Could you teach me how to install the package named "Zr" in R?

[liyuan-bioinfo]

Dear author,
It may difficult for me to use the R script named 1_zinc_to_chembl.R, because I don't know how to install the package named "Zr" after trying the method such as install.packages("Zr”), and I also don't understand what's the meaning of this codes source("~/work/sea/scripts/zinc_tools.R"). I want to get the information about zinc_id and drug info , I have tried to read your docoment named README, but I can't find any methods help me solve this. Could you help me to deal with this problem?

Your sincerely!
Li-Yuan

[momeara]

Dear Li-Yuan,
Thanks for your interest in the BioChemPantry package!

Zr is another package of mine used to access the ZINC15 webserver. You can find it here: https://github.com/momeara/Zr

source("~/work/sea/scripts/zinc_tools.R") Is a reference to a local file not in the package. I see that it appears in the chembl21 and chembl22 set vignettes. I would recommend using the most recent chembl vignette (chembl25) to get the most recent version of chembl loaded.

[liyuan-bioinfo]

Dear auther:
Thanks for your reply! I have installed Zr successful and it worked. but I want to know why not to use chembl vignette (chembl26) ? I guess ZINC only can download the most recent version of chembl25 by web service.
And when I try to run the codes:

 Zr::catalog_items(
  catalog_short_name="chembl25",
  count='all',
  verbose=T)

the R console shows some ERROR messages when send POST to ZINC web service:
ERROR: url='http://zinc15.docking.org/catalogs/chembl25/items.csv?output_fields=zinc_id%20supplier_code%20substance.preferred_name%20substance.smiles%20substance.purchasable%20substance.purchasability%20substance.gene_names%20substance.rb%20substance.reactive%20substance.features&count=all'
status_code='503'
I guess I should restart my network service or try to download it in another way.

[momeara]

we haven’t prepared the ChEMBL 26 set yet, if you would like to adapt the chembl25 vignette and do a pull request I would review it. For The ZINC catalog items, look at the options for the ZINC REST function in Zr, you can batch queries into chunks rather than getting it all at once, and set a higher retry rate. If you are having further issues with ZINC, I would reach out to their admin/support

…

On May 21, 2020, at 5:25 AM, liyuan-bioinfo ***@***.***> wrote:  Dear auther: Thanks for your reply! I have install Zr successful and it worked. but I want to know why not use chembl vignette (chembl26) ? I guess ZINC only can download the version of chemle by web service. And when I try to run the codes: Zr::catalog_items( catalog_short_name="chembl25", count='all', verbose=T) the R console shows some ERROR messages when send POST to ZINC web service: ERROR: url='http://zinc15.docking.org/catalogs/chembl25/items.csv?output_fields=zinc_id%20supplier_code%20substance.preferred_name%20substance.smiles%20substance.purchasable%20substance.purchasability%20substance.gene_names%20substance.rb%20substance.reactive%20substance.features&count=all' status_code='503' I guess I should restart my network service or try to download it in another way. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.