Hi @PaoloBnn ,

I tried the R commands in https://www.retip.app/ (with Windows 10 and R 4.1.3).

And I got the following errors and warning message in keras <- fit.keras(training,testing).

> keras <- fit.keras(training,testing)
2022-04-25 15:32:59.327894: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cudart64_110.dll'; dlerror: cudart64_110.dll not found
2022-04-25 15:32:59.328350: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Loaded Tensorflow version 2.8.0
2022-04-25 15:33:17.192953: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cudart64_110.dll'; dlerror: cudart64_110.dll not found
2022-04-25 15:33:17.193700: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cublas64_11.dll'; dlerror: cublas64_11.dll not found
2022-04-25 15:33:17.194395: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cublasLt64_11.dll'; dlerror: cublasLt64_11.dll not found
2022-04-25 15:33:17.195075: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cufft64_10.dll'; dlerror: cufft64_10.dll not found
2022-04-25 15:33:17.195800: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'curand64_10.dll'; dlerror: curand64_10.dll not found
2022-04-25 15:33:17.196466: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cusolver64_11.dll'; dlerror: cusolver64_11.dll not found
2022-04-25 15:33:17.197181: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cusparse64_11.dll'; dlerror: cusparse64_11.dll not found
2022-04-25 15:33:17.197862: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cudnn64_8.dll'; dlerror: cudnn64_8.dll not found
2022-04-25 15:33:17.197982: W tensorflow/core/common_runtime/gpu/gpu_device.cc:1850] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU. Follow the guide at https://www.tensorflow.org/install/gpu for how to download and setup the required libraries for your platform.
Skipping registering GPU devices...
2022-04-25 15:33:17.200959: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX AVX2
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
[1] "Computing model1 Keras  ... Please wait ..."
[1] "Computing model2 Keras  ... Please wait ..."
[1] "Computing model3 Keras  ... Please wait ..."
[1] "Mean absolute 1 error on test set: 1.04"
[1] "Mean absolute 2 error on test set: 0.96"
[1] "Mean absolute 3 error on test set: 0.95"
[1] "Return Model 3"
Warning messages:
1: In backcompat_fix_rename_lr_to_learning_rate(...) :
  the `lr` argument has been renamed to `learning_rate`.
2: In backcompat_fix_rename_lr_to_learning_rate(...) :
  the `lr` argument has been renamed to `learning_rate`.
3: In backcompat_fix_rename_lr_to_learning_rate(...) :
  the `lr` argument has been renamed to `learning_rate`.

I would appreciate it if you could let me know if we should care about these messages.

when I train the model use the function of fit.lightgbm(), is always shows a failure.

does anyone meet this problem?

Hi,

I was running Retip again yesterday. The fit.lightgbm() function error was showed again. I am wondering if you can reset parameter in the function. Thanks.

lightgbm <- fit.lightgbm(training,testing)
Error in lightgbm::lgb.cv(params, dtrain, nrounds = 5000, nfold = 10, :
unused arguments (max_depth = 4, max_leaf = 20, max_bin = 100)

Hi developers!

I am trying to install Retip and everything seems to work just until the very end, when I try to install keras.

library(keras)
install_keras()
Collecting package metadata (current_repodata.json): ...working... failed

CondaSSLError: OpenSSL appears to be unavailable on this machine. OpenSSL is required to
download and install packages.

Exception: HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /conda-forge/win-64/current_repodata.json (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available."))

It says OpenSSL is required but I manually installed this package in R and still get this error. Anybody can help me out?

many thanks!

Bas

while use function:
getCD(HILIC)
caused error
address 0x7ffeda268fd8, cause 'memory not mapped'

R version is 4.1.0

Hi,

I wanted to try the Retip package, but running your example it made R crash when it wants to compute the chemical descriptors.

In Rstudio I get this output:

[1] "Computing Chemical Descriptors 1 of 970 ... Please wait"
[80786:80786:20200826,091229.019964:ERROR process_memory_range.cc:86] read out of range
[80786:80786:20200826,091229.020011:ERROR elf_image_reader.cc:558] missing nul-terminator
[80786:80786:20200826,091229.020086:ERROR elf_dynamic_array_reader.h:61] tag not found
.
.
.
.
[80786:80786:20200826,091229.024746:ERROR elf_dynamic_array_reader.h:61] tag not found
[80786:80787:20200826,091229.053386:ERROR directory_reader_posix.cc:42] opendir: No such file or directory (2)

It outputs the line [80786:80786:20200826,091229.024746:ERROR elf_dynamic_array_reader.h:61] tag not found many many times. I also tried without parallel computing, but same issue. Can you help me with this?

My sessioninfo:

 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       Ubuntu 20.04.1 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Amsterdam            
 date     2020-08-26   

I have openjdk-11 installed. I also tried with openjdk-8, but same issue.

Cheers, Rico

Hi,
I want to install Retip but I am not able to install.
There is a problem when I try to install devtools::install_github("Paolobnn/Retiplib")
Error: Failed to install 'unknown package' from GitHub:
Failed to connect to api.github.com port 443: Connection refused
I don't know how to solve this problem.
Thanks.

hmdb_pred <- RT.spell(training,target="HMBD",model=keras,output="MSFINDER")

Fresh install on Win64 and R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

> library(rJava)
> .jinit()
> devtools::install_github("Paolobnn/Retiplib")
Downloading GitHub repo Paolobnn/Retiplib@HEAD
  
√  checking for file 'C:\Users\rj\AppData\Local\Temp\RtmpSgSOXC\remotes112061e521a3\PaoloBnn-Retiplib-49bd5fe/DESCRIPTION'

-  preparing 'Retiplib': (626ms)
   checking DESCRIPTION meta-information ...
   checking DESCRIPTION meta-information ... 
√  checking DESCRIPTION meta-information
Warning in as.POSIXlt.POSIXct(x, tz) :
   Warning in as.POSIXlt.POSIXct(x, tz) :
     unable to identify current timezone 'C':
   please set environment variable 'TZ'
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'Retiplib_0.2.1.tar.gz'

Error in strptime(xx, f, tz = tz) : 
  (converted from warning) unable to identify current timezone 'C':
please set environment variable 'TZ'
Error: Failed to install 'Retiplib' from GitHub:
  (converted from warning) installation of package ‘C:/Users/rj/AppData/Local/Temp/RtmpSgSOXC/file11203ea06479/Retiplib_0.2.1.tar.gz’ had non-zero exit status
> 

Potential solution: Define timezone or fix and request setting of time zone.
check timezone before:

Sys.timezone()
[1] "unknown"
Warning message:
In Sys.timezone() : unable to identify current timezone 'C':
please set environment variable 'TZ'

> Sys.setenv(TZ='GMT')
> Sys.timezone()
[1] "GMT"

Followed the step-by-step installation instructions, then used the demo workflow,
still got this error:

1) library(Retip)
2) prep.wizard() - Windows firewall warning (allow)
socket cluster with 72 nodes on host ‘localhost’
3) RP2 <- readxl::read_excel("Plasma_positive.xlsx", sheet = "lib_2", col_types = c("text","text", "text", "numeric"))
Error in loadNamespace(name) : there is no package called ‘readxl’

Potential solution, install

 install.packages("readxl")

Dear Developers,

I'm following the explanation in the retip and reached till the Building QSAR models:.

There, when running:

keras <- fit.keras(training,testing)

Receive this error:

2021-02-15 17:28:40.887108: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'cudart64_101.dll'; dlerror: cudart64_101.dll not found 2021-02-15 17:28:40.887560: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. Error:

And when trying again:

`

keras <- fit.keras(training,testing)
2021-02-15 17:29:17.094035: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library nvcuda.dll
2021-02-15 17:29:17.130586: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1561] Found device 0 with properties:
pciBusID: 0000:02:00.0 name: GeForce GT 710 computeCapability: 3.5
coreClock: 0.954GHz coreCount: 1 deviceMemorySize: 2.00GiB deviceMemoryBandwidth: 11.92GiB/s
2021-02-15 17:29:17.133583: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'cudart64_101.dll'; dlerror: cudart64_101.dll not found
2021-02-15 17:29:17.135754: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'cublas64_10.dll'; dlerror: cublas64_10.dll not found
2021-02-15 17:29:17.137999: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'cufft64_10.dll'; dlerror: cufft64_10.dll not found
2021-02-15 17:29:17.140565: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'curand64_10.dll'; dlerror: curand64_10.dll not found
2021-02-15 17:29:17.142849: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'cusolver64_10.dll'; dlerror: cusolver64_10.dll not found
2021-02-15 17:29:17.145072: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'cusparse64_10.dll'; dlerror: cusparse64_10.dll not found
2021-02-15 17:29:17.147183: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'cudnn64_7.dll'; dlerror: cudnn64_7.dll not found
2021-02-15 17:29:17.147632: W tensorflow/core/common_runtime/gpu/gpu_device.cc:1598] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU. Follow the guide at https://www.tensorflow.org/install/gpu for how to download and setup the required libraries for your platform.
Skipping registering GPU devices...
2021-02-15 17:29:17.149085: I tensorflow/core/platform/cpu_feature_guard.cc:143] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2
2021-02-15 17:29:17.163720: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x27ee1547440 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2021-02-15 17:29:17.164150: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
2021-02-15 17:29:17.164576: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1102] Device interconnect StreamExecutor with strength 1 edge matrix:
2021-02-15 17:29:17.164985: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1108]
[1] "Computing model1 Keras ... Please wait ..."
Error in py_call_impl(callable, dots$args, dots$keywords) :
ModuleNotFoundError: No module named 'rpytools'
`

I tried to follow this explantions:
Evaluation error: ModuleNotFoundError: No module named 'rpytools' #561

Evaluation error: ModuleNotFoundError: No module named 'rpytools'. #959

Any suggestions\ ideas \ thoughts to how to solve this will be appriciated
Many thanks

Hi,

Can you help me with that error obtained under Rstudio while running plasma tutorial example?

Train Model

setSessionTimeLimit(cpu = Inf, elapsed = Inf)
xgb <- fit.xgboost(training)
[1] "Computing model Xgboost ... Please wait ..."
Error in selectChildren(ac[!fin], -1) : reached CPU time limit

keras <- fit.keras(training,testing)
*** Error in `/usr/lib/rstudio-server/bin/rsession': munmap_chunk(): invalid pointer: 0x00007ffd60046b60 ***

others models are fine in my configuration

Many thanks
Yann

Hi,

I get an OpenSSL error while the openssl seems loaded, can you guys see what's going wrong here?

library(openssl)
Linking to: OpenSSL 1.1.1k 25 Mar 2021
keras <- fit.keras(training,testing)

• "C:/Users/Bas/AppData/Local/r-miniconda/condabin/conda.bat" "create" "--yes" "--prefix" "C:/Users/Bas/AppData/Local/r-miniconda/envs/r-reticulate" "python=3.8" "numpy" "--quiet" "-c" "conda-forge"
  Collecting package metadata (current_repodata.json): ...working... failed

CondaSSLError: OpenSSL appears to be unavailable on this machine. OpenSSL is required to
download and install packages.

Exception: HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /conda-forge/win-64/current_repodata.json (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available."))

Error: Error creating conda environment 'C:/Users/Bas/AppData/Local/r-miniconda/envs/r-reticulate' [exit code 1]

Hi!

Somehow this smile does not work in retip: "C1CN(CCN1CC/C=C\2/C3=CC=CC=C3SC4=C2C=C(C=C4)Cl)CCO"

getRT.smile("C1CN(CCN1CC/C=C\2/C3=CC=CC=C3SC4=C2C=C(C=C4)Cl)CCO",training,model=xgb)
Error in eval.desc(mol, descNames) : molecule must be an IAtomContainer
In addition: Warning message:
In parse.smiles(smile) :
1 out of 1 SMILES were not successfully parsed, resulting in NULLs.

I really don't understand why, because all my other SMILES work just fine.

Thanks again!

Bas

Dear Retip developer,
I'm haveing issues that could not solve in installing the packge.

My system :
> version _ platform x86_64-w64-mingw32 arch x86_64 os mingw32 system x86_64, mingw32 status major 3 minor 6.2 year 2019 month 12 day 12 svn rev 77560 language R version.string R version 3.6.2 (2019-12-12) nickname Dark and Stormy Night

I'm receiving this message:

``> devtools::install_github("Paolobnn/Retip", force = TRUE)
Downloading GitHub repo Paolobnn/Retip@HEAD
√ checking for file 'C:\Users\BCDD\AppData\Local\Temp\RtmpI7Ny7t\remotesc6984303216d\PaoloBnn-Retip-8c23eda/DESCRIPTION' (461ms)

• preparing 'Retip': (502ms)
  √ checking DESCRIPTION meta-information ...
• 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 'Retip_0.5.4.tar.gz' (3.1s)

Installing package into ‘D:/BCDD/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

• installing source package 'Retip' ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** byte-compile and prepare package for lazy loading
  Error: (converted from warning) package 'ggplot2' was built under R version 3.6.3
  Execution halted
  ERROR: lazy loading failed for package 'Retip'
• removing 'D:/BCDD/Documents/R/win-library/3.6/Retip'
  Error: Failed to install 'Retip' from GitHub:
  (converted from warning) installation of package ‘C:/Users/BCDD/AppData/Local/Temp/RtmpI7Ny7t/filec6987ea92c6b/Retip_0.5.4.tar.gz’ had non-zero exit status``

Any idea how to solve this?
(If is there any more info needed please tell me)

Many thanks,
Tal

Dear Developer,
I am running R 4.0.5 on Windows and keep getting this error when I run the keras <- fit.keras(training,testing) line when I follow the instructions on Win 10. I didn't find useful information online. Someone asked the same question on stackoverflow but nobody answered it. The traceback is pasted below:

Error in path.expand(path) : invalid 'path' argument
16.
path.expand(path)
15.
normalizePath(conda_envs, mustWork = FALSE)
14.
unique(normalizePath(conda_envs, mustWork = FALSE))
13.
conda_list(conda = conda)
12.
rbind(deparse.level, ...)
11.
rbind(conda_envs, conda_list(conda = conda))
10.
python_conda_versions()
9.
py_discover_config(required_module, use_environment)
8.
(function() {
op <- options(reticulate.python.initializing = TRUE)
on.exit(options(op), add = TRUE)
py_discover_config(required_module, use_environment) ...
7.
initialize_python(required_module, use_environment)
6.
ensure_python_initialized()
5.
tuple(shape)
4.
modifiers[nm]
3.
capture_args(match.call(), list(shape = normalize_shape, batch_shape = normalize_shape))
2.
layer_input(shape = ncol(train_data)) at model_keras.R#48
1.
fit.keras(training, testing)

Dear Retip developer,
I am trying to use this wonderful tool, However, I keep obtaining the following error.

the problem seems to be the rJava package, but I can correctly library rJava.
Do you have any clue?

best,
Sukis