| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-23 01:34:14 -0000 (Thu, 23 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4245 |
| 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 musicatk package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/musicatk.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. |
| Package 1301/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| musicatk 1.9.0 (landing page) Aaron Chevalier
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: musicatk |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings musicatk_1.9.0.tar.gz |
| StartedAt: 2023-02-22 08:57:16 -0000 (Wed, 22 Feb 2023) |
| EndedAt: 2023-02-22 09:06:12 -0000 (Wed, 22 Feb 2023) |
| EllapsedTime: 535.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: musicatk.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings musicatk_1.9.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘musicatk’ 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
Namespaces in Imports field not imported from:
‘TCGAbiolinks’ ‘shinyBS’ ‘shinyalert’ ‘shinybusy’ ‘shinydashboard’
‘shinyjqui’ ‘shinyjs’ ‘sortable’
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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
build_standard_table 10.846 0.847 11.712
extract_variants 5.772 0.052 5.824
plot_cluster 5.589 0.100 5.687
create_umap 5.415 0.176 5.589
plot_umap 5.051 0.088 5.136
* 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 ...
‘musicatk.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/musicatk.Rcheck/00check.log’
for details.
musicatk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL musicatk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘musicatk’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (musicatk)
musicatk.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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("musicatk")
Loading required package: NMF
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 31/32
To enable shared memory capabilities, try: install.extras('
NMF
')
Attaching package: 'NMF'
The following object is masked from 'package:testthat':
compare
>
> test_check("musicatk")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 42 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 42 ]
>
> proc.time()
user system elapsed
26.690 1.673 28.340
musicatk.Rcheck/musicatk-Ex.timings
| name | user | system | elapsed | |
| add_flank_to_variants | 3.557 | 0.280 | 3.839 | |
| add_variant_type | 0.019 | 0.000 | 0.019 | |
| annotate_replication_strand | 0.282 | 0.012 | 0.295 | |
| annotate_transcript_strand | 2.539 | 0.112 | 2.651 | |
| annotate_variant_length | 0.014 | 0.000 | 0.013 | |
| annotate_variant_type | 0.003 | 0.000 | 0.003 | |
| auto_predict_grid | 2.875 | 0.012 | 2.887 | |
| build_custom_table | 1.337 | 0.007 | 1.344 | |
| build_standard_table | 10.846 | 0.847 | 11.712 | |
| built_tables | 0.002 | 0.000 | 0.003 | |
| cluster_exposure | 0.019 | 0.000 | 0.019 | |
| combine_count_tables | 3.208 | 0.240 | 3.448 | |
| combine_predict_grid | 2.857 | 0.028 | 2.885 | |
| compare_cosmic_v2 | 3.582 | 0.032 | 3.614 | |
| compare_cosmic_v3 | 1.521 | 0.000 | 1.521 | |
| compare_results | 1.989 | 0.003 | 1.993 | |
| cosmic_v2_subtype_map | 0.002 | 0.000 | 0.001 | |
| create_musica | 0.968 | 0.163 | 1.136 | |
| create_umap | 5.415 | 0.176 | 5.589 | |
| discover_signatures | 0.873 | 0.072 | 0.946 | |
| drop_annotation | 0.002 | 0.000 | 0.003 | |
| exposure_differential_analysis | 0.016 | 0.008 | 0.023 | |
| exposures | 0.004 | 0.000 | 0.005 | |
| extract_count_tables | 0.005 | 0.000 | 0.005 | |
| extract_variants | 5.772 | 0.052 | 5.824 | |
| extract_variants_from_maf | 0.138 | 0.004 | 0.141 | |
| extract_variants_from_maf_file | 0.125 | 0.000 | 0.124 | |
| extract_variants_from_matrix | 0.146 | 0.000 | 0.144 | |
| extract_variants_from_vcf | 0.898 | 0.024 | 0.923 | |
| extract_variants_from_vcf_file | 0.683 | 0.008 | 0.691 | |
| generate_result_grid | 0.232 | 0.004 | 0.235 | |
| get_musica | 0.005 | 0.003 | 0.009 | |
| k_select | 1.237 | 0.016 | 1.254 | |
| musicatk | 0 | 0 | 0 | |
| name_signatures | 0.003 | 0.000 | 0.003 | |
| pipe | 0.003 | 0.000 | 0.003 | |
| plot_cluster | 5.589 | 0.100 | 5.687 | |
| plot_differential_analysis | 0.258 | 0.004 | 0.261 | |
| plot_exposures | 0.248 | 0.004 | 0.252 | |
| plot_heatmap | 1.006 | 0.020 | 1.027 | |
| plot_sample_counts | 0.480 | 0.000 | 0.481 | |
| plot_sample_reconstruction_error | 0.868 | 0.000 | 0.868 | |
| plot_signatures | 0.814 | 0.000 | 0.814 | |
| plot_umap | 5.051 | 0.088 | 5.136 | |
| predict_exposure | 1.724 | 0.104 | 1.828 | |
| rc | 0.002 | 0.000 | 0.002 | |
| samp_annot | 0.009 | 0.000 | 0.009 | |
| sample_names | 0.004 | 0.000 | 0.004 | |
| select_genome | 0 | 0 | 0 | |
| signatures | 0.002 | 0.004 | 0.006 | |
| subset_musica_by_annotation | 0.002 | 0.004 | 0.006 | |
| subset_musica_by_counts | 0.009 | 0.000 | 0.009 | |
| subset_variant_by_type | 0.006 | 0.000 | 0.006 | |
| subset_variants_by_samples | 0.006 | 0.000 | 0.005 | |
| table_selected | 0.000 | 0.002 | 0.002 | |
| tables | 0.005 | 0.005 | 0.010 | |
| umap | 0.004 | 0.000 | 0.004 | |
| variants | 0.009 | 0.000 | 0.009 | |