Lab 03: project_data_steps.R gives "object not found" errors

[mtwelker]

Prof. Stowers, On the first step of Lab 03, I'm getting errors when I try to run "project_data_steps.R":

> import::here("build_year",
+              "RELEVANT_FILES",
+              "obtain_crosswalk",
+              "create_final_metadata_file",
+              # notice the use of here::here() that points to the .R file
+              # where all these R objects are created
+              .from = here::here("labs/wk03/utilities.R"),
+              .character_only = TRUE)
Error: object 'build_year' not found
> 
> # for each relevant file, run the build_year() function ----
> # note: this populates the data/rodeo/ directory with clean files
> for (relevant_file in RELEVANT_FILES) {
+   print(paste0("Starting on ", relevant_file[["year"]]))
+   build_year(fn1 = relevant_file[["fullcount"]],
+              fn2 = relevant_file[["sample"]],
+              year = relevant_file[["year"]])
+   if (relevant_file[["year"]] < 2010) {
+     print("Finished! Moving onto the next decade.")
+   } else {
+     print("Finished! No more data to parse.")
+   }
+ }
Error in RELEVANT_FILES : object 'RELEVANT_FILES' not found
> 
> # load the crosswalk ----
> # note: this stores a copy in the data/raw/ directory
> cw <- obtain_crosswalk()
Error in obtain_crosswalk() : could not find function "obtain_crosswalk"
> 
> # create the final meta data file ----
> # note: this stores a copy within the data/rodeo/ directory
> create_final_metadata_file(file_names = RELEVANT_FILES,
+                            crosswalk = cw)
Error in create_final_metadata_file(file_names = RELEVANT_FILES, crosswalk = cw) : 
  could not find function "create_final_metadata_file"
> 
> # end of script #

I think it can't find the utilities in the utilities.R file, even though they're in the same directory. And I believe I'm in the right directory, because it said:

> library(here)
here() starts at C:/Users/mtwel/OneDrive/Documents/R/CPP 528 2021 Fall B/cpp-528-fall-2021-group-04

and that's where the utilities.R file is with those functions that errored out:

Am I missing something? Is there something else I need to run first? Thanks for any help you can offer!

[AmyTrumpower]

Did you load the import package?_

[castower]

Hello Michelle @mtwelker,

I was able to replicate your error on my computer.

Try the following steps:

1. Restart your R session and clear all output.

2. Update the renv:

 renv::restore()

#select y

3. Open utilities.R

If you get a pop-up on the top of the screen to install any packages, select install.

Next, highlight the libraries listed and run the code.

These are the libraries:

library( dplyr )
library( here )
library( knitr )
library( pander )

4. Open project_data_steps.R

If you get a pop-up to install any packages, click install.

Now run the code.

Let me know if you have any further difficulties!

[mtwelker]

That did the trick! Thank you!

[DMBurwell]

Prof. Stowers-

I completed the above steps after updating R and RStudio to the most recent versions and am still getting the same error messages mentioned above:

load necessary functions ----

note: all of these are R objects that will be used throughout this .rmd file

import::here("build_year",

• "RELEVANT_FILES",
• "obtain_crosswalk",
• "create_final_metadata_file",

• notice the use of here::here() that points to the .R file

• where all these R objects are created

• .from = here::here("labs/utilities.R"),
• .character_only = TRUE) Error in loadNamespace(name) : there is no package called ‘C:/Users/danic/OneDrive/Desktop/CPP528/labs/wk03/labs/utilities.R’

for each relevant file, run the build_year() function ----

note: this populates the data/rodeo/ directory with clean files

for (relevant_file in RELEVANT_FILES) {

• print(paste0("Starting on ", relevant_file[["year"]]))
• build_year(fn1 = relevant_file[["fullcount"]],
• fn2 = relevant_file[["sample"]],
• year = relevant_file[["year"]])
• if (relevant_file[["year"]] < 2010) {
• print("Finished! Moving onto the next decade.")
• } else {
• print("Finished! No more data to parse.")
• }
• } Error in RELEVANT_FILES : object 'RELEVANT_FILES' not found

load the crosswalk ----

note: this stores a copy in the data/raw/ directory

cw <- obtain_crosswalk() Error in obtain_crosswalk() : could not find function "obtain_crosswalk"

create the final meta data file ----

note: this stores a copy within the data/rodeo/ directory

create_final_metadata_file(file_names = RELEVANT_FILES,

• crosswalk = cw) Error in create_final_metadata_file(file_names = RELEVANT_FILES, crosswalk = cw) : could not find function "create_final_metadata_file"

end of script

[castower]

Hello Danica @DMBurwell,

.from = here::here("labs/utilities.R") 

should be

.from = here::here("labs/wk03/utilities.R") 

The file path needs to match the location of your utilities.R file.

Let me know if you run into any other issues!

[DMBurwell]

I updated this and am still getting the same error messages

[castower]

@DMBurwell have you installed the import package?

[bbmoren2]

I am having a similar issue. I followed the instructions here but still get errors running the project_data_steps.R code.

I run the utilities.R file successfully with the the here() library outputting:

> library( here )

here() starts at /Users/bbmoreno

The first error I get after running the project_data_utilities.R file:

> import::here("build_year",
+              "RELEVANT_FILES",
+              "obtain_crosswalk",
+              "create_final_metadata_file",
+              # notice the use of here::here() that points to the .R file
+              # where all these R objects are created
+              .from = here::here("cpp528/cpp-528-fall-2021-group-06/labs/wk03/utilities.R"),
+              .character_only = TRUE)

Error: Cannot assign name to different value in the given environment. Name already in use.

Then, when I run the first function:

for (relevant_file in RELEVANT_FILES) {
+              print(paste0("Starting on ", relevant_file[["year"]]))
+              build_year(fn1 = relevant_file[["fullcount"]],
+                            fn2 = relevant_file[["sample"]],
+                            year = relevant_file[["year"]])
+              if (relevant_file[["year"]] < 2010) {
+                 print("Finished! Moving onto the next decade.")
+              } else {
+                 print("Finished! No more data to parse.")
+              }
}

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt"):

And showing the traceback:

Error in file(file, "rt") : cannot open the connection 
5. file(file, "rt") 
4. read.table(file = file, header = header, sep = sep, quote = quote, 
    dec = dec, fill = fill, comment.char = comment.char, ...) 
3. read.csv(here::here(path), colClasses = "character") 
2. tidy_up_data(fn1) 
1. build_year(fn1 = relevant_file[["fullcount"]], fn2 = relevant_file[["sample"]], 
    year = relevant_file[["year"]])

Each subsequent function also has issues related to "cannot open the function" and/or "object 'x' not found".

I am assuming this is a file source issue? I have attempted using a different file path but it is also unsuccessful. I assume it requires the full path since my here() begins at bbmoreno/, but shortening the path is also unsuccessful. I have the utilities.R and project_data_steps.R files in labs/wk03 folder. Is there anything I should have in there at this time? I am wondering if I should also have my data in this folder.

Thanks for any and all help!

[castower]

Hello @bbmoren2,

If you notice, your here() package is starting at the user level of your computer. You must be inside of your repository's project for the code to work.

I would suggest re-opening your .Rproject file to ensure that here() starts in that folder.

[bbmoren2]

I figured it was related to that, thank you for clarifying!

Brittany

[bbmoren2]

Hi again, @castower. 😬

I successfully navigated to the correct path through my .Rproject file but am receiving the same errors when I run the for() function:

for (relevant_file in RELEVANT_FILES) {
+              print(paste0("Starting on ", relevant_file[["year"]]))
+              build_year(fn1 = relevant_file[["fullcount"]],
+                            fn2 = relevant_file[["sample"]],
+                            year = relevant_file[["year"]])
+              if (relevant_file[["year"]] < 2010) {
+                 print("Finished! Moving onto the next decade.")
+              } else {
+                 print("Finished! No more data to parse.")
+              }
}
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt"):

And showing the traceback:

Error in file(file, "rt") : cannot open the connection 
5. file(file, "rt") 
4. read.table(file = file, header = header, sep = sep, quote = quote, 
    dec = dec, fill = fill, comment.char = comment.char, ...) 
3. read.csv(here::here(path), colClasses = "character") 
2. tidy_up_data(fn1) 
1. build_year(fn1 = relevant_file[["fullcount"]], fn2 = relevant_file[["sample"]], 
    year = relevant_file[["year"]])

Is there another place I should be adding the correct directory or file path?

Thank you!

[castower]

Hello @bbmoren2 ,

Do you have the ltdb files stored in your data/raw folder?

[bbmoren2]

Nope 😅 Thank you, @castower!