Multiple platform build/check report for BioC 3.20 - CHECK results for RNAseqCovarImpute on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 RNAseqCovarImpute on kjohnson3

To the developers/maintainers of the RNAseqCovarImpute package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAseqCovarImpute.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: RNAseqCovarImpute

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAseqCovarImpute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAseqCovarImpute_1.4.0.tar.gz

StartedAt: 2024-11-09 11:41:20 -0500 (Sat, 09 Nov 2024)

EndedAt: 2024-11-09 11:45:43 -0500 (Sat, 09 Nov 2024)

EllapsedTime: 263.6 seconds

RetCode: 0

Status: OK

CheckDir: RNAseqCovarImpute.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAseqCovarImpute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAseqCovarImpute_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNAseqCovarImpute.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* this is package ‘RNAseqCovarImpute’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘RNAseqCovarImpute’ 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 ... NOTE
combine_rubins: no visible binding for global variable ‘probe’
combine_rubins: no visible binding for global variable ‘i’
combine_rubins: no visible binding for global variable ‘coef_combined’
combine_rubins: no visible binding for global variable ‘rubins_t_bayes’
combine_rubins: no visible binding for global variable ‘combined_p’
combine_rubins: no visible binding for global variable
  ‘combined_p_bayes’
limmavoom_imputed_data_list_helper: no visible binding for global
  variable ‘i’
limmavoom_imputed_data_list_helper: no visible binding for global
  variable ‘lm_predictor’
limmavoom_imputed_data_pca: no visible binding for global variable
  ‘probe’
lowess_all_gene_bins: no visible binding for global variable ‘gene_bin’
lowess_all_gene_bins: no visible binding for global variable ‘i’
voom_master_lowess: no visible global function definition for ‘is’
voom_master_lowess: no visible global function definition for ‘new’
voom_master_lowess: no visible global function definition for ‘lowess’
voom_master_lowess: no visible global function definition for
  ‘approxfun’
voom_sx_sy: no visible global function definition for ‘is’
voom_sx_sy: no visible global function definition for ‘new’
Undefined global functions or variables:
  approxfun coef_combined combined_p combined_p_bayes gene_bin i is
  lm_predictor lowess new probe rubins_t_bayes
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "approxfun", "lowess")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'impute_gene_bin_helper.Rd':
  ‘DGE’ ‘param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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
limmavoom_imputed_data_pca  5.214  0.753   4.146
limmavoom_imputed_data_list 4.788  0.650   1.307
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNAseqCovarImpute.Rcheck/00check.log’
for details.

Installation output

RNAseqCovarImpute.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNAseqCovarImpute
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘RNAseqCovarImpute’ ...
** using staged installation
** R
** data
** 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 (RNAseqCovarImpute)

Tests output

RNAseqCovarImpute.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(RNAseqCovarImpute)
> 
> test_check("RNAseqCovarImpute")

 iter imp variable
  1   1  y  z  a  b
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 iter imp variable
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 iter imp variable
  1   1  y  z  a  b
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 iter imp variable
  1   1  y  z  a  b
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 iter imp variable
  1   1  y  z  a  b
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  3   1  y  z  a  b
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  6   2  y  z  a  b
  7   1  y  z  a  b
  7   2  y  z  a  b
  8   1  y  z  a  b
  8   2  y  z  a  b
  9   1  y  z  a  b
  9   2  y  z  a  b
  10   1  y  z  a  b
  10   2  y  z  a  b

 iter imp variable
  1   1  y  z  a  b
  1   2  y  z  a  b
  2   1  y  z  a  b
  2   2  y  z  a  b
  3   1  y  z  a  b
  3   2  y  z  a  b
  4   1  y  z  a  b
  4   2  y  z  a  b
  5   1  y  z  a  b
  5   2  y  z  a  b
  6   1  y  z  a  b
  6   2  y  z  a  b
  7   1  y  z  a  b
  7   2  y  z  a  b
  8   1  y  z  a  b
  8   2  y  z  a  b
  9   1  y  z  a  b
  9   2  y  z  a  b
  10   1  y  z  a  b
  10   2  y  z  a  b


 iter imp variable
  1   1  y  z  a  b
  1   2  y  z  a  b
  2   1  y  z  a  b
  2   2  y  z  a  b
  3   1  y  z  a  b
  3   2  y  z  a  b
  4   1  y  z  a  b
  4   2  y  z  a  b
  5   1  y  z  a  b
  5   2  y  z  a  b
  6   1  y  z  a  b
  6   2  y  z  a  b
  7   1  y  z  a  b
  7   2  y  z  a  b
  8   1  y  z  a  b
  8   2  y  z  a  b
  9   1  y  z  a  b
  9   2  y  z  a  b
  10   1  y  z  a  b
  10   2  y  z  a  b

 iter imp variable
  1   1  y  z  a  b
  1   2  y  z  a  b
  2   1  y  z  a  b
  2   2  y  z  a  b
  3   1  y  z  a  b
  3   2  y  z  a  b
  4   1  y  z  a  b
  4   2  y  z  a  b
  5   1  y  z  a  b
  5   2  y  z  a  b
  6   1  y  z  a  b
  6   2  y  z  a  b
  7   1  y  z  a  b
  7   2  y  z  a  b
  8   1  y  z  a  b
  8   2  y  z  a  b
  9   1  y  z  a  b
  9   2  y  z  a  b
  10   1  y  z  a  b
  10   2  y  z  a  b

 iter imp variable
  1   1  y  z  a  b
  1   2  y  z  a  b
  2   1  y  z  a  b
  2   2  y  z  a  b
  3   1  y  z  a  b
  3   2  y  z  a  b
  4   1  y  z  a  b
  4   2  y  z  a  b
  5   1  y  z  a  b
  5   2  y  z  a  b
  6   1  y  z  a  b
  6   2  y  z  a  b
  7   1  y  z  a  b
  7   2  y  z  a  b
  8   1  y  z  a  b
  8   2  y  z  a  b
  9   1  y  z  a  b
  9   2  y  z  a  b
  10   1  y  z  a  b
  10   2  y  z  a  b


 iter imp variable
  1   1  y  z  a  b
  1   2  y  z  a  b
  2   1  y  z  a  b
  2   2  y  z  a  b
  3   1  y  z  a  b
  3   2  y  z  a  b
  4   1  y  z  a  b
  4   2  y  z  a  b
  5   1  y  z  a  b
  5   2  y  z  a  b
  6   1  y  z  a  b
  6   2  y  z  a  b
  7   1  y  z  a  b
  7   2  y  z  a  b
  8   1  y  z  a  b
  8   2  y  z  a  b
  9   1  y  z  a  b
  9   2  y  z  a  b
  10   1  y  z  a  b
  10   2  y  z  a  b

 iter imp variable
  1   1  y  z  a  b
  1   2  y  z  a  b
  2   1  y  z  a  b
  2   2  y  z  a  b
  3   1  y  z  a  b
  3   2  y  z  a  b
  4   1  y  z  a  b
  4   2  y  z  a  b
  5   1  y  z  a  b
  5   2  y  z  a  b
  6   1  y  z  a  b
  6   2  y  z  a  b
  7   1  y  z  a  b
  7   2  y  z  a  b
  8   1  y  z  a  b
  8   2  y  z  a  b
  9   1  y  z  a  b
  9   2  y  z  a  b
  10   1  y  z  a  b
  10   2  y  z  a  b

 iter imp variable
  1   1  y  z  a  b
  1   2  y  z  a  b
  2   1  y  z  a  b
  2   2  y  z  a  b
  3   1  y  z  a  b
  3   2  y  z  a  b
  4   1  y  z  a  b
  4   2  y  z  a  b
  5   1  y  z  a  b
  5   2  y  z  a  b
  6   1  y  z  a  b
  6   2  y  z  a  b
  7   1  y  z  a  b
  7   2  y  z  a  b
  8   1  y  z  a  b
  8   2  y  z  a  b
  9   1  y  z  a  b
  9   2  y  z  a  b
  10   1  y  z  a  b
  10   2  y  z  a  b

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  6.576   0.405   5.316

Example timings

RNAseqCovarImpute.Rcheck/RNAseqCovarImpute-Ex.timings

name	user	system	elapsed
combine_rubins	3.438	0.547	1.655
example_DGE	0.026	0.002	0.028
example_data	0.001	0.000	0.002
get_gene_bin_intervals	3.813	0.632	1.310
impute_by_gene_bin	2.261	0.334	1.294
limmavoom_imputed_data_list	4.788	0.650	1.307
limmavoom_imputed_data_pca	5.214	0.753	4.146