Keras failure in R after using in python with Anaconda #733

NigelKinney · 2019-04-08T07:32:45Z

Hello,

I have had some weird issues: I mainly used keras on R, but last week I had to do that in python, and then today I realized that my keras installation in RStudio.

I got this error for all keras functions; such as .

model <- keras_model_sequential()

or

rray_reshape(x = xtrain, dim = list(dim(xtrain)[1], 1, dim(xtrain)[2]))

keras Error: lexical error: invalid char in json text. WARNING: The conda.compat module

But when I uninstall anaconda, then I could use my keras.
Does anyone know what may be happening. (I am okay without Anaconda, but it is not that convenient as I do need to use Python occasionally)

BrianCollinss · 2019-04-08T09:41:11Z

I am working on Windows 10 and R/3.5.0. Apparently Keras has some incompatibility with Python 3.7. The thing is that Tensorflow 1.13.1 is dependent on Python 3.7! I don't know how I can install. I cannot get Tensorflow installed with Python 3.7 and 3.6 on Anacondra. It only works with stand-along installations of Python. Any solution?

ibrary(keras)
> install_keras()
Error: lexical error: invalid char in json text.
                                       WARNING: The conda.compat modul
                     (right here) ------^

> library(keras)
> install_keras(method='conda')
Error: lexical error: invalid char in json text.
                                       WARNING: The conda.compat modul
                     (right here) ------^

dfalbel · 2019-04-08T14:01:51Z

This may help: rstudio/tensorflow#311

This issue is probably related to reticulate and we already have 2 open issues there eg. rstudio/reticulate#475 and rstudio/reticulate#474

NigelKinney · 2019-04-08T16:55:40Z

@dfalbel @BenAbabaei . Thank you for your reply.

I think downgrading the python (#311) will help as I did a pip update python when I was writing the codes in jupyternotebooks, which created that problem. Thanks a lot!

dfalbel · 2019-04-08T20:41:12Z

This has been solved, see here: rstudio/reticulate#475

NigelKinney · 2019-04-08T20:45:04Z

I have seen the #475 reticulate post, but it does not solve my problem. Re-installing reticulate does not solve the problem.

The only solution I have now is to force to downward python 3.7 to python 3.6; then everything seems ok at the moment.

NigelKinney · 2019-04-09T00:32:17Z

devtools::install_github("rstudio/reticulate") does not help. I still got the same error. FCmodel <- keras_model_sequential() Error: lexical error: invalid char in json text. WARNING: The conda.compat modul (right here) ------^

…

On Mon, Apr 8, 2019 at 1:41 PM Daniel Falbel ***@***.***> wrote: This has been solved, see here: rstudio/reticulate#475 <rstudio/reticulate#475> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#733 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AURDFn0ckcJc3yqJLFDVkX-7H0Gcob0Wks5ve6lrgaJpZM4chflL> .

-- Jiancong (Nigel) || 陈见聪 Graduate Student Environmental Engineering UC Berkeley

dfalbel · 2019-04-09T01:08:56Z

Are you on a clean session? Can you share your tf_config() and sessionInfo() please?

NigelKinney · 2019-04-09T01:19:10Z

The reason I ran into this is because i updated my Anaconda and python to 3.7. Everything was fine when I was python 3.6. I just uninstall Anaconda, and R and RStudio. It seemed working now. I think maybe there’s a compile issue of reticulate in python 3.7

…

On Monday, April 8, 2019, Daniel Falbel ***@***.***> wrote: Are you on a clean session? Can you share your tf_config() and sessionInfo() please? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#733 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AURDFmwgomTVVYpL36MhmHJ0wSjI1-Cfks5ve-gqgaJpZM4chflL> .

-- Jiancong (Nigel) || 陈见聪 Graduate Student Environmental Engineering UC Berkeley

BrianCollinss · 2019-04-10T01:14:08Z

> library(keras)
> install_keras()
Error: lexical error: invalid char in json text.
                                       WARNING: The conda.compat modul
                     (right here) ------^
> 
> tf_config()
Error: lexical error: invalid char in json text.
                                       WARNING: The conda.compat modul
                     (right here) ------^
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252    

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

other attached packages:
[1] keras_2.2.4.1.9000     tensorflow_1.13.1.9000

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        compiler_3.5.3    prettyunits_1.0.2 base64enc_0.1-3   remotes_2.0.2     tools_3.5.3       zeallot_0.1.0    
 [8] testthat_2.0.1    digest_0.6.18     pkgbuild_1.0.3    pkgload_1.0.2     jsonlite_1.6      memoise_1.1.0     lattice_0.20-38  
[15] rlang_0.3.4       Matrix_1.2-15     cli_1.1.0         rstudioapi_0.10   curl_3.3          yaml_2.2.0        withr_2.1.2      
[22] generics_0.0.2    desc_1.2.0        fs_1.2.7          devtools_2.0.1    rprojroot_1.3-2   grid_3.5.3        reticulate_1.11.1
[29] glue_1.3.1        R6_2.4.0          processx_3.3.0    sessioninfo_1.1.1 callr_3.2.0       magrittr_1.5      whisker_0.3-2    
[36] backports_1.1.3   ps_1.3.0          tfruns_1.4        usethis_1.4.0     assertthat_0.2.1  crayon_1.3.4

dfalbel · 2019-04-10T01:16:36Z

Please install the dev version of reticulate:

devtools::install_github("rstudio/reticulate")

BrianCollinss · 2019-04-10T01:18:46Z

> devtools::install_github("rstudio/reticulate")
Downloading GitHub repo rstudio/reticulate@master
√  checking for file 'C:\Users\uqbababa\AppData\Local\Temp\RtmpMdeum0\remotes25010b153ef\rstudio-reticulate-41706b4/DESCRIPTION' ... 
-  preparing 'reticulate': (745ms)
√  checking DESCRIPTION meta-information ... 
-  cleaning src
-  checking for LF line-endings in source and make files and shell scripts (413ms)
-  checking for empty or unneeded directories
-  building 'reticulate_1.11.1-9000.tar.gz'
   
Installing package into ‘C:/Users/uqbababa/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package 'reticulate' ...
** libs

*** arch - i386
C:/RBuildTools/3.5/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/RBuildTools/3.5/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c event_loop.cpp -o event_loop.o
C:/RBuildTools/3.5/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c libpython.cpp -o libpython.o
C:/RBuildTools/3.5/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c output.cpp -o output.o
C:/RBuildTools/3.5/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c python.cpp -o python.o
C:/RBuildTools/3.5/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c readline.cpp -o readline.o
C:/RBuildTools/3.5/mingw_32/bin/g++ -shared -s -static-libgcc -o reticulate.dll tmp.def RcppExports.o event_loop.o libpython.o output.o python.o readline.o -LC:/PROGRA~1/R/R-35~1.3/bin/i386 -lR
installing to C:/Users/uqbababa/Documents/R/win-library/3.5/reticulate/libs/i386

*** arch - x64
C:/RBuildTools/3.5/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/RBuildTools/3.5/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c event_loop.cpp -o event_loop.o
C:/RBuildTools/3.5/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c libpython.cpp -o libpython.o
C:/RBuildTools/3.5/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c output.cpp -o output.o
C:/RBuildTools/3.5/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c python.cpp -o python.o
C:/RBuildTools/3.5/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG  -I"C:/Users/uqbababa/Documents/R/win-library/3.5/Rcpp/include"        -O2 -Wall  -mtune=generic -c readline.cpp -o readline.o
C:/RBuildTools/3.5/mingw_64/bin/g++ -shared -s -static-libgcc -o reticulate.dll tmp.def RcppExports.o event_loop.o libpython.o output.o python.o readline.o -LC:/PROGRA~1/R/R-35~1.3/bin/x64 -lR
installing to C:/Users/uqbababa/Documents/R/win-library/3.5/reticulate/libs/x64
Error in file.copy(files, dest, overwrite = TRUE) : 
  (converted from warning) problem copying .\reticulate.dll to C:\Users\uqbababa\Documents\R\win-library\3.5\reticulate\libs\x64\reticulate.dll: Permission denied
* removing 'C:/Users/uqbababa/Documents/R/win-library/3.5/reticulate'
* restoring previous 'C:/Users/uqbababa/Documents/R/win-library/3.5/reticulate'
Error in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) : 
  (converted from warning) problem copying C:\Users\uqbababa\Documents\R\win-library\3.5\00LOCK-reticulate\reticulate\libs\x64\reticulate.dll to C:\Users\uqbababa\Documents\R\win-library\3.5\reticulate\libs\x64\reticulate.dll: Permission denied
Execution halted
In R CMD INSTALL
Error in i.p(...) : 
  (converted from warning) installation of package ‘C:/Users/uqbababa/AppData/Local/Temp/RtmpMdeum0/file250374f2435/reticulate_1.11.1-9000.tar.gz’ had non-zero exit status

dfalbel · 2019-04-10T01:21:40Z

This seems like a "permission denied" issue. Are you admin on this machine?

BrianCollinss · 2019-04-10T01:23:19Z

@dfalbel I am. I just wonder why I get that error with 'conda' json file.

dfalbel · 2019-04-10T01:52:24Z

This error is related to reticulate and has been fixed in the dev version. See here: rstudio/reticulate#474

BrianCollinss · 2019-04-10T02:24:36Z

I reinstalled reticulate from GitHub and it worked! So much trouble for a warning :) Cheers.

rgurlek · 2019-04-10T12:18:54Z

Installing reticulate from Github worked. I had to use argument INSTALL_opts = c('--no-lock').

roberthadow mentioned this issue Apr 8, 2019

Error in data.frame(...): arguments imply differing number of rows: 2, 0 andrie/deepviz#5

Open

dfalbel closed this as completed Apr 8, 2019

BrianCollinss mentioned this issue Apr 10, 2019

install_keras() fails #367

Closed

dfalbel mentioned this issue Apr 10, 2019

Custom objects in R #723

Closed

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Keras failure in R after using in python with Anaconda #733

Keras failure in R after using in python with Anaconda #733

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Keras failure in R after using in python with Anaconda #733

Keras failure in R after using in python with Anaconda #733

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