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  • Jun 17 05:37
    eliotmcintire synchronize #216
  • Jun 17 05:37

    eliotmcintire on DotsBugFix

    whoops (compare)

  • Jun 16 22:51
    eliotmcintire synchronize #216
  • Jun 16 22:51

    eliotmcintire on DotsBugFix

    .fnCleanup -- deal with "unused… (compare)

  • Jun 16 21:45
    eliotmcintire synchronize #216
  • Jun 16 21:45

    eliotmcintire on DotsBugFix

    some weird duplication of showS… (compare)

  • Jun 16 21:08
    eliotmcintire synchronize #216
  • Jun 16 21:08

    eliotmcintire on DotsBugFix

    minor tweak of test (compare)

  • Jun 16 17:04
    eliotmcintire synchronize #216
  • Jun 16 17:04

    eliotmcintire on DotsBugFix

    rm stale comments add functionName to "similar" c… messageCache can set own colour… and 2 more (compare)

  • Jun 16 16:12
    eliotmcintire synchronize #216
  • Jun 16 16:12

    eliotmcintire on DotsBugFix

    correct the new test bump (compare)

  • Jun 16 15:51
    eliotmcintire synchronize #216
  • Jun 16 15:51

    eliotmcintire on DotsBugFix

    .cacheExtra (compare)

  • Jun 16 04:11
    eliotmcintire synchronize #216
  • Jun 16 04:11

    eliotmcintire on DotsBugFix

    bugfixes for nestedLev & unused… (compare)

  • Jun 15 23:11
    eliotmcintire opened #216
  • Jun 15 23:11

    eliotmcintire on DotsBugFix

    Cache --> don't dispatch on ...… bugfix lack of digest on ... .cacheExtra (compare)

  • Jun 15 19:24
    ianmseddy opened #215
  • Jun 10 15:48
    achubaty commented #214
Alex Chubaty
@achubaty
^^ nevermind! there were hidden spaces at the beginning and middile of each of the file names. :angry:
Eliot McIntire
@eliotmcintire
lol
Alex Chubaty
@achubaty
cannot see the spaces in the messages, especially when all files started with a space
ianmseddy
@ianmseddy
I have been having problems with package loading the last few days on two different machines. dplyr isn't loaded, so bind_rows isn't found during simInit. Neither are a few packages listed under the reqdPgks, e.g. mgcv. Anyone else experiencing this? I can file an issue, I just thought I'd check if there was some easy fix..
> packageVersion('SpaDES.core')
[1] ‘1.0.4.9003’
> packageVersion('Require')
[1] ‘0.0.9.9006
Eliot McIntire
@eliotmcintire
dplyr was removed from SpaDES.core ... so, if your metadata uses it in a module, then you have to put dplyr in the reqdPkgs
The newModule code now does not use bind_rows in the metadata, but old modules will. The simplest ways are either 1) add dplyr to your reqdPkgs or remove the _ in the function call so it is bindrows (in SpaDES.core)
i.e., this is not a bug
Alex Chubaty
@achubaty
the dplyr / bind_rows issue is annoying for backwards compatibility. we should enuser all module have this updated
Eliot McIntire
@eliotmcintire
search and replace whole github directories on one of our machines? I think it is easier to just tell everyone we know to update the modules they are using now. Alternatively, we mask the dplyr::bind_rows, which I don't like. Or we temporarily mask dplyr::bind_rows with a message to say, "change it"
Alex Chubaty
@achubaty
i've made this change in the following modules. just testing to make suro no issues before i push to develpoment branches.
image.png
Alex Chubaty
@achubaty
pushed
ianmseddy
@ianmseddy
alright, I made changes to PSP_Clean and Biomass_speciesParameters. I'm still having problems with nlme and mgcv failing to load, but as a work around I have specified the package with the function calls.
It might be my module's fault. I have to do weird things with environments to run mgcv::gamm, but I don't remember why :confused:
Eliot McIntire
@eliotmcintire
Dear maintainer,
Please see the problems shown on
https://cran.r-project.org/web/checks/check_results_reproducible.html.
Please correct before 2020-12-03 to safely retain your package on CRAN.
Best,
-k
Eliot McIntire
@eliotmcintire
@achubaty I will try to submit reproducible today or tomorrow. CRAN wants it by Dec 3.
Eliot McIntire
@eliotmcintire
@achubaty Can you please remove the failing bits of MacOS code on Github Actions or fix them? I believe that all the tests were passing on MacOS GA, but now the setup is failing. I want to submit to CRAN asap because I have a mental break right now.
Alex Chubaty
@achubaty
ok i'll take them out. i don't know why the binaries aren't being installed anymore :/
Eliot McIntire
@eliotmcintire

Re: file links in reproducible:

I see in the code that I am confounding things: there are 3 places that file.links could happen.
1) Cache objects (not the file backed rasters, but everything else)
e.g., Cache(mean, 1) should produce the same result as Cache(median, 1), so make a file.link. This is done in reproducible
2) preProcess via getOption("reproducible.inputPaths") ... if you are using this mechanism, and there are 2 preProcess calls that result in the same data file, then make a file.link. This is done in reproducible
3) Cache of file-backed rasters. Check for raster object on disk and if it is identical to one that is already there, then make a file.link. This is NOT currently done.

I don't recall what the decision was to not do the 3rd option. Or whether it was just a case of "not done yet". Can make an issue...
Eliot McIntire
@eliotmcintire

Dear maintainer,

Please see the problems shown on
https://cran.r-project.org/web/checks/check_results_reproducible.html.

Please correct before 2021-01-23 to safely retain your package on CRAN.

The CRAN Team

Alex Chubaty
@achubaty
are these coming from the RSQLite changes?
Eliot McIntire
@eliotmcintire
Yes.
I forgot, I fixed them! Lol!!
Eliot McIntire
@eliotmcintire

Dear maintainer,

Please see the problems shown on
https://cran.r-project.org/web/checks/check_results_reproducible.html.

Please correct before 2021-02-06 to safely retain your package on CRAN.

Note that this will be the final reminder.

The CRAN Team

Alex Chubaty
@achubaty
@eliotmcintire the polygon shortcut seems to cause problems when running LandWeb. I've disabled it using options("reproducible.polygonShortcut" = FALSE) but it's worth noting. I've put a TODO note in the LandWeb code for now.
2 replies
Ceres Barros
@CeresBarros
this started happening today, after having worked several times (with the same cache call/object):
source("Rscripts/Data_prep/newScripts_inProg/CompileRes_allMetrics.R") ## cache id f240263cfe4a88bc
  ...(Object to retrieve (f240263cfe4a88bc.rds) is large: 708.5 Mb)
     loaded cached result from previous loadResultsMetrics call, 
Waiting for 3.4 seconds to retry; the attempt is failing
tries to do it and keeps failing
this, however, works:
loadFromCache(cacheId = "f240263cfe4a88bc")
will post an issue on GitHub
Alex Chubaty
@achubaty
is the cache in use elsewhere else, or only in this one R session?
Ceres Barros
@CeresBarros
only in this R Session
tried restarting R/RStudio/PC, none worked
loadFromCache is working
Eliot McIntire
@eliotmcintire
Sadness
Does it happen to have lots of file-backed rasters?
Ceres Barros
@CeresBarros
nope. its a data.table
I'm easily bypassing this with loadFromCache and I have the feeling it's something to do with my hard drive or something, because it was working fine. Maybe I accessed it so many times that something got corrupted some how.
Eliot McIntire
@eliotmcintire
You know what, is it possible that it loads fine and that the "waiting" is from a different step in your source?
Ceres Barros
@CeresBarros
Sorry to answer so late to this - as always I forget to come here :/
so I don't think it's waiting for anything, It's just a "normal" Cache call that used to be running fine.
I also just found out the issue is also happening in the ubuntu VBM in the BC cluster - so not a problem related to my HDD
Eliot McIntire
@eliotmcintire
The new reproducible may have fixed this. This is the type of issue that was happening that I fixed. You will have to set options("reproducible.useNewDigestAlgorith" = 2)
The source version is on CRAN now ... 1.2.6 ... install.packages("reproducible", type = "source")
Ceres Barros
@CeresBarros
thanks Eliot. I'll need to test this eventually, but still haven't gone around to it!
Eliot McIntire
@eliotmcintire
I need to start a blog post ... tricks with SpaDES/reproducible/etc... I look at other people's code and get "inspired"... here's the next one:
The options("reproducible.inputPaths") is intended to be used across projects ... so it should be set to a place outside the project folders, e.g., for me ~/data. It is not intended to be a "human readable" location. It is simply a common repository so that large objects, e.g., KNN_whatever, only has one copy on a disk drive, no matter how many projects are being run on that disk.
options("reproducible.inputPaths" = "~/data")
Ana Raymundo
@araymund83
please do !
Ceres Barros
@CeresBarros
x-posted in Gitter:
did prepInputs/postProcess change in the way they process and save rasters?
I'm getting this error with gdaldem but the input DEM raster is not supposed to be a brick . I didn't have any issues before - and mind you that "before" is likely many many versions of reproducible ago because I haven't need to prepInputs/postProcess this layer in ages (working from a clean project for the first time in months/years...)
slopeRas <- gdaldem(mode = "slope",
                      # input_dem = filename(sim$DEMRas),
                      input_dem = "D:/GitHub/FoothillsBurnSeasonality/inputs/DEMRas_NA.tif",
                      output = file.path(inputPath(sim), "slopeRas.tif"),
                      output_Raster = TRUE,
                      compute_edges = TRUE,
                      p = TRUE)
Error in .local(.Object, ...) : 
In addition: Warning message:
In system(cmd, intern = TRUE) :
  running command '"C:\Program Files\QGIS 3.16\bin\gdaldem.exe" "slope" "D:/GitHub/FoothillsBurnSeasonality/inputs/DEMRas_NA.tif"  "D:/GitHub/FoothillsBurnSeasonality/inputs/slopeRas.tif" -compute_edges  -p ' had status 5
Error in .rasterObjectFromFile(x, objecttype = "RasterBrick", ...) : 
  Cannot create a RasterLayer object from this file.
Browse[1]> sim$DEMRas
class      : RasterLayer 
dimensions : 1081, 408, 441048  (nrow, ncol, ncell)
resolution : 250, 250  (x, y)
extent     : -1405750, -1303750, 6777500, 7047750  (xmin, xmax, ymin, ymax)
crs        : +proj=lcc +lat_0=0 +lon_0=-95 +lat_1=49 +lat_2=77 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs 
source     : D:/GitHub/FoothillsBurnSeasonality/inputs/DEMRas_NA.tif 
names      : DEMRas_NA 
values     : 0, 3148.289  (min, max)
Browse[1]> class(sim$DEMRas)
[1] "RasterLayer"
attr(,"package")
[1] "raster"
Eliot McIntire
@eliotmcintire
This ended up being a non-reproducible issue, but a gdal issue
Ceres Barros
@CeresBarros
correct, thanks Eliot