| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:19 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1779/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAseqCovarImpute 1.0.2 (landing page) Brennan Baker
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: RNAseqCovarImpute |
| Version: 1.0.2 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RNAseqCovarImpute.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RNAseqCovarImpute_1.0.2.tar.gz |
| StartedAt: 2024-04-16 03:10:55 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 03:13:16 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 141.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNAseqCovarImpute.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RNAseqCovarImpute.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RNAseqCovarImpute_1.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RNAseqCovarImpute.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* this is package ‘RNAseqCovarImpute’ version ‘1.0.2’
* 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 ‘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 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 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 ... 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’
get_gene_bin_intervals: no visible binding for global variable ‘end’
get_gene_bin_intervals: no visible binding for global variable ‘start’
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’
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 end gene_bin i is
lm_predictor lowess new probe rubins_t_bayes start
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "approxfun", "end", "lowess", "start")
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 ... 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 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_list 12.137 2.170 4.800
impute_by_gene_bin 11.742 1.644 4.391
combine_rubins 11.896 1.110 5.040
get_gene_bin_intervals 11.098 1.311 4.023
* 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 ...
‘Example_Data_for_RNAseqCovarImpute.Rmd’ using ‘UTF-8’... OK
‘Impute_Covariate_Data_in_RNA_sequencing_Studies.Rmd’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/RNAseqCovarImpute.Rcheck/00check.log’
for details.
RNAseqCovarImpute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL RNAseqCovarImpute ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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)
RNAseqCovarImpute.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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.
> # 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")
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iter imp variable
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
20.730 1.066 16.774
RNAseqCovarImpute.Rcheck/RNAseqCovarImpute-Ex.timings
| name | user | system | elapsed | |
| combine_rubins | 11.896 | 1.110 | 5.040 | |
| example_DGE | 0.065 | 0.004 | 0.068 | |
| example_data | 0.003 | 0.000 | 0.002 | |
| get_gene_bin_intervals | 11.098 | 1.311 | 4.023 | |
| impute_by_gene_bin | 11.742 | 1.644 | 4.391 | |
| limmavoom_imputed_data_list | 12.137 | 2.170 | 4.800 | |