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ZhuMetLab / AllCCS

Source code of AllCCS. Prediction function was provided in AllCCS web server (http://allccs.zhulab.cn/).
http://allccs.zhulab.cn/
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Error in is.data.frame(x) : object 'md_hmdb_pos' not found #3

Open gzu300 opened 2 years ago

gzu300 commented 2 years ago

Hi,

I tried to run throught the example code provided in the package. test <- read.csv(system.file("extdata", "demo_data.csv", package="AllCCS"), stringsAsFactors = F) test <- MdGet(mol_smiles = test$smiles, mol_names = test$id_allccs, rep(c('Valid'), length(test$id_allccs)), base_dir = '.')

But had the error mentioned in the title of the issue. I looked into the code. 'md_hmdb_pos' is indded not assigned anywhere above this line. Here's the link. https://github.com/ZhuMetLab/AllCCS/blob/f92b428e06617fb723ee9ec6c3ee2a11a0573e6d/R/AllCcsMdFun.R#L161

Could you correct it? Or explains what kind of object it is? Thanks

JustinZZW commented 2 years ago

Hi Guanchen,

Sorry for the late reply. The MD values and final SVR model were intentionally removed in the package due to copyright. The github package is only used for source code demonstration purpose.

Please use the web server for completed functions.

Best,

Zhiwei

Zhiwei Zhou, Ph.D.

Interdisciplinary Research Center on Biology and Chemistry (IRCBC)

Shanghai Institute of Organic Chemistry

Chinese Academy of Sciences

From: @. @.> On Behalf Of Guanchen Zhu Sent: Thursday, September 8, 2022 7:17 AM To: ZhuMetLab/AllCCS @.> Cc: Subscribed @.> Subject: [ZhuMetLab/AllCCS] Error in is.data.frame(x) : object 'md_hmdb_pos' not found (Issue #3)

Hi,

I tried to run throught the example code provided in the package. test <- read.csv(system.file("extdata", "demo_data.csv", package="AllCCS"), stringsAsFactors = F) test <- MdGet(mol_smiles = test$smiles, mol_names = test$id_allccs, rep(c('Valid'), length(test$id_allccs)), base_dir = '.')

But had the error mentioned in the title of the issue. I looked into the code. 'md_hmdb_pos' is indded nto assigned anywhere. Here's the link. https://github.com/ZhuMetLab/AllCCS/blob/f92b428e06617fb723ee9ec6c3ee2a11a0573e6d/R/AllCcsMdFun.R#L161

Could you correct it? Or explains what kind of object it is? Thanks

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