db_create() / Error reading from the connection

[bioxenia]

Hello again.
I am trying to run the restez package. I tried that on Windows10 but I got UTF-8 errors, so I installed a different OS, Ubuntu specifically, via Vitrual Box. But now an other error occured.
I am trying to download the invertebrate data, and after making the connection and running the db_create command I get the error:

Error in readLines(con = connection) : error reading from the connection In addition: Warning message: In readLines(con = connection) : invalid or incomplete compressed data Error: callr subprocess failed: error reading from the connection
Do you have any ideas?
Thank you!

[jeroen]

You need to be more specific about what code you ran, and the context of the error. Both on Windows and Ubuntu. From your error message above it is impossible to guess what went wrong.

Did you install the latest version of restez?

[bioxenia]

Yes, I have the latest version of restez.
The code I ran and the error I get on Windows:

`

library(restez)
rstz_pth <- file.path(tempdir(), 'database')
if (!dir.exists(rstz_pth)) {
dir.create(rstz_pth)
}
restez_path_set(filepath = rstz_pth)
db_download()
restez_connect()
db_create()
Adding 204 file(s) to the database ...
... 'gbinv1.seq.gz' (1/204)
... 'gbinv10.seq.gz' (2/204)
... 'gbinv100.seq.gz' (3/204)
... 'gbinv101.seq.gz' (4/204)
... 'gbinv102.seq.gz' (5/204)
... 'gbinv103.seq.gz' (6/204)
: Invalid argument
Error in gsub("\n", " ", res, fixed = TRUE) :
input string 1 is invalid UTF-8
Error: callr subprocess failed: input string 1 is invalid UTF-8
Type .Last.error.trace to see where the error occured
.Last.error.trace

Stack trace:

Process 11096:

1. restez:::db_create()
2. restez:::gb_build2(dpth = dpth, seq_files = seq_files, max_length = max_length, ...
3. callr::r(func = function(restez_path, gb_build, dpth, seq_files, ...
4. callr:::get_result(output = out, options)
5. throw(newerr, parent = remerr[[2]])

x callr subprocess failed: input string 1 is invalid UTF-8

Process 11636:
17. (function (restez_path, gb_build, dpth, seq_files, max_length, ...
18. restez:::gb_build(dpth = dpth, seq_files = seq_files, max_length = max_length, ...
19. restez:::gb_sql_add(df = df)
20. DBI::dbWriteTable(conn = connection, name = "nucleotide", value = df, ...
21. DBI::dbWriteTable(conn = connection, name = "nucleotide", value = df, ...
22. MonetDBLite:::.local(conn, name, value, ...)
23. DBI:::dbCommit(conn)
24. MonetDBLite:::dbCommit(conn)
25. DBI:::dbSendQuery(conn, "COMMIT")
26. MonetDBLite:::dbSendQuery(conn, "COMMIT")
27. MonetDBLite:::.local(conn, statement, ...)
28. MonetDBLite:::monetdb_embedded_query(conn@connenv$conn, statement, ...
29. base:::gsub("\n", " ", res, fixed = TRUE)
30. base:::.handleSimpleError(function (e) ...
31. h(simpleError(msg, call))

x input string 1 is invalid UTF-8
`

and these are on Ubuntu:

`

db_create()
Adding 204 file(s) to the database ...
... 'gbinv1.seq.gz' (1/204)
... 'gbinv10.seq.gz' (2/204)
... 'gbinv100.seq.gz' (3/204)
Error in readLines(con = connection) : error reading from the connection
In addition: Warning message:
In readLines(con = connection) : invalid or incomplete compressed data
Error: callr subprocess failed: error reading from the connection
Type .Last.error.trace to see where the error occurred
Last.error.trace
Error: object 'Last.error.trace' not found
.Last.error.trace

Stack trace:

Process 13829:

1. restez:::db_create()
2. restez:::gb_build2(dpth = dpth, seq_files = seq_files, max_length ...
3. callr::r(func = function(restez_path, gb_build, dpth, seq_files, ...
4. callr:::get_result(output = out, options)
5. throw(newerr, parent = remerr[[2]])

x callr subprocess failed: error reading from the connection

Process 22214:
17. (function (restez_path, gb_build, dpth, seq_files, max_length, ...
18. restez:::gb_build(dpth = dpth, seq_files = seq_files, max_length = max_leng ...
19. restez:::flatfile_read(flpth = flpth)
20. base:::readLines(con = connection)
21. base:::.handleSimpleError(function (e) ...
22. h(simpleError(msg, call))

x error reading from the connection
`
Thank you for your help!

[maelle]

For info, we're looking for a new maintainer / a new maintainer team for this package, see #23. If you read this and are a restez user, feel free to volunteer, we'd be happy to help.

[joelnitta]

I am the new maintainer.

The OP didn't mention it, but it looks like they selected 'Invertebrate' to download (as of GenBank release 250, this is 715 files and 62.6 GB in compressed, downloaded files).

I will try running the code with the current version of restez, but the download is quite large so it may take some time.