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This page was generated on 2023-01-02 09:00:40 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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

CHECK results for musicatk on palomino5


To the developers/maintainers of the musicatk package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1297/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.9.0  (landing page)
Aaron Chevalier
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: master
git_last_commit: 69829e2
git_last_commit_date: 2022-11-01 11:23:15 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: musicatk
Version: 1.9.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings musicatk_1.9.0.tar.gz
StartedAt: 2022-12-29 01:44:59 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 01:50:00 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 301.5 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:musicatk.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings musicatk_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/musicatk.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.9.0'
* 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 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 7.33   1.34    8.67
plot_cluster         3.94   0.19    5.01
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/musicatk.Rcheck/00check.log'
for details.



Installation output

musicatk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library 'F:/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)

Tests output

musicatk.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: windows] | Cores 31/32

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 
  15.93    1.01   16.90 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants1.720.201.92
add_variant_type0.010.010.03
annotate_replication_strand0.800.020.81
annotate_transcript_strand0.920.050.97
annotate_variant_length0.020.000.02
annotate_variant_type0.010.000.01
auto_predict_grid1.910.011.94
build_custom_table0.750.020.77
build_standard_table7.331.348.67
built_tables000
cluster_exposure0.000.030.03
combine_count_tables2.180.332.52
combine_predict_grid202
compare_cosmic_v21.860.001.85
compare_cosmic_v30.790.030.82
compare_results1.060.001.06
cosmic_v2_subtype_map000
create_musica0.840.241.14
create_umap3.770.083.89
discover_signatures0.580.120.70
drop_annotation000
exposure_differential_analysis0.010.000.02
exposures000
extract_count_tables0.000.010.01
extract_variants3.520.063.58
extract_variants_from_maf0.090.000.09
extract_variants_from_maf_file0.110.000.11
extract_variants_from_matrix0.160.000.16
extract_variants_from_vcf0.540.040.58
extract_variants_from_vcf_file0.470.010.48
generate_result_grid0.330.000.32
get_musica0.020.000.02
k_select0.650.040.70
musicatk000
name_signatures0.000.020.02
pipe000
plot_cluster3.940.195.01
plot_differential_analysis0.160.000.16
plot_exposures0.140.000.16
plot_heatmap0.560.010.58
plot_sample_counts0.270.000.26
plot_sample_reconstruction_error0.470.000.47
plot_signatures0.420.000.42
plot_umap3.390.063.47
predict_exposure1.030.111.14
rc000
samp_annot0.030.000.03
sample_names000
select_genome000
signatures0.020.000.02
subset_musica_by_annotation0.000.020.01
subset_musica_by_counts0.010.000.02
subset_variant_by_type000
subset_variants_by_samples0.020.000.01
table_selected000
tables0.000.020.02
umap0.000.010.02
variants0.000.020.01