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This page was generated on 2024-05-04 11:38:10 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1392/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.14.0  (landing page)
Joshua D. Campbell
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: RELEASE_3_19
git_last_commit: a447ad6
git_last_commit_date: 2024-04-30 11:28:39 -0400 (Tue, 30 Apr 2024)
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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for musicatk on palomino3


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: 1.14.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings musicatk_1.14.0.tar.gz
StartedAt: 2024-05-04 05:56:47 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 06:03:50 -0400 (Sat, 04 May 2024)
EllapsedTime: 422.9 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings musicatk_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/musicatk.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'musicatk/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'musicatk' version '1.14.0'
* 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 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 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 8.08   1.86    9.95
plot_cluster         5.55   0.26    5.87
extract_variants     5.50   0.11    5.61
create_umap          5.45   0.10    5.74
plot_umap            5.39   0.04    5.48
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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


Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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)

Tests output

musicatk.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: windows] | Cores 2/2

Attaching package: 'NMF'

The following object is masked from 'package:testthat':

    compare

> 
> test_check("musicatk")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  24.76    2.29   25.86 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants3.740.454.19
add_variant_type0.000.020.01
annotate_replication_strand0.160.010.17
annotate_transcript_strand1.540.001.55
annotate_variant_length0.020.020.03
annotate_variant_type000
auto_predict_grid3.610.103.72
build_custom_table1.010.061.08
build_standard_table8.081.869.95
built_tables0.000.010.02
cluster_exposure0.000.020.01
combine_count_tables2.600.362.96
combine_predict_grid2.110.062.19
compare_cosmic_v23.140.093.25
compare_cosmic_v31.500.021.51
compare_results1.620.031.66
cosmic_v2_subtype_map000
create_musica0.880.311.34
create_umap5.450.105.74
discover_signatures0.800.120.92
drop_annotation000
exposure_differential_analysis0.020.000.02
exposures000
extract_count_tables000
extract_variants5.500.115.61
extract_variants_from_maf0.130.000.13
extract_variants_from_maf_file0.110.000.11
extract_variants_from_matrix0.120.020.14
extract_variants_from_vcf0.670.010.69
extract_variants_from_vcf_file0.470.020.49
generate_result_grid0.340.010.36
get_musica0.020.000.01
k_select0.700.020.72
musicatk000
name_signatures0.000.020.02
pipe000
plot_cluster5.550.265.87
plot_differential_analysis0.470.020.48
plot_exposures0.260.010.29
plot_heatmap1.000.570.86
plot_sample_counts0.960.370.73
plot_sample_reconstruction_error1.120.021.14
plot_signatures1.110.001.11
plot_umap5.390.045.48
predict_exposure1.640.281.93
rc000
samp_annot0.000.040.03
sample_names0.000.010.01
select_genome000
signatures0.020.000.02
subset_musica_by_annotation0.010.020.03
subset_musica_by_counts0.020.000.02
subset_variant_by_type0.010.000.01
subset_variants_by_samples0.020.000.02
table_selected0.000.010.01
tables0.000.020.02
umap0.000.010.01
variants0.030.000.03