| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:34 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
To the developers/maintainers of the chimeraviz package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 320/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chimeraviz 1.25.0 (landing page) Stian Lågstad
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: chimeraviz |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings chimeraviz_1.25.0.tar.gz |
| StartedAt: 2023-04-12 05:16:29 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 05:30:20 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 831.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings chimeraviz_1.25.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/chimeraviz.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘1.25.0’
* 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 loading without being on the library search path ... 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 33.024 2.668 36.520
plot_transcripts 18.200 0.611 18.812
plot_fusion_transcript 15.379 0.372 15.751
plot_fusion_transcript_with_protein_domain 9.928 0.144 10.073
plot_fusion_transcripts_graph 9.610 0.172 9.782
get_transcripts_ensembl_db 6.304 0.272 6.576
select_transcript 5.911 0.036 5.947
* 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 ...
‘chimeraviz-vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)
chimeraviz.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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
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, aperm, 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
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 0 | PASS 224 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
180.128 7.284 188.033
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| add_fusion_reads_alignment | 0.867 | 0.013 | 0.880 | |
| create_fusion_report | 3.167 | 0.162 | 3.343 | |
| decide_transcript_category | 0.214 | 0.000 | 0.215 | |
| down_shift | 0.072 | 0.000 | 0.071 | |
| downstream_partner_gene | 0.068 | 0.000 | 0.068 | |
| fetch_reads_from_fastq | 0 | 0 | 0 | |
| fusion_spanning_reads_count | 0.033 | 0.000 | 0.033 | |
| fusion_split_reads_count | 0.032 | 0.000 | 0.032 | |
| fusion_to_data_frame | 0.033 | 0.000 | 0.034 | |
| get_ensembl_ids | 0.538 | 0.036 | 0.573 | |
| get_fusion_by_chromosome | 0.029 | 0.000 | 0.029 | |
| get_fusion_by_gene_name | 0.028 | 0.000 | 0.027 | |
| get_fusion_by_id | 0.03 | 0.00 | 0.03 | |
| get_transcripts_ensembl_db | 6.304 | 0.272 | 6.576 | |
| import_aeron | 0.480 | 0.000 | 0.481 | |
| import_chimpipe | 0.104 | 0.000 | 0.104 | |
| import_defuse | 0.103 | 0.000 | 0.103 | |
| import_ericscript | 0.104 | 0.000 | 0.104 | |
| import_fusioncatcher | 0.109 | 0.004 | 0.113 | |
| import_fusionmap | 0.117 | 0.004 | 0.121 | |
| import_infusion | 0.094 | 0.000 | 0.095 | |
| import_jaffa | 0.09 | 0.00 | 0.09 | |
| import_oncofuse | 0.129 | 0.000 | 0.129 | |
| import_prada | 0.088 | 0.000 | 0.088 | |
| import_soapfuse | 0.082 | 0.000 | 0.082 | |
| import_squid | 0.086 | 0.000 | 0.085 | |
| import_starfusion | 0.089 | 0.000 | 0.089 | |
| partner_gene_ensembl_id | 0.066 | 0.000 | 0.067 | |
| partner_gene_junction_sequence | 0.039 | 0.000 | 0.040 | |
| plot_circle | 2.177 | 0.204 | 2.382 | |
| plot_fusion | 33.024 | 2.668 | 36.520 | |
| plot_fusion_reads | 2.233 | 0.153 | 2.385 | |
| plot_fusion_transcript | 15.379 | 0.372 | 15.751 | |
| plot_fusion_transcript_with_protein_domain | 9.928 | 0.144 | 10.073 | |
| plot_fusion_transcripts_graph | 9.610 | 0.172 | 9.782 | |
| plot_transcripts | 18.200 | 0.611 | 18.812 | |
| select_transcript | 5.911 | 0.036 | 5.947 | |
| split_on_utr_and_add_feature | 0.355 | 0.004 | 0.359 | |
| upstream_partner_gene | 0.068 | 0.004 | 0.072 | |
| write_fusion_reference | 0.038 | 0.000 | 0.039 | |