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This page was generated on 2023-11-02 11:40:59 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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

Package 1375/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.12.0  (landing page)
Aaron Chevalier
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: RELEASE_3_18
git_last_commit: 69a345e
git_last_commit_date: 2023-10-24 11:27:12 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 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 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for musicatk on kunpeng2


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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: musicatk
Version: 1.12.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings musicatk_1.12.0.tar.gz
StartedAt: 2023-11-02 12:35:09 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 12:43:38 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 508.6 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings musicatk_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/musicatk.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.12.0’
* 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 11.426  0.599  12.507
plot_cluster          6.322  0.148   6.562
create_umap           6.053  0.172   6.264
extract_variants      5.981  0.080   6.080
plot_umap             5.496  0.028   5.536
* 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: OK


Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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)

Tests output

musicatk.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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 
 27.401   1.392  28.971 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants4.0110.3164.472
add_variant_type0.0170.0000.018
annotate_replication_strand0.1700.0040.174
annotate_transcript_strand2.7840.1272.943
annotate_variant_length0.0130.0000.013
annotate_variant_type0.0020.0000.003
auto_predict_grid2.8310.0502.902
build_custom_table1.3130.0121.331
build_standard_table11.426 0.59912.507
built_tables0.0000.0020.002
cluster_exposure0.0170.0010.025
combine_count_tables3.2940.1883.489
combine_predict_grid2.8440.0242.888
compare_cosmic_v23.7790.0243.864
compare_cosmic_v32.2400.0002.245
compare_results2.5960.0202.622
cosmic_v2_subtype_map0.0000.0020.002
create_musica1.0600.1521.714
create_umap6.0530.1726.264
discover_signatures0.8910.0710.998
drop_annotation0.0020.0000.002
exposure_differential_analysis0.0150.0000.019
exposures0.0040.0000.004
extract_count_tables0.0050.0000.005
extract_variants5.9810.0806.080
extract_variants_from_maf0.1460.0040.148
extract_variants_from_maf_file0.1270.0000.125
extract_variants_from_matrix0.2370.0040.239
extract_variants_from_vcf0.9640.0361.004
extract_variants_from_vcf_file0.6720.0070.681
generate_result_grid0.2370.0010.237
get_musica0.0090.0000.008
k_select1.1900.0191.215
musicatk000
name_signatures0.0030.0000.003
pipe0.0000.0030.003
plot_cluster6.3220.1486.562
plot_differential_analysis0.2620.0040.266
plot_exposures0.2680.0080.277
plot_heatmap1.0380.0161.057
plot_sample_counts0.7660.0000.769
plot_sample_reconstruction_error1.0820.0321.118
plot_signatures1.1280.0041.135
plot_umap5.4960.0285.536
predict_exposure1.7500.0401.795
rc0.0000.0030.004
samp_annot0.010.000.01
sample_names0.0030.0000.003
select_genome000
signatures0.0050.0000.006
subset_musica_by_annotation0.0060.0000.007
subset_musica_by_counts0.0050.0040.008
subset_variant_by_type0.0060.0000.006
subset_variants_by_samples0.0050.0000.005
table_selected0.0030.0000.002
tables0.010.000.01
umap0.0040.0000.004
variants0.0090.0000.009