Package check result: NOTE

Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: ‘Dylan Beaudette <dylan.beaudette@usda.gov>’
  
  Found the following (possibly) invalid URLs:
    URL: https://ncsslabdatamart.sc.egov.usda.gov/
      From: man/ca630.Rd
      Status: Error
      Message: Operation timed out after 60000 milliseconds with 312216 out of 335991 bytes received
    URL: https://nrcspad.sc.egov.usda.gov/DistributionCenter/product.aspx?ProductID=991
      From: man/SoilTextureLevels.Rd
            man/hzDistinctnessCodeToOffset.Rd
            man/hzTopographyCodeToLineType.Rd
            man/hzTopographyCodeToOffset.Rd
            man/lookup_taxpartsize.Rd
      Status: Error
      Message: server verification failed: certificate signer not trusted. (CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none)

Changes to worse in reverse depends:

Package: soilassessment
Check: examples
New result: ERROR
  Running examples in ‘soilassessment-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: depthharm
  > ### Title: A function for harmonizing soil property between uniform depth
  > ###   intervals in observation pits
  > ### Aliases: depthharm
  > 
  > ### ** Examples
  > 
  > library(aqp)
  This is aqp 2.1.0
  > library(plyr)
  > library(sp)
  
  Attaching package: ‘sp’
  
  The following objects are masked from ‘package:aqp’:
  
      coordinates, coordinates<-, proj4string, proj4string<-
  
  > x=c(rep(2.12,4),rep(2.05,4))
  > y=c(rep(9.34,4),rep(8.17,4))
  > pit=c(rep(1,4),rep(2,4))
  > depthcode=c(1,2,3,4,1,2,3,4)
  > upper=c(0,18,25,35,0,12,33,50)
  > lower=c(10,25,35,67,12,33,50,100)
  > pH=c(6.7,5.5,5.1,6.7,6.4,5.8,5.3,5.0)
  > df=data.frame(pit,x,y,upper,lower,depthcode,pH)
  > lat=df$x;lon=df$y;id=df$pit;top=df$upper;
  > bottom=df$lower;horizon=df$depthcode;Varn=df$pH
  > 
  > soildata <- join(data.frame(id, top, bottom, Varn, horizon),
  +               data.frame(id, lat, lon), type='inner')
  Joining by: id
  > depths(soildata) <- id ~ top + bottom
  > site(soildata) <- ~ lat + lon
  > coordinates(soildata) <- ~ lat + lon
  Error: unable to find an inherited method for function ‘coordinates<-’ for signature ‘object = "SoilProfileCollection"’
  Execution halted