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CHECK report for chimeraviz on tokay2

This page was generated on 2018-10-17 08:43:14 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings chimeraviz_1.6.2.tar.gz
StartedAt: 2018-10-17 01:03:35 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:17:56 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 861.7 seconds
RetCode: 0
Status:  OK  
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings chimeraviz_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/chimeraviz.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.2'
* 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 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                            user system elapsed
plot_fusion                                22.59   0.80   23.67
plot_transcripts                           15.34   0.66   16.06
plot_fusion_transcript                     10.82   0.06   10.89
plot_fusion_transcripts_graph              10.24   0.04   10.28
plot_fusion_transcript_with_protein_domain  8.97   0.07    9.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                            user system elapsed
plot_fusion                                31.61   0.71   32.35
plot_transcripts                           16.75   0.34   17.09
plot_fusion_transcript                     14.41   0.11   14.51
plot_fusion_transcripts_graph              12.41   0.07   12.49
plot_fusion_transcript_with_protein_domain 10.20   0.04   10.25
get_transcripts_ensembl_db                  7.49   0.06    7.55
select_transcript                           6.15   0.02    6.17
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/chimeraviz.Rcheck/00check.log'
for details.



Installation output

chimeraviz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/chimeraviz_1.6.2.tar.gz && rm -rf chimeraviz.buildbin-libdir && mkdir chimeraviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chimeraviz.buildbin-libdir chimeraviz_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL chimeraviz_1.6.2.zip && rm chimeraviz_1.6.2.tar.gz chimeraviz_1.6.2.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 2463k  100 2463k    0     0  29.4M      0 --:--:-- --:--:-- --:--:-- 32.0M

install for i386

* installing *source* package 'chimeraviz' ...
** 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_defuse                           html  
    import_ericscript                       html  
    import_function_non_ucsc                html  
    import_fusioncatcher                    html  
    import_fusionmap                        html  
    import_infusion                         html  
    import_jaffa                            html  
    import_prada                            html  
    import_soapfuse                         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_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_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
In R CMD INSTALL

install for x64

* installing *source* package 'chimeraviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chimeraviz' as chimeraviz_1.6.2.zip
* DONE (chimeraviz)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'chimeraviz' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

chimeraviz.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, 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

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: 144 SKIPPED: 2 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 111.43    4.67  118.40 

chimeraviz.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, 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

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: 144 SKIPPED: 2 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 119.21    3.25  123.68 

Example timings

chimeraviz.Rcheck/examples_i386/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment1.580.091.75
create_fusion_report2.760.834.27
decide_transcript_category0.230.000.27
down_shift0.060.000.06
downstream_partner_gene0.100.010.11
fetch_reads_from_fastq000
fusion_spanning_reads_count0.060.000.06
fusion_split_reads_count0.050.000.05
fusion_to_data_frame0.060.020.08
get_ensembl_ids0.550.190.73
get_fusion_by_chromosome0.060.010.08
get_fusion_by_gene_name0.010.070.08
get_fusion_by_id0.040.040.08
get_transcripts_ensembl_db4.180.134.31
import_defuse0.110.000.11
import_ericscript0.210.010.30
import_fusioncatcher0.190.000.25
import_fusionmap0.190.000.35
import_infusion0.170.000.28
import_jaffa0.220.000.28
import_prada0.170.000.25
import_soapfuse0.210.000.27
import_starfusion0.180.000.25
partner_gene_ensembl_id0.110.000.11
partner_gene_junction_sequence0.070.000.06
plot_circle0.860.361.22
plot_fusion22.59 0.8023.67
plot_fusion_reads2.020.112.21
plot_fusion_transcript10.82 0.0610.89
plot_fusion_transcript_with_protein_domain8.970.079.03
plot_fusion_transcripts_graph10.24 0.0410.28
plot_transcripts15.34 0.6616.06
select_transcript4.240.004.24
split_on_utr_and_add_feature0.290.000.30
upstream_partner_gene0.080.010.09
write_fusion_reference0.060.000.06

chimeraviz.Rcheck/examples_x64/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment0.810.000.81
create_fusion_report3.100.624.31
decide_transcript_category0.320.000.32
down_shift0.070.000.08
downstream_partner_gene0.070.030.09
fetch_reads_from_fastq000
fusion_spanning_reads_count0.040.000.05
fusion_split_reads_count0.050.000.04
fusion_to_data_frame0.050.000.05
get_ensembl_ids0.620.100.72
get_fusion_by_chromosome0.080.000.08
get_fusion_by_gene_name0.060.000.06
get_fusion_by_id0.080.000.08
get_transcripts_ensembl_db7.490.067.55
import_defuse0.210.000.21
import_ericscript0.240.000.24
import_fusioncatcher0.20.00.2
import_fusionmap0.220.000.22
import_infusion0.220.000.21
import_jaffa0.20.00.2
import_prada0.140.000.14
import_soapfuse0.120.000.13
import_starfusion1.240.001.23
partner_gene_ensembl_id0.090.000.10
partner_gene_junction_sequence0.050.000.04
plot_circle0.560.320.89
plot_fusion31.61 0.7132.35
plot_fusion_reads2.000.112.11
plot_fusion_transcript14.41 0.1114.51
plot_fusion_transcript_with_protein_domain10.20 0.0410.25
plot_fusion_transcripts_graph12.41 0.0712.49
plot_transcripts16.75 0.3417.09
select_transcript6.150.026.17
split_on_utr_and_add_feature0.520.010.53
upstream_partner_gene0.150.000.16
write_fusion_reference0.150.000.14