curl_fetch_memory

[mccannpeter]

Hi,
I am having an issue in the pathway annotation in ggpicrust2. I have tried the other workflow with the same results. I'm not behind a firewall or proxy, I can access the url on my browser and have everything up to date including ssl certificates. Any help would be greatly appreciated. TIA

results_file_input <- ggpicrust2(file = abundance_file,
metadata = metadata,
group = "infection", # For example dataset, group = "Environment"
pathway = "KO",
daa_method = "LinDA",
ko_to_kegg = TRUE,
order = "pathway_class",
p_values_bar = TRUE,
x_lab = "pathway_name")
Starting the ggpicrust2 analysis...

Converting KO to KEGG...

Loading data from file...
Rows: 7600 Columns: 11
── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (1): #NAME
dbl (10): NMRI_SNAIL_NAIVE_1, NMRI_SNAIL_INFECTED_1, NMRI_SNAIL_NAIVE_2, NMR...

ℹ Use spec() to retrieve the full column specification for this data.
ℹ Specify the column types or set show_col_types = FALSE to quiet this message.
Loading KEGG reference data. This might take a while...
Performing KO to KEGG conversion. Please be patient, this might take a while...
|======================================================================| 100%
KO to KEGG conversion completed. Time elapsed: 7.17 seconds.
Removing KEGG pathways with zero abundance across all samples...
KEGG abundance calculation completed successfully.
Performing pathway differential abundance analysis...

Sample names extracted.
Identifying matching columns in metadata...
Matching columns identified: sample_name . This is important for ensuring data consistency.
Using all columns in abundance.
Converting abundance to a matrix...
Reordering metadata...
Converting metadata to a matrix and data frame...
Extracting group information...
Running LinDA analysis...
Performing LinDA analysis...
0 features are filtered!
The filtered data has 10 samples and 237 features will be tested!
Imputation approach is used.
Fit linear models ...
Completed.
Processing LinDA results...
LinDA analysis is complete.
Success: Found 28 statistically significant biomarker(s) in the dataset.
Annotating pathways...

Starting pathway annotation...
DAA results data frame is not null. Proceeding...
KO to KEGG is set to TRUE. Proceeding with KEGG pathway annotations...
We are connecting to the KEGG database to get the latest results, please wait patiently.

Processing pathways in chunks...

| | 0%
Error in curl::curl_fetch_memory(url, handle = handle) :
OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0

[cafferychen777]

Hi @mccannpeter,

Thank you for reaching out. The error you encountered, OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, is typically related to an internet connection issue. This is a common problem for users in China, where a VPN may be required to access certain databases. If you are not in China, it could be an issue with your WiFi network. I suggest trying the following:

1. If you are in China, please ensure that your VPN is active and functioning correctly.
2. If you are outside of China, try switching to a different network or resetting your current network connection.

Please let me know if this resolves the issue or if you have any further questions.

Best regards,
Chen YANG

[mccannpeter]

Hi Caffrey,

I'm in Europe and have tried on 3 different WiFi networks but the problem persists.

Thanks,
Peter

[cafferychen777]

Hi Peter,

Thank you for the update and for trying different WiFi networks. Since the issue persists across multiple networks, it might be worth exploring other potential solutions:

1. Could you try using your mobile phone as a hotspot to see if connecting through a different type of network helps?
2. If possible, try running the process on a different computer to determine if the issue might be specific to your current machine.

These steps can help isolate whether the problem is related to the network environment or perhaps to something specific with your primary computer.

Please keep me posted on your progress or if you encounter any further issues.

Best regards,
Caffery

[mccannpeter]

Hi,

I tried to run the package with mobile hotspot and it didn't work. I assume then it is something to do with my computer, possibly a version compatibility as I know other groups at the university that use ggpicrust2 without issue.

Thanks,
Peter