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CHECK report for chimeraviz on malbec2

This page was generated on 2019-10-16 12:10:05 -0400 (Wed, 16 Oct 2019).

Package 255/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.10.0
Stian Lågstad
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/chimeraviz
Branch: RELEASE_3_9
Last Commit: c764369
Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chimeraviz
Version: 1.10.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings chimeraviz_1.10.0.tar.gz
StartedAt: 2019-10-16 00:26:29 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:35:03 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 513.9 seconds
RetCode: 0
Status:  OK 
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings chimeraviz_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/chimeraviz.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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 ... OK
* 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 or elapsed time > 5s
                                             user system elapsed
plot_transcripts                           19.862  0.331  20.355
plot_fusion                                18.180  0.111  18.342
plot_fusion_transcript                     16.659  0.012  16.991
plot_fusion_transcript_with_protein_domain 11.982  0.016   9.156
plot_fusion_transcripts_graph               8.925  0.008   8.967
get_transcripts_ensembl_db                  5.902  0.124   6.026
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.



Installation output

chimeraviz.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL chimeraviz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 171 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 97.998   1.819  96.707 

Example timings

chimeraviz.Rcheck/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment1.7570.0081.772
create_fusion_report4.3130.3844.833
decide_transcript_category0.2580.0080.279
down_shift0.0740.0080.082
downstream_partner_gene0.1110.0080.119
fetch_reads_from_fastq0.0010.0000.001
fusion_spanning_reads_count0.0570.0080.065
fusion_split_reads_count0.0560.0040.060
fusion_to_data_frame0.0560.0080.064
get_ensembl_ids0.6070.0360.643
get_fusion_by_chromosome0.0660.0040.070
get_fusion_by_gene_name0.0690.0040.073
get_fusion_by_id0.0610.0040.065
get_transcripts_ensembl_db5.9020.1246.026
import_defuse0.1640.0000.164
import_ericscript0.1680.0000.292
import_fusioncatcher0.1580.0000.212
import_fusionmap0.130.000.30
import_infusion0.1340.0000.134
import_jaffa0.130.000.13
import_oncofuse0.1340.0000.134
import_prada0.1480.0000.149
import_soapfuse0.1270.0000.126
import_starfusion0.1250.0040.129
partner_gene_ensembl_id0.0910.0000.092
partner_gene_junction_sequence0.0510.0040.055
plot_circle0.9360.0320.969
plot_fusion18.180 0.11118.342
plot_fusion_reads3.6610.0243.702
plot_fusion_transcript16.659 0.01216.991
plot_fusion_transcript_with_protein_domain11.982 0.016 9.156
plot_fusion_transcripts_graph8.9250.0088.967
plot_transcripts19.862 0.33120.355
select_transcript3.6240.0013.624
split_on_utr_and_add_feature0.3560.0000.356
upstream_partner_gene0.1190.0000.120
write_fusion_reference0.070.000.07