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cffdrs log file (check_x86_64_linux)

Tue Jul 12 05:52:09 2022: Checking package cffdrs (SVN revision 157) ...
* using log directory ‘/srv/rf/building/build_2022-07-12-05-51/RF_PKG_CHECK/PKGS/cffdrs.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82572)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘cffdrs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cffdrs’ version ‘1.8.19’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Alan Cantin ’

New maintainer:
  Alan Cantin 
Old maintainer(s):
  Alan Cantin 

Found the following (possibly) invalid URLs:
  URL: http://cfs.nrcan.gc.ca/pubwarehouse/pdfs/10068.pdf (moved to https://cfs.nrcan.gc.ca:443/pubwarehouse/pdfs/10068.pdf)
    From: DESCRIPTION
          man/cffdrs-package.Rd
          man/fbp.Rd
          man/fbpRaster.Rd
    Status: 200
    Message: OK
  URL: http://cfs.nrcan.gc.ca/pubwarehouse/pdfs/19927.pdf (moved to https://cfs.nrcan.gc.ca:443/pubwarehouse/pdfs/19927.pdf)
    From: man/fwi.Rd
          man/fwiRaster.Rd
    Status: 200
    Message: OK
  URL: http://cfs.nrcan.gc.ca/pubwarehouse/pdfs/19973.pdf (moved to https://cfs.nrcan.gc.ca:443/pubwarehouse/pdfs/19973.pdf)
    From: man/fwi.Rd
          man/fwiRaster.Rd
          man/test_fwi.Rd
          man/test_sdmc.Rd
    Status: 200
    Message: OK
  URL: http://cfs.nrcan.gc.ca/pubwarehouse/pdfs/23550.pdf (moved to https://cfs.nrcan.gc.ca:443/pubwarehouse/pdfs/23550.pdf)
    From: man/wDC.Rd
    Status: 200
    Message: OK
  URL: http://cfs.nrcan.gc.ca/pubwarehouse/pdfs/25591.pdf (moved to https://cfs.nrcan.gc.ca:443/pubwarehouse/pdfs/25591.pdf)
    From: man/gfmc.Rd
          man/hffmc.Rd
          man/hffmcRaster.Rd
    Status: 200
    Message: OK
  URL: http://cfs.nrcan.gc.ca/pubwarehouse/pdfs/29152.pdf (moved to https://cfs.nrcan.gc.ca:443/pubwarehouse/pdfs/29152.pdf)
    From: man/fireSeason.Rd
          man/fwi.Rd
          man/fwiRaster.Rd
          man/wDC.Rd
    Status: 200
    Message: OK
  URL: http://cfs.nrcan.gc.ca/pubwarehouse/pdfs/31414.pdf (moved to https://cfs.nrcan.gc.ca:443/pubwarehouse/pdfs/31414.pdf)
    From: man/test_fbp.Rd
    Status: 200
    Message: OK
  URL: http://cwfis.cfs.nrcan.gc.ca/background/summary/fbp (moved to https://cwfis.cfs.nrcan.gc.ca/background/summary/fbp)
    From: man/cffdrs-package.Rd
    Status: 200
    Message: OK
  URL: http://cwfis.cfs.nrcan.gc.ca/background/summary/fdr (moved to https://cwfis.cfs.nrcan.gc.ca/background/summary/fdr)
    From: man/cffdrs-package.Rd
    Status: 200
    Message: OK
  URL: http://cwfis.cfs.nrcan.gc.ca/background/summary/fwi (moved to https://cwfis.cfs.nrcan.gc.ca/background/summary/fwi)
    From: man/cffdrs-package.Rd
    Status: 200
    Message: OK
  URL: http://publications.gc.ca/collections/collection_2010/nrcan/Fo123-2-10-2009-eng.pdf (moved to https://publications.gc.ca/collections/collection_2010/nrcan/Fo123-2-10-2009-eng.pdf)
    From: man/cffdrs-package.Rd
          man/fbp.Rd
          man/fbpRaster.Rd
    Status: 200
    Message: OK
  URL: http://www.ualberta.ca/~flanniga/publications/1993_Wotton_Flannigan.pdf (moved to https://www.ualberta.ca/~flanniga/publications/1993_Wotton_Flannigan.pdf)
    From: man/fireSeason.Rd
    Status: 200
    Message: OK
* 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 serialization versions ... OK
* checking whether package ‘cffdrs’ can be installed ... [18s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Maintainer field differs from that derived from Authors@R
  Maintainer: ‘Alan Cantin ’
  Authors@R:  ‘Xianli Wang ’

* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 use of S3 registration ... 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 ... [26s/24s] NOTE
Found if() conditions comparing class() to string:
File ‘cffdrs/R/getvaluesblock_stackfix.r’: if (class(x) == "RasterStack") ...
File ‘cffdrs/R/getvaluesblock_stackfix.r’: if (class(x) == "RasterLayer" || nlayers(x) == 1) ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘gfmcRaster’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Variables with usage in documentation object 'test_fbpRaster' but not in code:
  ‘test_fbpRaster’

Variables with usage in documentation object 'test_rast_day01' but not in code:
  ‘test_rast_day01’

Variables with usage in documentation object 'test_rast_day02' but not in code:
  ‘test_rast_day02’

Variables with usage in documentation object 'test_rast_hour01' but not in code:
  ‘test_rast_hour01’

Variables with usage in documentation object 'test_rast_hour02' but not in code:
  ‘test_rast_hour02’

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [10s/9s] ERROR
Running examples in ‘cffdrs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fwi
> ### Title: Fire Weather Index System
> ### Aliases: fwi
> ### Keywords: methods
> 
> ### ** Examples
> 
> library(cffdrs)
> # The test data is a standard test
> # dataset for FWI system (Van Wagner and Pickett 1985) 
> data("test_fwi")
> # Show the data, which is already sorted by time:
> head(test_fwi)
  long lat   yr mon day temp rh ws prec
1 -100  40 1985   4  13 17.0 42 25  0.0
2 -100  40 1985   4  14 20.0 21 25  2.4
3 -100  40 1985   4  15  8.5 40 17  0.0
4 -100  40 1985   4  16  6.5 25  6  0.0
5 -100  40 1985   4  17 13.0 34 24  0.0
6 -100  40 1985   4  18  6.0 40 22  0.4
> #long  lat	yr	mon	day	temp	rh	ws	prec
> #-100	40	1985	4	13	17	42	25	0
> #-100	40	1985	4	14	20	21	25	2.4
> #-100	40	1985	4	15	8.5	40	17	0
> #-100	40	1985	4	16	6.5	25	6	0
> #-100	40	1985	4	17	13	34	24	0
> # (1) FWI System variables for a single weather station:
> # Using the default initial values and batch argument, 
> # the function calculate FWI variables chronically:
> fwi.out1<-fwi(test_fwi) 				
> # Using a different set of initial values:
> fwi.out2<-fwi(test_fwi,init=data.frame(ffmc=80, dmc=10,dc=16, lat=50))
> # This could also be done as the following:
> fwi.out2<-fwi(test_fwi,init=data.frame(80,10,6,50))
> # Or:
> fwi.out2<-fwi(test_fwi,init=c(80,10,6,50))
> # Latitude could be ignored, and the default value (55) will 
> # be used:
> fwi.out2<-fwi(test_fwi,init=data.frame(80,10,6))
> # (2) FWI for one or multiple stations in a single day:
> # Change batch argument to FALSE, fwi calculates FWI 
> # components based on previous day's fwi outputs:
> fwi.out3<-fwi(test_fwi,init=fwi.out1,batch=FALSE)                 
Error in if (prec <= 1.5) { : the condition has length > 1
Calls: fwi -> .dmcCalc
Execution halted
* checking examples with --run-donttest ... [10s/9s] ERROR
Running examples in ‘cffdrs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fwi
> ### Title: Fire Weather Index System
> ### Aliases: fwi
> ### Keywords: methods
> 
> ### ** Examples
> 
> library(cffdrs)
> # The test data is a standard test
> # dataset for FWI system (Van Wagner and Pickett 1985) 
> data("test_fwi")
> # Show the data, which is already sorted by time:
> head(test_fwi)
  long lat   yr mon day temp rh ws prec
1 -100  40 1985   4  13 17.0 42 25  0.0
2 -100  40 1985   4  14 20.0 21 25  2.4
3 -100  40 1985   4  15  8.5 40 17  0.0
4 -100  40 1985   4  16  6.5 25  6  0.0
5 -100  40 1985   4  17 13.0 34 24  0.0
6 -100  40 1985   4  18  6.0 40 22  0.4
> #long  lat	yr	mon	day	temp	rh	ws	prec
> #-100	40	1985	4	13	17	42	25	0
> #-100	40	1985	4	14	20	21	25	2.4
> #-100	40	1985	4	15	8.5	40	17	0
> #-100	40	1985	4	16	6.5	25	6	0
> #-100	40	1985	4	17	13	34	24	0
> # (1) FWI System variables for a single weather station:
> # Using the default initial values and batch argument, 
> # the function calculate FWI variables chronically:
> fwi.out1<-fwi(test_fwi) 				
> # Using a different set of initial values:
> fwi.out2<-fwi(test_fwi,init=data.frame(ffmc=80, dmc=10,dc=16, lat=50))
> # This could also be done as the following:
> fwi.out2<-fwi(test_fwi,init=data.frame(80,10,6,50))
> # Or:
> fwi.out2<-fwi(test_fwi,init=c(80,10,6,50))
> # Latitude could be ignored, and the default value (55) will 
> # be used:
> fwi.out2<-fwi(test_fwi,init=data.frame(80,10,6))
> # (2) FWI for one or multiple stations in a single day:
> # Change batch argument to FALSE, fwi calculates FWI 
> # components based on previous day's fwi outputs:
> fwi.out3<-fwi(test_fwi,init=fwi.out1,batch=FALSE)                 
Error in if (prec <= 1.5) { : the condition has length > 1
Calls: fwi -> .dmcCalc
Execution halted
* checking PDF version of manual ... OK
* skipping checking HTML version of manual: no command ‘tidy’ found
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 3 NOTEs
See
  ‘/srv/rf/building/build_2022-07-12-05-51/RF_PKG_CHECK/PKGS/cffdrs.Rcheck/00check.log’
for details.

Run time: 168.84 seconds.