joeroe / coincalc Goto Github PK

==> devtools::check()

══ Building ═══════════════════════════════════════════════════════════════════════════════════════════════
Setting env vars:
• CFLAGS    : -Wall -pedantic -fdiagnostics-color=always
• CXXFLAGS  : -Wall -pedantic -fdiagnostics-color=always
• CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/home/joeroe/g/CoinCalc/DESCRIPTION’ ...
─  preparing ‘CoinCalc’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘CoinCalc_2.0.tar.gz’
   
══ Checking ═══════════════════════════════════════════════════════════════════════════════════════════════
Setting env vars:
• _R_CHECK_CRAN_INCOMING_REMOTE_               : FALSE
• _R_CHECK_CRAN_INCOMING_                      : FALSE
• _R_CHECK_FORCE_SUGGESTS_                     : FALSE
• _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
• NOT_CRAN                                     : true
── R CMD check ────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/home/joeroe/g/CoinCalc.Rcheck’
─  using R version 4.3.3 (2024-02-29)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  R was compiled by
       gcc (GCC) 13.2.1 20230801
       GNU Fortran (GCC) 13.2.1 20230801
─  running under: Manjaro Linux
─  using session charset: UTF-8
─  using options ‘--no-manual --as-cran’
✔  checking for file ‘CoinCalc/DESCRIPTION’
─  checking extension type ... Package
─  this is package ‘CoinCalc’ version ‘2.0’
✔  checking package namespace information ...
✔  checking package dependencies (653ms)
✔  checking if this is a source package ...
✔  checking if there is a namespace
✔  checking for executable files ...
✔  checking for hidden files and directories
✔  checking for portable file names
✔  checking for sufficient/correct file permissions
✔  checking serialization versions
✔  checking whether package ‘CoinCalc’ can be installed (1.2s)
✔  checking installed package size ...
✔  checking package directory ...
✔  checking for future file timestamps ...
N  checking DESCRIPTION meta-information ...
   Malformed Description field: should contain one or more complete sentences.
N  checking top-level files
   File
     LICENSE
   is not mentioned in the DESCRIPTION file.
✔  checking for left-over files
✔  checking index information
✔  checking package subdirectories ...
✔  checking R files for non-ASCII characters ...
✔  checking R files for syntax errors ...
✔  checking whether the package can be loaded ...
✔  checking whether the package can be loaded with stated dependencies ...
✔  checking whether the package can be unloaded cleanly ...
✔  checking whether the namespace can be loaded with stated dependencies ...
✔  checking whether the namespace can be unloaded cleanly ...
✔  checking loading without being on the library search path ...
✔  checking dependencies in R code ...
✔  checking S3 generic/method consistency ...
✔  checking replacement functions ...
✔  checking foreign function calls ...
N  checking R code for possible problems (2.6s)
   CC.binarize: no visible global function definition for ‘quantile’
   CC.ceca.ts: no visible global function definition for ‘ecdf’
   CC.eca.es: no visible global function definition for ‘ecdf’
   CC.eca.ts: no visible global function definition for ‘ecdf’
   CC.plot: no visible global function definition for ‘par’
   CC.plot: no visible global function definition for ‘rgb’
   CC.plot: no visible global function definition for ‘arrows’
   CC.plot: no visible global function definition for ‘points’
   CC.plot: no visible global function definition for ‘text’
   CC.plot: no visible global function definition for ‘title’
   CC.plot: no visible global function definition for ‘polygon’
   Undefined global functions or variables:
     arrows ecdf par points polygon quantile rgb text title
   Consider adding
     importFrom("grDevices", "rgb")
     importFrom("graphics", "arrows", "par", "points", "polygon", "text",
                "title")
     importFrom("stats", "ecdf", "quantile")
   to your NAMESPACE file.
✔  checking Rd files ...
✔  checking Rd metadata ...
N  checking Rd line widths ...
   Rd file 'CC.binarize.Rd':
     \examples lines wider than 100 characters:
        # Load April temperature data set for the phenological station of Niederrimbach (supplied by Coincalc)
   
   Rd file 'CC.ceca.ts.Rd':
     \usage lines wider than 90 characters:
        CC.ceca.ts(seriesA,seriesB,seriesC,alpha=0.05,delT=0,delT.cond=0,sym=FALSE,sym.cond=FALSE,tau=0,tau.cond=0,sigtest="poisson",reps=1000)
   
   Rd file 'CC.eca.es.Rd':
     \examples lines wider than 100 characters:
        # Lets see if CC.eca.es fill find significant coincidences (of which we already know that they exist!).
        # Note, that when executing CC.eca.es for these event series, we need to define delT>=1 in order to find
   
   Rd file 'CC.eca.ts.Rd':
     \usage lines wider than 90 characters:
        CC.eca.ts(seriesA, seriesB, alpha=0.05, delT=0, sym=FALSE, tau=0, sigtest="poisson", reps=1000)
     \examples lines wider than 100 characters:
        Flow_bin=CC.binarize(CC.Example.Data1$DOY_Lilac_Flowering,ev.def="percentile",thres=0.1,event="lower")
   
   Rd file 'CC.es2ts.Rd':
     \examples lines wider than 100 characters:
        # 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
   
   These lines will be truncated in the PDF manual.
✔  checking Rd cross-references ...
✔  checking for missing documentation entries ...
✔  checking for code/documentation mismatches ...
✔  checking Rd \usage sections ...
✔  checking Rd contents ...
✔  checking for unstated dependencies in examples ...
✔  checking contents of ‘data’ directory (523ms)
✔  checking data for non-ASCII characters ...
W  checking data for ASCII and uncompressed saves (8s)
     
     Note: significantly better compression could be obtained
           by using R CMD build --resave-data
                          old_size new_size compress
     CC.Example.Data3.rda    3.2Mb    1.8Mb    bzip2
✔  checking examples (410ms)
✔  checking for non-standard things in the check directory
✔  checking for detritus in the temp directory
   
   See
     ‘/home/joeroe/g/CoinCalc.Rcheck/00check.log’
   for details.
   
   
── R CMD check results ────────────────────────────────────────────────────────────────── CoinCalc 2.0 ────
Duration: 16.3s

❯ checking data for ASCII and uncompressed saves ... WARNING
    
    Note: significantly better compression could be obtained
          by using R CMD build --resave-data
                         old_size new_size compress
    CC.Example.Data3.rda    3.2Mb    1.8Mb    bzip2

❯ checking DESCRIPTION meta-information ... NOTE
  Malformed Description field: should contain one or more complete sentences.

❯ checking top-level files ... NOTE
  File
    LICENSE
  is not mentioned in the DESCRIPTION file.

❯ checking R code for possible problems ... NOTE
  CC.binarize: no visible global function definition for ‘quantile’
  CC.ceca.ts: no visible global function definition for ‘ecdf’
  CC.eca.es: no visible global function definition for ‘ecdf’
  CC.eca.ts: no visible global function definition for ‘ecdf’
  CC.plot: no visible global function definition for ‘par’
  CC.plot: no visible global function definition for ‘rgb’
  CC.plot: no visible global function definition for ‘arrows’
  CC.plot: no visible global function definition for ‘points’
  CC.plot: no visible global function definition for ‘text’
  CC.plot: no visible global function definition for ‘title’
  CC.plot: no visible global function definition for ‘polygon’
  Undefined global functions or variables:
    arrows ecdf par points polygon quantile rgb text title
  Consider adding
    importFrom("grDevices", "rgb")
    importFrom("graphics", "arrows", "par", "points", "polygon", "text",
               "title")
    importFrom("stats", "ecdf", "quantile")
  to your NAMESPACE file.

❯ checking Rd line widths ... NOTE
  Rd file 'CC.binarize.Rd':
    \examples lines wider than 100 characters:
       # Load April temperature data set for the phenological station of Niederrimbach (supplied by Coincalc)
  
  Rd file 'CC.ceca.ts.Rd':
    \usage lines wider than 90 characters:
       CC.ceca.ts(seriesA,seriesB,seriesC,alpha=0.05,delT=0,delT.cond=0,sym=FALSE,sym.cond=FALSE,tau=0,tau.cond=0,sigtest="poisson",reps=1000)
  
  Rd file 'CC.eca.es.Rd':
    \examples lines wider than 100 characters:
       # Lets see if CC.eca.es fill find significant coincidences (of which we already know that they exist!).
       # Note, that when executing CC.eca.es for these event series, we need to define delT>=1 in order to find
  
  Rd file 'CC.eca.ts.Rd':
    \usage lines wider than 90 characters:
       CC.eca.ts(seriesA, seriesB, alpha=0.05, delT=0, sym=FALSE, tau=0, sigtest="poisson", reps=1000)
    \examples lines wider than 100 characters:
       Flow_bin=CC.binarize(CC.Example.Data1$DOY_Lilac_Flowering,ev.def="percentile",thres=0.1,event="lower")
  
  Rd file 'CC.es2ts.Rd':
    \examples lines wider than 100 characters:
       # 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
  
  These lines will be truncated in the PDF manual.

0 errors ✔ | 1 warning ✖ | 4 notes ✖
Error: R CMD check found WARNINGs
Execution halted

Exited with status 1.