there is no package "testthat"

[turgut090]

Hi,
I have just updated R to 3.6.0 version and cannot install lightgbm

The problem is with testthatpackage. I installed that library but when I try to run

Rscript build_r.R

It throws an error: there is no testthat package from the terminal.

Ошибка в library(testthat) :нет пакета под названием ‘testthat’
Выполнение остановлено

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] testthat_2.1.0

loaded via a namespace (and not attached):
[1] compiler_3.6.0 magrittr_1.5   R6_2.4.0       tools_3.6.0    rlang_0.3.4   

[jameslamb]

@henry090 thanks for reporting. I don't understand how that error message and that sessionInfo() could possibly happen together, but I do know I need to do some re-reading on how package installs work in R 3.6.0.

Either way, I have a workaround for you! On advice from @Laurae2 , I put up #2123 to remove all R dependencies not available in common distributions from the build process. Until that PR is reviewed and merged, you could replace your local build.R with that one and I think it should work!

Will you try and let me know?

[turgut090]

I have all of the libraries... (‘data.table’, ‘Matrix’)

Предупреждение: неизвестная опция ‘--keep_empty-dirs’
* checking for file ‘lightgbm_r/DESCRIPTION’ ... OK
* preparing ‘lightgbm’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘lightgbm_2.2.4.tar.gz’

* installing to library ‘/anaconda3/lib/R/library’
ERROR: dependencies ‘data.table’, ‘Matrix’ are not available for package ‘lightgbm’
* removing ‘/anaconda3/lib/R/library/lightgbm’
Ошибка в .run_shell_command(cmd) :Command failed with exit code: 1
Выполнение остановлено

[Laurae2]

@jameslamb @henry090 This might be because R is inside Anaconda. Not sure how the R shell behaves inside a conda + macOS environment.

@jameslamb Can you test what happens inside a macOS environment using conda, assuming a precompiled data.table and Matrix packages from conda R repositories?

[turgut090]

Hi, @Laurae2 .
I removed Anaconda from Mac OS and tried again. It helped! Thank you!

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lightgbm_2.2.4 R6_2.4.0      

loaded via a namespace (and not attached):
[1] compiler_3.6.0    magrittr_1.5      tools_3.6.0       data.table_1.12.2 jsonlite_1.6 

[jameslamb]

@henry090 wait does that mean it worked? When you say you "removed" Anaconda does that mean you completely uninstalled it, or just moved out of a conda environment into a vanilla R session?

@Laurae2 yes I'll try to reproduce this this week on my Mac. I believe when you use R within a conda environment, packages you installed with install.packages() in a non-conda session will not be found (since they won't be in a library path like /something/miniconda/lib/R/library.

[turgut090]

@henry090 wait does that mean it worked? When you say you "removed" Anaconda does that mean you completely uninstalled it, or just moved out of a conda environment into a vanilla R session?

"you completely uninstalled it" - Yes.

[jameslamb]

closing this as I think it's now working. @henry090 thanks for the thorough report. If you are still experiencing problems, please open a new issue.