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CHECK report for gemini on merida1

This page was generated on 2021-05-06 12:35:03 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the gemini package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 678/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemini 1.4.0  (landing page)
Sidharth Jain
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/gemini
Branch: RELEASE_3_12
Last Commit: ee4db06
Last Changed Date: 2020-10-27 11:47:20 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: gemini
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gemini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gemini_1.4.0.tar.gz
StartedAt: 2021-05-06 01:58:20 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:01:29 -0400 (Thu, 06 May 2021)
EllapsedTime: 189.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: gemini.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gemini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gemini_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/gemini.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemini/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gemini’ version ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gemini’ 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
gemini_boxplot : <anonymous>: no visible binding for global variable
  ‘.’
gemini_boxplot: no visible binding for global variable ‘.’
gemini_boxplot : <anonymous>: no visible binding for global variable
  ‘gi’
gemini_boxplot : <anonymous>: no visible binding for global variable
  ‘hj’
gemini_boxplot: no visible binding for global variable ‘label’
gemini_boxplot: no visible binding for global variable ‘y’
gemini_calculate_lfc: no visible binding for global variable ‘.’
update_s_pb: no visible binding for global variable ‘.’
update_tau_pb: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . gi hj label y
* 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
gemini_inference  26.945  3.410  30.395
update_tau_pb     12.216  1.658  13.899
update_x_pb       10.118  1.430  11.562
gemini_initialize  7.968  0.068   8.050
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gemini)
  > 
  > test_check("gemini")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_data.R:31:5): Input object is reproducible ────────────────────
  `Input.new` not equal to `Input`.
  Component "sample.annot": Attributes: < Component "row.names": Mean relative difference: 0.5454545 >
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/gemini.Rcheck/00check.log’
for details.


Installation output

gemini.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gemini
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘gemini’ ...
** using staged installation
** R
** data
** 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 (gemini)

Tests output

gemini.Rcheck/tests/testthat.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(gemini)
> 
> test_check("gemini")
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test_data.R:31:5): Input object is reproducible ────────────────────
`Input.new` not equal to `Input`.
Component "sample.annot": Attributes: < Component "row.names": Mean relative difference: 0.5454545 >

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted

Example timings

gemini.Rcheck/gemini-Ex.timings

nameusersystemelapsed
Sgene2Pguides_hash0.0010.0010.001
Sguide2Pguides_hash0.0010.0000.000
compound0.0010.0010.001
dot-median_normalize0.0000.0010.000
gemini_boxplot3.8750.0713.951
gemini_calculate_lfc0.4610.0210.482
gemini_create_input0.3800.0100.389
gemini_inference26.945 3.41030.395
gemini_initialize7.9680.0688.050
gemini_plot_mae0.8640.0100.875
gemini_prepare_input0.4500.0040.455
gemini_score0.9750.0090.985
initialize_s1.8920.0231.918
initialize_tau2.6940.0272.723
initialize_x4.0120.0254.041
initialize_y0.7770.0340.811
pipe000
update_mae1.5670.0111.581
update_s_pb2.2170.0962.317
update_tau_pb12.216 1.65813.899
update_x_pb10.118 1.43011.562
update_y_pb3.5240.0623.593