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CHECK report for chimeraviz on malbec2

This page was generated on 2018-10-17 08:29:42 -0400 (Wed, 17 Oct 2018).

Package 226/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.6.2
Stian Lågstad
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/chimeraviz
Branch: RELEASE_3_7
Last Commit: 7dc4fd3
Last Changed Date: 2018-09-19 14:15:16 -0400 (Wed, 19 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chimeraviz
Version: 1.6.2
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings chimeraviz_1.6.2.tar.gz
StartedAt: 2018-10-15 23:07:39 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:14:12 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 392.6 seconds
RetCode: 0
Status:  OK 
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings chimeraviz_1.6.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/chimeraviz.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.2’
* 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_fusion                                23.704  0.540  24.346
plot_transcripts                           12.752  0.276  13.036
plot_fusion_transcript                     11.636  0.004  11.647
plot_fusion_transcripts_graph               7.556  0.008   7.572
plot_fusion_transcript_with_protein_domain  6.984  0.000   7.154
get_transcripts_ensembl_db                  4.932  0.064   5.001
* 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-3.7-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.



Installation output

chimeraviz.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL chimeraviz
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘chimeraviz’ ...
** 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
* DONE (chimeraviz)

Tests output

chimeraviz.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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: 149 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 85.896   2.136  88.250 

Example timings

chimeraviz.Rcheck/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment0.6800.0120.705
create_fusion_report2.6520.2763.519
decide_transcript_category0.2280.0120.237
down_shift0.0480.0000.050
downstream_partner_gene0.0800.0120.095
fetch_reads_from_fastq0.0000.0000.001
fusion_spanning_reads_count0.0480.0000.047
fusion_split_reads_count0.0440.0040.049
fusion_to_data_frame0.0480.0040.052
get_ensembl_ids0.3720.0080.377
get_fusion_by_chromosome0.0360.0080.045
get_fusion_by_gene_name0.0400.0040.044
get_fusion_by_id0.0440.0000.048
get_transcripts_ensembl_db4.9320.0645.001
import_defuse0.1160.0000.116
import_ericscript0.1200.0000.125
import_fusioncatcher0.1240.0000.137
import_fusionmap0.1200.0040.122
import_infusion0.1240.0000.122
import_jaffa0.1200.0000.119
import_prada0.1440.0000.145
import_soapfuse0.1160.0000.115
import_starfusion0.1240.0000.125
partner_gene_ensembl_id0.0840.0000.086
partner_gene_junction_sequence0.0480.0000.047
plot_circle0.7320.0160.746
plot_fusion23.704 0.54024.346
plot_fusion_reads1.6760.0241.713
plot_fusion_transcript11.636 0.00411.647
plot_fusion_transcript_with_protein_domain6.9840.0007.154
plot_fusion_transcripts_graph7.5560.0087.572
plot_transcripts12.752 0.27613.036
select_transcript4.2760.0004.281
split_on_utr_and_add_feature0.2840.0000.284
upstream_partner_gene0.0840.0000.082
write_fusion_reference0.0520.0000.050