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This page was generated on 2024-03-28 11:36:47 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1373/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.13.0  (landing page)
Aaron Chevalier
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: devel
git_last_commit: 9bedf9c
git_last_commit_date: 2023-10-24 11:27:12 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for musicatk on nebbiolo1


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.

raw results


Summary

Package: musicatk
Version: 1.13.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings musicatk_1.13.0.tar.gz
StartedAt: 2024-03-28 00:40:39 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 00:48:03 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 444.1 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings musicatk_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.13.0’
* 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 code 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 ... NOTE
checkRd: (-1) plot_umap.Rd:53: Lost braces
    53 | code{color_by = "annotation"}. This not recommended if the annotation is
       |     ^
checkRd: (-1) plot_umap.Rd:58: Lost braces
    58 | code{color_by = "annotation"} and \code{add_annotation_labels = TRUE}.
       |     ^
checkRd: (-1) plot_umap.Rd:62: Lost braces
    62 | to improve readability. Only used if code{color_by = "annotation"} and
       |                                          ^
* 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 6.880  1.132   8.012
plot_cluster         5.201  0.700   5.902
create_umap          5.127  0.128   5.254
plot_umap            4.786  0.364   5.149
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck/00check.log’
for details.


Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 20.687   1.362  22.075 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants2.9070.3323.240
add_variant_type0.0180.0010.019
annotate_replication_strand0.1130.0110.125
annotate_transcript_strand1.2210.0491.268
annotate_variant_length0.0140.0000.014
annotate_variant_type0.0000.0020.002
auto_predict_grid2.8720.0492.921
build_custom_table0.9030.0280.931
build_standard_table6.8801.1328.012
built_tables0.0020.0000.002
cluster_exposure0.0110.0030.015
combine_count_tables2.3080.3442.653
combine_predict_grid1.6450.0111.656
compare_cosmic_v22.6070.0602.668
compare_cosmic_v31.4480.0161.464
compare_results1.6460.0161.662
cosmic_v2_subtype_map0.0010.0000.002
create_musica0.7590.2921.033
create_umap5.1270.1285.254
discover_signatures0.6740.0880.763
drop_annotation0.0000.0030.003
exposure_differential_analysis0.0100.0010.011
exposures0.0040.0000.004
extract_count_tables0.0050.0000.004
extract_variants4.0370.1084.098
extract_variants_from_maf0.1400.0000.115
extract_variants_from_maf_file0.1100.0080.088
extract_variants_from_matrix0.1230.0040.103
extract_variants_from_vcf0.6350.0640.699
extract_variants_from_vcf_file0.4460.0400.485
generate_result_grid0.1550.0040.159
get_musica0.0060.0040.010
k_select0.7880.0960.885
musicatk0.0000.0000.001
name_signatures0.0030.0000.003
pipe0.0030.0000.003
plot_cluster5.2010.7005.902
plot_differential_analysis0.2780.0080.285
plot_exposures0.1510.0160.167
plot_heatmap0.6930.0840.777
plot_sample_counts0.5000.0280.529
plot_sample_reconstruction_error0.7290.0430.773
plot_signatures0.6630.0150.679
plot_umap4.7860.3645.149
predict_exposure1.0070.1321.138
rc0.0030.0000.002
samp_annot0.0060.0030.009
sample_names0.0030.0000.003
select_genome000
signatures0.0040.0020.006
subset_musica_by_annotation0.0040.0020.005
subset_musica_by_counts0.0060.0040.009
subset_variant_by_type0.0060.0000.006
subset_variants_by_samples0.0060.0000.006
table_selected0.0020.0000.002
tables0.0090.0000.008
umap0.0040.0000.004
variants0.0070.0040.011