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hypertidy / ncmeta

Tidy NetCDF metadata
https://hypertidy.github.io/ncmeta/
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CRAN Debian check problem #38

Closed mdsumner closed 4 years ago

mdsumner commented 4 years ago

https://github.com/mjwoods/RNetCDF/issues/75

This is CRAN pretest for 0.2.5, it seems we could set values for all the chunking, chunksizes, deflate in var.def.nc() or wait for RNetCDF: 

* using log directory ‘/srv/hornik/tmp/CRAN/ncmeta.Rcheck’
* using R Under development (unstable) (2020-04-28 r78328)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ncmeta/DESCRIPTION’ ... OK
* this is package ‘ncmeta’ version ‘0.2.5’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: ‘Michael Sumner <mdsumner@gmail.com>’
* 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 ‘ncmeta’ can be installed ... [4s/4s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 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 ... [6s/6s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 examples ... [1s/1s] ERROR
Running examples in ‘ncmeta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nc_coord_var
> ### Title: Get Coordinate Variables for Given Variable
> ### Aliases: nc_coord_var nc_coord_var.character nc_coord_var.NetCDF
> 
> ### ** Examples
> 
> f <- system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package = "ncmeta")
> nc_coord_var(f, "chlor_a")
Error in RNetCDF::var.inq.nc(x, i) : 
  NetCDF: Filter error: filter not defined for variable
Calls: nc_coord_var ... lapply -> FUN -> nc_var -> nc_var.NetCDF -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4s/4s] ERROR
  Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncmeta)
  > skip_on_os("solaris")
  > test_check("ncmeta")
  ── 1. Failure: nc_atts works (@test-attributes.R#73)  ──────────────────────────
  nrow(nc_atts(f)) not equal to 87.
  1/1 mismatches
  [1] 65 - 87 == -22

  ── 2. Failure: nc_atts works (@test-attributes.R#74)  ──────────────────────────
  nrow(nc_atts(f, "chlor_a")) not equal to 12.
  1/1 mismatches
  [1] 65 - 12 == 53

  ── 3. Failure: nc_atts works (@test-attributes.R#75)  ──────────────────────────
  nrow(nc_atts(f, "lon")) not equal to 5.
  1/1 mismatches
  [1] 65 - 5 == 60

  ── 4. Error: nc_coord_var brings back expected content for one variable (@test-c
  NetCDF: Filter error: filter not defined for variable
  Backtrace:
    1. testthat::expect_equivalent(...)
    5. ncmeta:::nc_coord_var.character(f, "chlor_a")
    8. ncmeta:::nc_vars.NetCDF(nc)
    9. ncmeta:::nc_vars_internal(x, nvars)
   16. base::lapply(seq_len(nvars), function(i) nc_var(x, i - 1))
   17. ncmeta:::FUN(X[[i]], ...)
   19. ncmeta:::nc_var.NetCDF(x, i - 1)
   20. RNetCDF::var.inq.nc(x, i)

  ── 5. Error: nc_coord_vars brings back expected content for sample (@test-coord.
  NetCDF: Filter error: filter not defined for variable
  Backtrace:
    1. ncmeta::nc_coord_var(f)
    2. ncmeta:::nc_coord_var.character(f)
    5. ncmeta:::nc_vars.NetCDF(nc)
    6. ncmeta:::nc_vars_internal(x, nvars)
   13. base::lapply(seq_len(nvars), function(i) nc_var(x, i - 1))
   14. ncmeta:::FUN(X[[i]], ...)
   16. ncmeta:::nc_var.NetCDF(x, i - 1)
   17. RNetCDF::var.inq.nc(x, i)

  ── 6. Error: vars works (@test-vars.R#5)  ──────────────────────────────────────
  NetCDF: Filter error: filter not defined for variable
  Backtrace:
    1. ncmeta::nc_vars(f)
    2. ncmeta:::nc_vars.character(f)
    4. ncmeta:::nc_vars.NetCDF(nc)
    5. ncmeta:::nc_vars_internal(x, nvars)
   12. base::lapply(seq_len(nvars), function(i) nc_var(x, i - 1))
   13. ncmeta:::FUN(X[[i]], ...)
   15. ncmeta:::nc_var.NetCDF(x, i - 1)
   16. RNetCDF::var.inq.nc(x, i)

  ── 7. Error: nc4 bug (@test-vars.R#33)  ────────────────────────────────────────
  NetCDF: Filter error: filter not defined for variable
  Backtrace:
    1. ncmeta::nc_vars(f)
    2. ncmeta:::nc_vars.character(f)
    4. ncmeta:::nc_vars.NetCDF(nc)
    5. ncmeta:::nc_vars_internal(x, nvars)
   12. base::lapply(seq_len(nvars), function(i) nc_var(x, i - 1))
   13. ncmeta:::FUN(X[[i]], ...)
   15. ncmeta:::nc_var.NetCDF(x, i - 1)
   16. RNetCDF::var.inq.nc(x, i)

  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 103 | SKIPPED: 9 | WARNINGS: 4 | FAILED: 7 ]
  1. Failure: nc_atts works (@test-attributes.R#73) 
  2. Failure: nc_atts works (@test-attributes.R#74) 
  3. Failure: nc_atts works (@test-attributes.R#75) 
  4. Error: nc_coord_var brings back expected content for one variable (@test-coord.R#8) 
  5. Error: nc_coord_vars brings back expected content for sample (@test-coord.R#23) 
  6. Error: vars works (@test-vars.R#5) 
  7. Error: nc4 bug (@test-vars.R#33) 

  Error: testthat unit tests failed
  Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs

Current CRAN status: ERROR: 1, OK: 11
See: <https://CRAN.R-project.org/web/checks/check_results_ncmeta.html>

Version: 0.2.0
Check: tests, Result: ERROR
    Running ‘testthat.R’
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ncmeta)
    > skip_on_os("solaris")
    Error: Reason: On Solaris
    Execution halted
See: <https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/ncmeta-00check.html>
mdsumner commented 4 years ago

Here it is, fix by 15 May

mjwoods commented 4 years ago

My apologies, Michael. I have fixed the problem in the latest release of RNetCDF (2.3-1), which should appear on CRAN soon. I ran R CMD check with the latest ncmeta-0.2.5 (from your master branch), and it works with the new RNetCDF release.

mdsumner commented 4 years ago

Hey no problem, thank you for fixing!