plzmsu commented 4 years ago

I added the .Rmd files and PDF files associated w Lab5. It looks great when I do: rmarkdown: render_site("lab5_variograms.Rmd") but when I try to do the whole site with rmarkdown: render_site() there are issues popping up in previous labs for some reason.

Any ideas? @billspat

I didn't commit the .html versions in /docs in case that messes it up.

billspat commented 4 years ago

what happens when you, say render an earlier lab by itself like you did lab5? It could be that some Rmd files have side effects that break the next lab. Would you please post the error messages either here or as new github issues? TBH I haven't taken the time to fix the labs on my own computer and use the working fdata links etc so I'm sure I would have issues also if I re-rendered them as is.

plzmsu commented 4 years ago

Entire site rendering:

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

rmarkdown::render_site()

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Error in x$.self$finalize() : attempt to apply non-function In addition: Warning messages: 1: In readOGR(file.path(data_path, "cb_2014_us_nation_20m.shp")) : Z-dimension discarded 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum unknown in CRS definition Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply 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: attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in (function (x) : attempt to apply non-function Error in (function (x) : attempt to apply non-function Error in (function (x) : attempt to apply non-function |............................................................................. | 89% ordinary text without R code

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zip' length 108492 bytes (105 KB)

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/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS lab2_scale.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lab2_scale.html --email-obfuscation none --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --include-before-body /var/folders/ry/9bc9_2p54c94dtmtxzy91dxm0000gv/T//Rtmp1Q8htE/rmarkdown-str2362222dc79d.html --variable navbar=1 --variable body_padding=51 --variable header_padding=56 --variable 'theme:bootstrap' --include-in-header /var/folders/ry/9bc9_2p54c94dtmtxzy91dxm0000gv/T//Rtmp1Q8htE/rmarkdown-str23626b8c25f2.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/lua/latex-div.lua

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Error in FUN(X[[i]], ...) : object 'bryce_NED_1' not found In addition: Warning messages: 1: In readOGR(file.path(data_path, "cb_2014_us_region_20m.shp")) : Z-dimension discarded 2: In readOGR(file.path(data_path, "cb_2014_us_state_20m.shp")) : Z-dimension discarded 3: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded ellps WGS 84 in CRS definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs 4: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum WGS_1984 in CRS definition 5: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded ellps WGS 84 in CRS definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs 6: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum WGS_1984 in CRS definition 7: Transformation introduced infinite values in continuous x-axis 8: Removed 3943 rows containing non-finite values (stat_density). 9: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum Unknown based on WGS84 ellipsoid in CRS definition

plzmsu commented 4 years ago

Lab2 rendering alone: (these errors are the same I was getting earlier in the semester but it still renders)

Output created: docs/lab2_scale.html Warning messages: 1: In readOGR(file.path(data_path, "cb_2014_us_nation_20m.shp")) : Z-dimension discarded 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum unknown in CRS definition 3: In unzip(file.path(data_path, "usr.zip"), exdir = data_path) : error 1 in extracting from zip file 4: In readOGR(file.path(data_path, "cb_2014_us_region_20m.shp")) : Z-dimension discarded

plzmsu commented 4 years ago

Lab3 rendering alone:

Output created: docs/lab3_patch_design.html Warning messages: 1: In readOGR(file.path(data_path, "cb_2014_us_state_20m.shp")) : Z-dimension discarded 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded ellps WGS 84 in CRS definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs 3: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum WGS_1984 in CRS definition 4: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded ellps WGS 84 in CRS definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs 5: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum WGS_1984 in CRS definition 6: Transformation introduced infinite values in continuous x-axis 7: Removed 3943 rows containing non-finite values (stat_density).

plzmsu commented 4 years ago

Lab4 alone:

Output created: docs/lab4_autocorrelation.html Warning messages: 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum Unknown based on WGS84 ellipsoid in CRS definition 2: In plot.xy(xy, type, ...) : plot type 'black' will be truncated to first character 3: In doTryCatch(return(expr), name, parentenv, handler) : plot type 'black' will be truncated to first character

plzmsu commented 4 years ago

Lab5 render alone:

Output created: docs/lab5_variograms.html Warning messages: 1: In system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1 2: some mark values are NA in the point pattern Y 3: some mark values are NA in the point pattern object

plzmsu commented 4 years ago

i've been able to push 1 lab at a time and it's working. I'll hold off on updating the lab4 docs since they are working on it this week.

SpaCE-Lab-MSU / MSUGradSpatialEcology

Lab5 and re-rendering not working #7

trying URL 'http://www2.census.gov/geo/tiger/GENZ2014/shp/cb_2014_us_region_20m.zip' Content type 'application/zip' length 108492 bytes (105 KB)