| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:39 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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To the developers/maintainers of the musicatk package: - 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 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 1325/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| musicatk 1.11.0 (landing page) Aaron Chevalier
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: musicatk |
| Version: 1.11.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings musicatk_1.11.0.tar.gz |
| StartedAt: 2023-05-30 13:21:34 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 13:31:38 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 603.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: musicatk.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings musicatk_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/musicatk.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.11.0’
* 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 loading without being on the library search path ... 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 ... 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 10.074 0.784 10.859
plot_cluster 6.180 0.132 6.310
extract_variants 5.889 0.152 6.041
create_umap 5.803 0.192 5.992
plot_umap 5.520 0.136 5.653
* 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: OK
musicatk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL musicatk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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: bigmemory] | Cores 2/2
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
28.671 1.004 29.654
musicatk.Rcheck/musicatk-Ex.timings
| name | user | system | elapsed | |
| add_flank_to_variants | 3.859 | 0.520 | 4.379 | |
| add_variant_type | 0.015 | 0.003 | 0.018 | |
| annotate_replication_strand | 0.163 | 0.012 | 0.175 | |
| annotate_transcript_strand | 1.655 | 0.012 | 1.668 | |
| annotate_variant_length | 0.013 | 0.000 | 0.014 | |
| annotate_variant_type | 0.003 | 0.000 | 0.003 | |
| auto_predict_grid | 4.112 | 0.032 | 4.146 | |
| build_custom_table | 1.281 | 0.050 | 1.331 | |
| build_standard_table | 10.074 | 0.784 | 10.859 | |
| built_tables | 0.003 | 0.000 | 0.002 | |
| cluster_exposure | 0.015 | 0.004 | 0.019 | |
| combine_count_tables | 3.322 | 0.184 | 3.506 | |
| combine_predict_grid | 2.929 | 0.080 | 3.009 | |
| compare_cosmic_v2 | 3.699 | 0.076 | 3.775 | |
| compare_cosmic_v3 | 2.088 | 0.000 | 2.088 | |
| compare_results | 2.394 | 0.000 | 2.393 | |
| cosmic_v2_subtype_map | 0.001 | 0.000 | 0.001 | |
| create_musica | 1.011 | 0.129 | 1.163 | |
| create_umap | 5.803 | 0.192 | 5.992 | |
| discover_signatures | 0.928 | 0.056 | 0.985 | |
| drop_annotation | 0.002 | 0.000 | 0.003 | |
| exposure_differential_analysis | 0.005 | 0.008 | 0.013 | |
| exposures | 0.001 | 0.004 | 0.005 | |
| extract_count_tables | 0.005 | 0.000 | 0.005 | |
| extract_variants | 5.889 | 0.152 | 6.041 | |
| extract_variants_from_maf | 0.145 | 0.004 | 0.148 | |
| extract_variants_from_maf_file | 0.119 | 0.016 | 0.134 | |
| extract_variants_from_matrix | 0.150 | 0.000 | 0.148 | |
| extract_variants_from_vcf | 0.997 | 0.044 | 1.040 | |
| extract_variants_from_vcf_file | 0.650 | 0.048 | 0.699 | |
| generate_result_grid | 0.241 | 0.004 | 0.245 | |
| get_musica | 0.009 | 0.000 | 0.010 | |
| k_select | 1.266 | 0.088 | 1.355 | |
| musicatk | 0 | 0 | 0 | |
| name_signatures | 0.003 | 0.000 | 0.004 | |
| pipe | 0.003 | 0.000 | 0.004 | |
| plot_cluster | 6.180 | 0.132 | 6.310 | |
| plot_differential_analysis | 0.261 | 0.004 | 0.265 | |
| plot_exposures | 0.274 | 0.000 | 0.274 | |
| plot_heatmap | 0.990 | 0.008 | 0.998 | |
| plot_sample_counts | 0.741 | 0.000 | 0.741 | |
| plot_sample_reconstruction_error | 1.092 | 0.004 | 1.095 | |
| plot_signatures | 1.075 | 0.000 | 1.075 | |
| plot_umap | 5.520 | 0.136 | 5.653 | |
| predict_exposure | 1.778 | 0.112 | 1.890 | |
| rc | 0.002 | 0.000 | 0.003 | |
| samp_annot | 0.01 | 0.00 | 0.01 | |
| sample_names | 0.003 | 0.000 | 0.004 | |
| select_genome | 0 | 0 | 0 | |
| signatures | 0.006 | 0.000 | 0.006 | |
| subset_musica_by_annotation | 0.007 | 0.000 | 0.007 | |
| subset_musica_by_counts | 0.010 | 0.000 | 0.009 | |
| subset_variant_by_type | 0.003 | 0.003 | 0.006 | |
| subset_variants_by_samples | 0.006 | 0.000 | 0.005 | |
| table_selected | 0.000 | 0.002 | 0.002 | |
| tables | 0.009 | 0.001 | 0.010 | |
| umap | 0.005 | 0.000 | 0.005 | |
| variants | 0.006 | 0.004 | 0.010 | |