Error in rbind(deparse.level, ...) in addition SSL certificate problem: certificate has expired

[biomendi]

Hi. I used rfishbase a few months ago with no issues. However, I am now trying to use it again and somehow the package is not working on my system. The below error shows up when trying to run any command. Any idea on how to solve it? Thanks.

> validate_names("Abramites ternetzi")
Error in rbind(deparse.level, ...) :
numbers of columns of arguments do not match
In addition: Warning messages:
1: Error in curl::curl_fetch_memory(file, handle): SSL certificate problem: certificate has expired
2: Error in curl::curl_fetch_memory(file, handle): SSL certificate problem: certificate has expired
3: Error in curl::curl_fetch_memory(file, handle): SSL certificate problem: certificate has expired
4: Error in curl::curl_fetch_memory(file, handle): SSL certificate problem: certificate has expired
5: In curl::curl_fetch_memory(url, handle = handle) :
SSL certificate problem: certificate has expired
6: In curl::curl_fetch_memory(url, handle = handle) :
SSL certificate problem: certificate has expired

Session Info

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_1.0.9     rfishbase_4.0.0

loaded via a namespace (and not attached):
 [1] pillar_1.7.0      compiler_4.2.0    dbplyr_2.1.1      remotes_2.4.2     prettyunits_1.1.1 tools_4.2.0       progress_1.2.2   
 [8] pkgbuild_1.3.1    bit_4.0.4         contentid_0.0.15  jsonlite_1.8.0    memoise_2.0.1     lifecycle_1.0.1   tibble_3.1.7     
[15] pkgconfig_2.0.3   rlang_1.0.2       rstudioapi_0.13   DBI_1.1.2         cli_3.3.0         parallel_4.2.0    curl_4.3.2       
[22] fastmap_1.1.0     withr_2.5.0       duckdb_0.3.2-2    httr_1.4.3        stringr_1.4.0     generics_0.1.2    fs_1.5.2         
[29] vctrs_0.4.1       askpass_1.1       hms_1.1.1         rprojroot_2.0.3   bit64_4.0.5       tidyselect_1.1.2  glue_1.6.2       
[36] R6_2.5.1          processx_3.5.3    fansi_1.0.3       vroom_1.5.7       callr_3.7.0       purrr_0.3.4       readr_2.1.2      
[43] tzdb_0.3.0        magrittr_2.0.3    ps_1.7.0          ellipsis_0.3.2    assertthat_0.2.1  utf8_1.2.2        stringi_1.7.6    
[50] openssl_2.0.0     cachem_1.0.6      crayon_1.5.1 

[angle-zhang]

Having the same problem as well!

[cboettig]

sorry of the slow reply, having trouble reproducing this. Please ensure your system is up to date, in particular, your authority certificates? (On linux systems this is usually something like apt-get install ca-certificates, but not sure on the Mac, probably part of the standard OS update though...)

[Lithobius]

Hi. I used rfishbase a few months ago with no issues. However, I am now trying to use it again and somehow the package is not working on my system. The below error shows up when trying to run any command. Any idea on how to solve it? Thanks.

validate_names("Abramites ternetzi")
Error in rbind(deparse.level, ...) :
numbers of columns of arguments do not match
In addition: Warning messages:
1: Error in curl::curl_fetch_memory(file, handle): SSL certificate problem: certificate has expired
2: Error in curl::curl_fetch_memory(file, handle): SSL certificate problem: certificate has expired
3: Error in curl::curl_fetch_memory(file, handle): SSL certificate problem: certificate has expired
4: Error in curl::curl_fetch_memory(file, handle): SSL certificate problem: certificate has expired
5: In curl::curl_fetch_memory(url, handle = handle) :
SSL certificate problem: certificate has expired
6: In curl::curl_fetch_memory(url, handle = handle) :
SSL certificate problem: certificate has expired

Session Info

I also had this problem, and I used this solution in terminal:
ropensci-archive/rbhl#28 (comment)

Some months ago I had the same issue with taxize, then today I had the same problem with rfishbase after updating R. I've used this solution on 3 different computers each using a different OSX version.

It is a hard to replicate problem, has more to do with stuff in terminal than any given R package.

[cboettig]

Thanks @Lithobius for linking that solution for Mac!