_fusion51.030 0.97953.210
plot_fusion_reads2.9790.0263.009
plot_fusion_transcript27.425 0.10327.579
plot_fusion_transcript_with_protein_domain17.938 0.06918.032
plot_fusion_transcripts_graph17.828 0.09317.950
plot_transcripts35.181 0.55135.799
select_transcript10.818 0.02410.857
split_on_utr_and_add_feature0.7050.0040.710
upstream_partner_gene0.1270.0010.128
write_fusion_reference0.0710.0010.073