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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:RMassBank.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings RMassBank_3.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RMassBank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RMassBank’ version ‘3.14.0’
* 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 hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RMassBank’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ChemmineOB’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘MSnbase:::writeMgfContent’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analyzeMsMs.formula.optimized: no visible binding for global variable
  ‘occurrenceMatrix’
msmsRead.ticms2: no visible global function definition for
  ‘c.msmsWSspecs’
reanalyzeFailpeak: no visible binding for global variable ‘mass.calc’
updateObject,RmbSpectraSet: no visible global function definition for
  ‘updateObjectFromSlots’
Undefined global functions or variables:
  c.msmsWSspecs mass.calc occurrenceMatrix updateObjectFromSlots
* checking Rd files ... NOTE
checkRd: (-1) RmbSettings.Rd:11-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:17-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:21-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:28-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:36-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:63-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:68-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:73-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:79-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:82-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:87-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:90-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:100-134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RmbSettings.Rd:135-149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) checkIsotopes.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) filterPeaksMultiplicity.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findMsMsHR.Rd:49: Lost braces
    49 | to use for formula lookup. Note: In \\code{findMsMsHR.mass}, this is entirely optional and
       |                                           ^
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RMassBank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CAS2SMILES
> ### Title: Convert CAS to SMILES
> ### Aliases: CAS2SMILES
> 
> ### ** Examples
> 
> SMILES_ethanol <- CAS2SMILES("64-17-5", "Ethanol")
Error in curl::curl_fetch_memory(url, handle = handle): Timeout was reached: [cactus.nci.nih.gov] Failed to connect to cactus.nci.nih.gov port 80 after 5700 ms: Connection timed out
Request failed [ERROR]. Retrying in 1 seconds...
Error in curl::curl_fetch_memory(url, handle = handle): Timeout was reached: [cactus.nci.nih.gov] Failed to connect to cactus.nci.nih.gov port 80 after 5202 ms: Connection timed out
Request failed [ERROR]. Retrying in 1.5 seconds...
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [cactus.nci.nih.gov] Failed to connect to cactus.nci.nih.gov port 80 after 5201 ms: Connection timed out
Service not available. Returning NA.
Error in cir_query(CAS_number, from = "cas", to = "smiles") : 
Calls: CAS2SMILES -> cir_query
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/RMassBank.Rcheck/00check.log’
for details.