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daveauty authored Mar 2, 2020
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#### FIXES

1. This fix breaks backward compatibiliy. In `catalog_apply()` if `automerge = TRUE` and the output contains a `list` of strings the list was expected to be merged into a character vector. But the raw list was actually returned. This was not the intended behavior. This appends with `Spatial*` and `sf` objects and with `data.frame`. This bug should not have affected a lot of people.
1. This fix breaks backward compatibility. In `catalog_apply()` if `automerge = TRUE` and the output contains a `list` of strings the list was expected to be merged into a character vector. But actually, the raw list was returned, which was not the intended behavior. This appends with `Spatial*` and `sf` objects and with `data.frame`. This bug should not have affected too many people.

```r
opt_output_files(ctg) <- paste0(tempdir(), "/{ORIGINALFILENAME}")
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#> "/tmp/RtmpV4CQll/file38f1.txt" "/tmp/RtmpV4CQll/file38g.txt" "/tmp/RtmpV4CQll/file38h.txt" "/tmp/RtmpV4CQll/file38i.txt"
```

2. When using a `grid_*` function with a `RasterLayer` used as layout, if the layout was not empty or full of NAs, the values of the layout were transferd to the NA cells of the output [#318](https://github.com/Jean-Romain/lidR/issues/318).
2. When using a `grid_*` function with a `RasterLayer` used as layout, if the layout was not empty or full of NAs, the values of the layout were transferred to the NA cells of the output [#318](https://github.com/Jean-Romain/lidR/issues/318).

3. `lascheck()` no longer warn about "proj4string found but no CRS in the header". This was a false positive. On overall CRS are better checked.
3. `lascheck()` no longer warns about "proj4string found but no CRS in the header". This was a false positive. Overall, CRS are better checked.

### ENHANCEMENTS

1. `opt_output_files()` now prints a message when using the `ORIGINALFILENAME` template with a chunk size that is not 0 to inform that it does not make sense.
1. `opt_output_files()` now prints a message when using the `ORIGINALFILENAME` template with a chunk size that is not 0 to inform users that it does not make sense.

```r
opt_chunk_size(ctg) <- 800
opt_output_files(ctg) <- "{ORIGINALFILENAME}"
#> ORIGINALFILENAME template has been used but the chunk size is not 0. This template makes sense only when processing by file.
```

2. Internally when building the chunks an informative error is now thrown when using the `ORIGINALFILENAME` template with a chunk size that is not 0 to inform that it does not make sense instead of the former uninformative error `Error in eval(parse(text = text, keep.source = FALSE), envir) : objet 'ORIGINALFILENAME' not found`.
2. Internally when building the chunks an informative error is now thrown when using the `ORIGINALFILENAME` template with a chunk size that is not 0 to inform users that it does not make sense instead of the former uninformative error, `Error in eval(parse(text = text, keep.source = FALSE), envir) : objet 'ORIGINALFILENAME' not found`.

```r
#> Erreur : The template {ORIGINALFILENAME} makes sense only when processing by file (chunk size = 0). It is undefined otherwise.
```

3. When using a "by file" processing strategy + a buffer around each file, up to 9 files may be read. Internally the chunks (`LAScluster`) are now built in such a way that the first file read is the main one (and not one of the "buffer file"). This way, if the 9 files do not have the same scales and the same offsets, the main file has the precedence on the other ones when rescaling and reoffsetting one-the-fly. This reduce the risk of incompatibilities and preserve the original pattern when processing a LAScatalog.
3. When using a "by file" processing strategy + a buffer around each file, up to 9 files may be read. Internally the chunks (`LAScluster`) are now built in such a way that the first file read is the main one (and not one of the "buffer file"). This way, if the 9 files do not have the same scales and the same offsets, the main file has precedence over the other ones when rescaling and re-offsetting on-the-fly. This reduces the risk of incompatibilities and preserves the original pattern when processing a LAScatalog.

4. `grid_metrics()` now constructs a `RasterBrick` in a better way and this reduce the risk of bug with user's functions that sometime return 0 length objects. The `RasterBrick` will now be properly filled with `NAs`.
4. `grid_metrics()` now constructs a `RasterBrick` in a better way and this reduces the risk of bugs with users' functions that sometimes return 0 length objects. The `RasterBrick` will now be properly filled with `NAs`.
5. `lascheck()` now reports information if some points are flagged 'withheld', 'synthetic' or 'keypoint'
5. `lascheck()` now reports information if some points are flagged 'withheld', 'synthetic' or 'keypoint'.
6. We moved the internal logic of chunk realignment with a raster from `catalog_apply()` to the internal function `catalog_makecluster()`. This simplifies the source code, make it easier to maintain and test and will enable us to provide access, at the user level, to more internal functions in next releases.
6. We moved the internal logic of chunk realignment with a raster from `catalog_apply()` to the internal function `catalog_makecluster()`. This simplifies the source code, make it easier to maintain and test and will enable us to provide access, at the user level, to more internal functions in future releases.
## lidR v2.2.2
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