- using R version 4.4.0 (2024-04-24)
- using platform: x86_64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.3.1
- using session charset: UTF-8
- checking for file ‘cmmr/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘cmmr’ version ‘0.1.2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘cmmr’ can be installed ... [1s/1s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] OK
- checking whether startup messages can be suppressed ... [0s/0s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [1s/1s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
- checking examples ... [0s/12s] ERROR
Running examples in ‘cmmr-Ex.R’ failed
The error most likely occurred in:
> ### Name: advanced_batch_search
> ### Title: Encapsulation of CEU Mass Mediator advanced batch search API.
> ### Aliases: advanced_batch_search
>
> ### ** Examples
>
> df <- advanced_batch_search(
+ cmm_url = paste0(
+ 'http://ceumass.eps.uspceu.es/mediator/api/v3/',
+ 'advancedbatch'),
+ chemical_alphabet = 'all',
+ modifiers_type = 'none',
+ metabolites_type = 'all-except-peptides',
+ databases = '["hmdb"]',
+ masses_mode = 'mz',
+ ion_mode = 'positive',
+ adducts = '["all"]',
+ deuterium = 'false',
+ tolerance = '7.5',
+ tolerance_mode = 'ppm',
+ masses = '[400.3432, 288.2174]',
+ all_masses = '[]',
+ retention_times = '[18.842525, 4.021555]',
+ all_retention_times = '[]',
+ composite_spectra = paste0(
+ '[[{ "mz": 400.3432, "intensity": 307034.88 }, ',
+ '{ "mz": 311.20145, "intensity": 400.03336 }]]'
+ ))
Using the CEU Mass Mediator server API.
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [ceumass.eps.uspceu.es] Resolving timed out after 10007 milliseconds
Calls: advanced_batch_search ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [1s/1s] OK
Running ‘testthat.R’ [1s/1s]
- checking PDF version of manual ... [6s/6s] OK
- DONE
Status: 1 ERROR, 1 NOTE
- using check arguments '--no-clean-on-error '