An error and warnings in initialization

JohannesTan commented 5 years ago

Hi

I got an error and warnings after executing packrat::init() as follows.

> packrat::init()
Initializing packrat project in directory:
- "~/docdis"
Error: Unable to retrieve package records for the following packages:
- "rethinking"
In addition: There were 15 warnings (use warnings() to see them)

> warnings()
 警告メッセージ: 
1: In fileDependencies.R(file) :
  Failed to parse C:/Users/yohei/Documents/docdis/model/ch3/修正前/run-model-treghapSNC_simpmatx2.R ; dependencies in this file will not be discovered.
2: In FUN(X[[i]], ...) :
  Package 'rethinking' not available in repository or locally
3: In FUN(X[[i]], ...) :
  Failed to infer source for package 'GGally'; using latest available version on CRAN instead
4: In FUN(X[[i]], ...) :
  Failed to infer source for package 'MCMCpack'; using latest available version on CRAN instead
5: In FUN(X[[i]], ...) :
  Failed to infer source for package 'MatrixModels'; using latest available version on CRAN instead
6: In FUN(X[[i]], ...) :
  Failed to infer source for package 'SparseM'; using latest available version on CRAN instead
7: In FUN(X[[i]], ...) :
  Failed to infer source for package 'ellipse'; using latest available version on CRAN instead
8: In FUN(X[[i]], ...) :
  Failed to infer source for package 'gcookbook'; using latest available version on CRAN instead
9: In FUN(X[[i]], ...) :
  Failed to infer source for package 'ggmcmc'; using latest available version on CRAN instead
10: In FUN(X[[i]], ...) :
  Failed to infer source for package 'makedummies'; using latest available version on CRAN instead
11: In FUN(X[[i]], ...) :
  Failed to infer source for package 'mcmc'; using latest available version on CRAN instead
12: In FUN(X[[i]], ...) :
  Failed to infer source for package 'msm'; using latest available version on CRAN instead
13: In FUN(X[[i]], ...) :
  Failed to infer source for package 'quantreg'; using latest available version on CRAN instead
14: In FUN(X[[i]], ...) :
  Failed to infer source for package 'reshape'; using latest available version on CRAN instead
15: In FUN(X[[i]], ...) :
  Failed to infer source for package 'vcd'; using latest available version on CRAN instead

Then, I updated all packages and tried to install the package "rethinking", but...

> install.packages("rethinking")
Warning in install.packages :
  package ‘rethinking’ is not available (for R version 3.5.3)

I am unsure what I should do next to resolve these problems. Thanks!

Johannes

cderv commented 5 years ago

The issue here is that your project depends on a package, rethinking, that you don't have installed apparently.

You either

need to install the library - which is not on CRAN i think. I believe this is this one
Check if you you really need this package for your project, and if not remove the dependency from your call. (any call to library(rethinking), require(rethinking), rethinking::<fun>, ...)

JohannesTan commented 5 years ago

Thank you for your advice! I installed the package by following the github page you mentioned. I resolved the problem after that.

install.packages(c("coda","mvtnorm","devtools","loo"))
library(devtools)
devtools::install_github("rmcelreath/rethinking")

I learned, thanks to your comment, that this package is not on CRAN, so I could not install it with install.packages() function.

Johannes

leomarameo7 commented 4 years ago

Please, I have a conflict with "rethinking" and "packrat". I tried to initiate "packrat", with my existing project, but here's the error:

packrat::init() Initializing packrat project in directory:

"~/Desktop/functional_response_herbivore_fish" Error: Unable to retrieve package records for the following packages: 'rethinking' In addition: Warning messages: 1: In FUN(X[[i]], ...) : Package 'rethinking' not available in repository or locally 2: In FUN(X[[i]], ...) : Failed to infer source for package 'bdsmatrix'; using latest available version on CRAN instead

So I follow rstudio/packrat#553 (comment) , but it did not solve the problem. Line command### options(repos=c(getOption('repos'), rethinking='http://xcelab.net/R')) install.packages('rethinking',type='source') Installing package into ‘/Users/leonardocapitani/Library/R/3.6/library’ (as ‘lib’ is unspecified) trying URL 'http://xcelab.net/R/src/contrib/rethinking_2.00.tar.gz' Content type 'application/x-tar' length 2241087 bytes (2.1 MB)

downloaded 2.1 MB Error in file(filename, "r", encoding = encoding) : cannot open the connection Calls: source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'packrat/init.R': No such file or directory Execution halted Warning in install.packages : installation of package ‘rethinking’ had non-zero exit status The downloaded source packages are in ‘/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/RtmpXDBdZO/downloaded_packages’

rstudio / packrat

An error and warnings in initialization #553

My hardware: