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CHECK report for chimeraviz on tokay1

This page was generated on 2020-08-10 12:21:42 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE chimeraviz PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 269/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.15.0
Stian Lågstad
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/chimeraviz
Branch: master
Last Commit: 82f67eb
Last Changed Date: 2020-05-24 06:06:11 -0400 (Sun, 24 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: chimeraviz
Version: 1.15.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings chimeraviz_1.15.0.tar.gz
StartedAt: 2020-08-10 03:32:45 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 03:53:26 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 1241.1 seconds
RetCode: 0
Status:  OK  
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings chimeraviz_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/chimeraviz.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chimeraviz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimeraviz' version '1.15.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
plot_fusion                                41.01   1.02   42.83
plot_transcripts                           28.31   1.34   30.38
plot_fusion_transcript                     19.23   0.03   19.27
plot_fusion_transcripts_graph              15.55   0.05   15.59
plot_fusion_transcript_with_protein_domain 13.17   0.05   13.48
select_transcript                           9.75   0.02   10.19
get_transcripts_ensembl_db                  8.66   1.00    9.66
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
plot_fusion                                38.34   0.89   39.90
plot_transcripts                           20.73   0.23   20.97
plot_fusion_transcript                     18.75   0.07   18.81
plot_fusion_transcript_with_protein_domain 13.83   0.04   13.87
plot_fusion_transcripts_graph              11.58   0.02   11.60
get_transcripts_ensembl_db                 10.11   0.19   10.29
select_transcript                           7.39   0.02    7.40
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/chimeraviz.Rcheck/00check.log'
for details.



Installation output

chimeraviz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/chimeraviz_1.15.0.tar.gz && rm -rf chimeraviz.buildbin-libdir && mkdir chimeraviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chimeraviz.buildbin-libdir chimeraviz_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL chimeraviz_1.15.0.zip && rm chimeraviz_1.15.0.tar.gz chimeraviz_1.15.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2620k  100 2620k    0     0  24.0M      0 --:--:-- --:--:-- --:--:-- 25.0M

install for i386

* installing *source* package 'chimeraviz' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chimeraviz'
    finding HTML links ... done
    Fusion-class                            html  
    PartnerGene-class                       html  
    add_fusion_reads_alignment              html  
    chimeraviz-internals-fusions_to_gene_label_data
                                            html  
    chimeraviz-internals-fusions_to_link_data
                                            html  
    chimeraviz-internals-scaleListToInterval
                                            html  
    chimeraviz                              html  
    create_fusion_report                    html  
    decide_transcript_category              html  
    down_shift                              html  
    downstream_partner_gene                 html  
    fetch_reads_from_fastq                  html  
    fusion_spanning_reads_count             html  
    fusion_split_reads_count                html  
    fusion_to_data_frame                    html  
    get_ensembl_ids                         html  
    get_fusion_by_chromosome                html  
    get_fusion_by_gene_name                 html  
    get_fusion_by_id                        html  
    get_transcripts_ensembl_db              html  
    import_aeron                            html  
    import_chimpipe                         html  
    import_defuse                           html  
    import_ericscript                       html  
    import_function_non_ucsc                html  
    import_fusioncatcher                    html  
    import_fusionmap                        html  
    import_infusion                         html  
    import_jaffa                            html  
    import_oncofuse                         html  
    import_prada                            html  
    import_soapfuse                         html  
    import_squid                            html  
    import_starfusion                       html  
    partner_gene_ensembl_id                 html  
    partner_gene_junction_sequence          html  
    plot_circle                             html  
    plot_fusion                             html  
    plot_fusion_reads                       html  
    plot_fusion_transcript                  html  
    plot_fusion_transcript_with_protein_domain
                                            html  
    plot_fusion_transcripts_graph           html  
    plot_transcripts                        html  
    raw_Homo_sapiens.GRCh37.74              html  
    raw_chimpipe                            html  
    raw_cytobandhg19                        html  
    raw_cytobandhg38                        html  
    raw_defuse                              html  
    raw_ericscript                          html  
    raw_fusion5267proteindomains            html  
    raw_fusion5267reads                     html  
    raw_fusion5267readsBedGraph             html  
    raw_fusioncatcher                       html  
    raw_fusionmap                           html  
    raw_infusion                            html  
    raw_jaffa                               html  
    raw_oncofuse                            html  
    raw_prada                               html  
    raw_soapfuse                            html  
    raw_starfusion                          html  
    select_transcript                       html  
    show-Fusion-method                      html  
    show-PartnerGene-method                 html  
    split_on_utr_and_add_feature            html  
    upstream_partner_gene                   html  
    write_fusion_reference                  html  
** 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

install for x64

* installing *source* package 'chimeraviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chimeraviz' as chimeraviz_1.15.0.zip
* DONE (chimeraviz)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'chimeraviz' successfully unpacked and MD5 sums checked

Tests output

chimeraviz.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.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

Attaching package: 'IRanges'

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

    windows

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: 219 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 182.43    8.28  193.00 

chimeraviz.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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
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.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

Attaching package: 'IRanges'

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

    windows

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: 219 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 264.43    4.89  273.92 

Example timings

chimeraviz.Rcheck/examples_i386/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment0.810.100.91
create_fusion_report2.540.944.02
decide_transcript_category0.280.010.30
down_shift0.150.000.15
downstream_partner_gene0.110.000.11
fetch_reads_from_fastq000
fusion_spanning_reads_count0.070.000.07
fusion_split_reads_count0.060.000.06
fusion_to_data_frame0.050.000.05
get_ensembl_ids0.530.050.58
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_db8.661.009.66
import_aeron0.810.010.87
import_chimpipe0.190.000.19
import_defuse0.140.000.14
import_ericscript0.110.020.13
import_fusioncatcher0.090.000.09
import_fusionmap0.090.000.10
import_infusion0.100.000.09
import_jaffa0.090.000.09
import_oncofuse0.10.00.1
import_prada0.090.000.09
import_soapfuse0.090.000.09
import_squid0.110.000.11
import_starfusion0.110.000.11
partner_gene_ensembl_id0.060.000.07
partner_gene_junction_sequence0.050.000.04
plot_circle0.660.621.28
plot_fusion41.01 1.0242.83
plot_fusion_reads2.130.092.22
plot_fusion_transcript19.23 0.0319.27
plot_fusion_transcript_with_protein_domain13.17 0.0513.48
plot_fusion_transcripts_graph15.55 0.0515.59
plot_transcripts28.31 1.3430.38
select_transcript 9.75 0.0210.19
split_on_utr_and_add_feature0.580.000.57
upstream_partner_gene0.080.000.08
write_fusion_reference0.050.000.05

chimeraviz.Rcheck/examples_x64/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment0.950.010.97
create_fusion_report2.950.724.27
decide_transcript_category0.300.000.29
down_shift0.100.000.11
downstream_partner_gene0.130.000.13
fetch_reads_from_fastq000
fusion_spanning_reads_count0.060.000.06
fusion_split_reads_count0.060.000.06
fusion_to_data_frame0.070.000.07
get_ensembl_ids0.650.010.67
get_fusion_by_chromosome0.070.000.06
get_fusion_by_gene_name0.060.000.06
get_fusion_by_id0.060.000.07
get_transcripts_ensembl_db10.11 0.1910.29
import_aeron101
import_chimpipe0.220.000.22
import_defuse0.170.000.17
import_ericscript0.170.000.18
import_fusioncatcher0.150.000.16
import_fusionmap0.180.000.17
import_infusion0.170.000.17
import_jaffa0.170.000.17
import_oncofuse0.160.000.16
import_prada0.180.000.19
import_soapfuse0.180.000.17
import_squid0.170.010.19
import_starfusion0.190.000.18
partner_gene_ensembl_id0.100.000.11
partner_gene_junction_sequence0.080.000.08
plot_circle0.920.331.25
plot_fusion38.34 0.8939.90
plot_fusion_reads2.380.102.47
plot_fusion_transcript18.75 0.0718.81
plot_fusion_transcript_with_protein_domain13.83 0.0413.87
plot_fusion_transcripts_graph11.58 0.0211.60
plot_transcripts20.73 0.2320.97
select_transcript7.390.027.40
split_on_utr_and_add_feature0.450.000.46
upstream_partner_gene0.080.000.07
write_fusion_reference0.050.000.05