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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
351 stars 79 forks source link

Error for library SCP #168

Closed TPOW-001 closed 11 months ago

TPOW-001 commented 11 months ago

Here is the error information when I library SCP, please help me to resolve this problem:

Error: package or namespace load failed for ‘SCP’:
 .onAttach failed in attachNamespace() for 'SCP', details:
  call: NULL
  error: lexical error: invalid char in json text.
                                       'Analysis' <a4><a3><ac>O<a4><ba
                     (right here) ------^
TPOW-001 commented 11 months ago

https://github.com/rstudio/reticulate/issues/1274 According to above issues of reticulate, I got some information after run:

>debug(jsonlite:::parse_string)
> library(SCP)
debugging in: parse_string(txt, bigint_as_char)
debug: {
    if (length(txt) > 1) {
        txt <- paste(txt, collapse = "\n")
    }
    .Call(R_parse, txt, bigint_as_char)
}
Browse[2]> txt
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[67] "  \"user_rc_path\": \"C:\\\\Users\\\\TPOW31714\\\\Documents\\\\.condarc\","                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
[68] "  \"virtual_pkgs\": ["                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
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[70] "      \"__cuda\","                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
[71] "      \"12.2\""                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
[72] "    ]"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
[73] "  ]"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
[74] "}"
zhanghao-njmu commented 11 months ago

I am not sure what caused the error. However, you can try solving it by following these steps:

  1. Start a new R session.
  2. Run SCP::PrepareEnv(force = TRUE) to reinstall the SCP python environment.
  3. library(SCP)

If these steps do not work, please inform me so that I can assist you further.

TPOW-001 commented 11 months ago

I start a new R session, run following codes, but still got the same results:

> SCP::PrepareEnv(force = TRUE)
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)

Error: lexical error: invalid char in json text.
                                       'Analysis' <a4><a3><ac>O<a4><ba
                     (right here) ------^
zhanghao-njmu commented 11 months ago

You can try running the following code again: SCP::PrepareEnv(conda=NULL, force=TRUE) conda=NULL means that the latest version of conda will be downloaded and installed. Please give this command a try and check if the issue persists.

TPOW-001 commented 11 months ago

Thanks for the assitance! Your help made it possible for me to run your remarkable package, and I greatly appreciate it.