Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:13 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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? 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 301/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.23.0  (landing page)
Stian Lågstad
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/chimeraviz
git_branch: master
git_last_commit: 43ccf13
git_last_commit_date: 2022-06-16 08:24:37 -0400 (Thu, 16 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: chimeraviz
Version: 1.23.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings chimeraviz_1.23.0.tar.gz
StartedAt: 2022-06-24 00:07:29 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 00:17:23 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 593.8 seconds
RetCode: 0
Status:   OK  
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings chimeraviz_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/chimeraviz.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.23.0'
* 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
* 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                                32.51   0.50   34.09
plot_transcripts                           18.43   0.48   18.91
plot_fusion_transcript                     14.79   0.20   15.00
plot_fusion_transcript_with_protein_domain  9.30   0.07    9.36
plot_fusion_transcripts_graph               9.09   0.06    9.15
get_transcripts_ensembl_db                  6.11   0.34    6.45
select_transcript                           6.20   0.05    6.25
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/chimeraviz.Rcheck/00check.log'
for details.



Installation output

chimeraviz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/chimeraviz_1.23.0.tar.gz && rm -rf chimeraviz.buildbin-libdir && mkdir chimeraviz.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chimeraviz.buildbin-libdir chimeraviz_1.23.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL chimeraviz_1.23.0.zip && rm chimeraviz_1.23.0.tar.gz chimeraviz_1.23.0.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 2627k  100 2627k    0     0  13.2M      0 --:--:-- --:--:-- --:--:-- 13.2M
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'chimeraviz' as chimeraviz_1.23.0.zip
* DONE (chimeraviz)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'chimeraviz' successfully unpacked and MD5 sums checked

Tests output

chimeraviz.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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

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

Attaching package: 'IRanges'

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

    windows

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 2 | PASS 219 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 219 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 160.03    4.50  166.01 

Example timings

chimeraviz.Rcheck/chimeraviz-Ex.timings

nameusersystemelapsed
add_fusion_reads_alignment1.800.031.83
create_fusion_report1.560.784.14
decide_transcript_category0.230.020.25
down_shift0.090.000.09
downstream_partner_gene0.10.00.1
fetch_reads_from_fastq000
fusion_spanning_reads_count0.050.000.05
fusion_split_reads_count0.030.000.03
fusion_to_data_frame0.030.000.03
get_ensembl_ids1.680.031.70
get_fusion_by_chromosome0.040.000.05
get_fusion_by_gene_name0.050.000.05
get_fusion_by_id0.050.000.05
get_transcripts_ensembl_db6.110.346.45
import_aeron0.450.000.47
import_chimpipe0.080.000.08
import_defuse0.100.000.09
import_ericscript0.090.000.10
import_fusioncatcher0.080.000.08
import_fusionmap0.090.000.10
import_infusion0.100.000.09
import_jaffa0.070.000.08
import_oncofuse0.080.000.08
import_prada0.110.000.11
import_soapfuse0.090.000.09
import_squid0.090.000.10
import_starfusion0.100.000.09
partner_gene_ensembl_id0.040.020.06
partner_gene_junction_sequence0.030.000.03
plot_circle0.600.340.97
plot_fusion32.51 0.5034.09
plot_fusion_reads2.020.082.10
plot_fusion_transcript14.79 0.2015.00
plot_fusion_transcript_with_protein_domain9.300.079.36
plot_fusion_transcripts_graph9.090.069.15
plot_transcripts18.43 0.4818.91
select_transcript6.200.056.25
split_on_utr_and_add_feature0.340.020.36
upstream_partner_gene0.080.000.08
write_fusion_reference0.060.000.06