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This page was generated on 2021-10-15 15:05:46 -0400 (Fri, 15 Oct 2021).

CHECK results for musicatk on nebbiolo1

To the developers/maintainers of the musicatk package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1235/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
musicatk 1.2.0  (landing page)
Aaron Chevalier
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/musicatk
git_branch: RELEASE_3_13
git_last_commit: c207280
git_last_commit_date: 2021-05-19 12:57:08 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: musicatk
Version: 1.2.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings musicatk_1.2.0.tar.gz
StartedAt: 2021-10-14 10:45:44 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:51:20 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 336.4 seconds
RetCode: 0
Status:   OK  
CheckDir: musicatk.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:musicatk.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings musicatk_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/musicatk.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘musicatk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘musicatk’ version ‘1.2.0’
* 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 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 ... NOTE
plot_heatmap: no visible binding for global variable ‘.’
Undefined global functions or variables:
  .
* 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 10.094  1.620  11.716
create_umap           5.631  0.537   6.198
plot_cluster          5.434  0.100   5.546
plot_umap             5.345  0.069   5.429
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/musicatk.Rcheck/00check.log’
for details.



Installation output

musicatk.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL musicatk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 71/72
  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 1 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 19.508   0.913  20.428 

Example timings

musicatk.Rcheck/musicatk-Ex.timings

nameusersystemelapsed
add_flank_to_variants3.3000.3283.628
add_variant_type0.0130.0040.016
annotate_replication_strand0.1320.0080.139
annotate_transcript_strand2.5150.0642.578
annotate_variant_length0.0130.0000.013
annotate_variant_type0.0060.0000.007
auto_predict_grid1.5470.0401.588
build_custom_table0.9780.0321.009
build_standard_table10.094 1.62011.716
built_tables0.0000.0030.003
cluster_exposure0.0190.0000.019
combine_count_tables3.0410.9844.025
combine_predict_grid1.5880.0721.661
compare_cosmic_v21.8060.0121.818
compare_cosmic_v30.7990.0040.804
compare_results1.0550.0001.055
cosmic_v2_subtype_map0.0010.0000.001
create_musica0.9980.2531.222
create_umap5.6310.5376.198
discover_signatures0.7890.1560.946
drop_annotation0.0030.0000.003
exposure_differential_analysis0.0170.0040.021
exposures0.0010.0030.004
extract_count_tables0.0010.0040.005
extract_variants4.8630.0364.845
extract_variants_from_maf0.1360.0000.113
extract_variants_from_maf_file0.1180.0000.093
extract_variants_from_matrix0.1430.0000.116
extract_variants_from_vcf0.8000.0040.804
extract_variants_from_vcf_file0.5440.0000.544
generate_result_grid0.1470.0000.146
get_musica0.0090.0000.008
k_select0.7820.0150.797
name_signatures0.0020.0010.003
pipe0.0030.0000.002
plot_cluster5.4340.1005.546
plot_differential_analysis0.1330.0040.137
plot_exposures0.1390.0000.140
plot_heatmap0.6730.0070.682
plot_sample_counts0.2520.0000.251
plot_sample_reconstruction_error0.450.000.45
plot_signatures0.4450.0040.449
plot_umap5.3450.0695.429
predict_exposure1.1820.1721.355
rc0.0020.0000.003
samp_annot0.0090.0000.009
sample_names0.0030.0000.004
select_genome0.0000.0000.001
signatures0.0000.0080.008
subset_musica_by_annotation0.0030.0040.008
subset_musica_by_counts0.0080.0000.009
subset_variant_by_type0.0060.0000.006
subset_variants_by_samples0.0000.0050.005
table_selected0.0000.0020.002
tables0.0050.0040.009
umap0.0020.0020.004
variants0.0070.0010.009