Stian Lågstad
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/chimeraviz |
| git_branch: RELEASE_3_13 |
| git_last_commit: bc2b277 |
| git_last_commit_date: 2021-05-19 12:24:46 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 289/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chimeraviz 1.18.0 (landing page) Stian Lågstad
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: chimeraviz |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chimeraviz_1.18.0.tar.gz |
| StartedAt: 2021-10-14 20:58:02 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:16:36 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 1113.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chimeraviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chimeraviz_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/chimeraviz.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.18.0'
* 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 35.34 0.91 38.90
plot_transcripts 18.86 0.46 19.31
plot_fusion_transcript 16.44 0.11 16.57
plot_fusion_transcripts_graph 10.56 0.01 10.58
plot_fusion_transcript_with_protein_domain 10.34 0.03 10.37
get_transcripts_ensembl_db 7.61 0.86 8.46
select_transcript 5.93 0.00 5.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_fusion 37.15 0.75 39.92
plot_transcripts 28.56 0.48 29.05
plot_fusion_transcript 19.47 0.09 19.56
plot_fusion_transcript_with_protein_domain 15.51 0.06 15.58
plot_fusion_transcripts_graph 15.30 0.07 15.36
select_transcript 9.50 0.14 9.64
get_transcripts_ensembl_db 7.40 0.08 7.49
* 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-3.13-bioc/meat/chimeraviz.Rcheck/00check.log'
for details.
chimeraviz.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/chimeraviz_1.18.0.tar.gz && rm -rf chimeraviz.buildbin-libdir && mkdir chimeraviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chimeraviz.buildbin-libdir chimeraviz_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL chimeraviz_1.18.0.zip && rm chimeraviz_1.18.0.tar.gz chimeraviz_1.18.0.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
0 2623k 0 1135 0 0 14048 0 0:03:11 --:--:-- 0:03:11 14012
75 2623k 75 1990k 0 0 1839k 0 0:00:01 0:00:01 --:--:-- 1839k
100 2623k 100 2623k 0 0 2009k 0 0:00:01 0:00:01 --:--:-- 2010k
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_1.18.0.zip
* DONE (chimeraviz)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'chimeraviz' successfully unpacked and MD5 sums checked
|
chimeraviz.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 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")
== 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
205.50 8.57 217.31
|
chimeraviz.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 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")
== 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
187.01 3.71 193.98
|
|
chimeraviz.Rcheck/examples_i386/chimeraviz-Ex.timings
|
chimeraviz.Rcheck/examples_x64/chimeraviz-Ex.timings
|