updated base/db #2758 #2774

moki1202 · 2021-02-19T06:29:23Z

fixed tidyverse notes "no visible binding for global variable" for "name, id, created_at, updated_at, pft_id" in clone_pft.R

fixed tidyverse notes "no visible binding for global variable" for "container_type, container_id, machine_id, updated_at" in dbfiles.R

fixed tidyverse notes "no visible binding for global variable" for "sync_host_id, run_id, id, workflow_id, posix, folder, ensemble_id"

fixed tidyverse notes "no visible binding for global variable" for " pft_id, created_at, stat, trait "

fixed tidyverse notes "no visible binding for global variable" for "id, name, collect"

ixed tidyverse notes "no visible binding for global variable" for "name, pft_type, name.mt, cultivar_id, specie_id, genus, species, scientificname, name.cv"

fixed tidyverse notes "no visible binding for global variable" for "name"

fixed tidyverse notes "no visible binding for global variable" for "score, author, author_family, author_given, issued"

removed relevant "no visible binding for global variable" lines from the file .

moki1202 · 2021-02-19T08:02:34Z

tried my best to update base/db files. cross-checked them multiple times to be sure.

base/db/R/clone_pft.R

base/db/R/get.trait.data.pft.R

base/db/R/insert.format.vars.R

base/db/R/query.dplyr.R

base/db/R/query.pft.R

base/db/R/search_references.R

base/db/R/get.trait.data.pft.R

base/db/R/dbfiles.R

base/db/R/insert.format.vars.R

base/db/R/query.traits.R

ashiklom

Thanks @moki1202 ! Overall, this looks good, but please see my suggested changes.

Most of them refer to one of two situations where using .data is incorrect:

On the lefthand side of assignment (=, but not ==!) expressions. E.g., dplyr::mutate(newvariable = .data$oldvariable) or dplyr::select(new_name = .data$old_name) -- newvariable and new_name are being created inside the data frame, so no ambiguity and therefore no need for the .data pronoun. In fact, it will not work on the left side of expressions.
Inside strings. E.g., dplyr::left_join(table1, table2, by = c("t1_col" = "t2_col")) -- strings are evaluated as-is and not treated as variables, so there's no need for the .data pronoun. In fact, it will not work -- ".data$t1_col" will look for a column with that exact name (including the .data$ prefix), which does not exist.

removed/added '.data' pronoun where required.

added '.data' pronoun to 'file_name' and 'file_path'.

fixed by removing ' .data ' at appropriate places.

removed ' .data' from collect() function and added dplyr Namespace.

removed ' .data' pronoun from appropriate places.

infotroph · 2021-02-20T09:43:30Z

/document

base/db/R/search_references.R

Mostly to trigger a CI rebuild

Co-authored-by: Alexey Shiklomanov <alexey.shiklomanov@gmail.com>

infotroph · 2021-02-21T22:13:08Z

base/db/tests/Rcheck_reference.log

 match_dbcols: no visible global function definition for ‘head’
 match_dbcols: no visible binding for global variable ‘.’
 match_dbcols: no visible binding for global variable ‘as’
-query_pfts: no visible binding for global variable ‘name’


@moki1202 The current CI failure is because this warning hasn't been fixed yet. Confusingly, we have files named both query.pft.R (which you have cleaned up in this PR) and query_pfts.R (which you haven't yet modified). To fix the build error you can either do the updates in query_pfts.R, or re-add this line to Rcheck_reference.log and save the cleanup in query_pfts for another PR -- either way is OK with me.

ill fix this file as soon as my classes are over @infotroph

@infotroph just updated query_pfts.R, turns out I did forget to update this file. I apologize.

added ' .data ' pronoun to appropriate places.

infotroph · 2021-03-02T00:08:07Z

@ashiklom Have all your change requests been resolved here?

moki1202 added 2 commits February 19, 2021 11:57

updated base/db/R/clone_pft.R

abf2763

fixed tidyverse notes "no visible binding for global variable" for "name, id, created_at, updated_at, pft_id" in clone_pft.R

updated dbfiles.R

6f6f1c1

fixed tidyverse notes "no visible binding for global variable" for "container_type, container_id, machine_id, updated_at" in dbfiles.R

moki1202 changed the title ~~updated base/db/R/clone_pft.R #2758~~ updated base/db #2758 Feb 19, 2021

moki1202 added 8 commits February 19, 2021 12:44

updated query.dplyr.R

c6ff211

fixed tidyverse notes "no visible binding for global variable" for "sync_host_id, run_id, id, workflow_id, posix, folder, ensemble_id"

updated get.trait.data.pft.R

f144376

fixed tidyverse notes "no visible binding for global variable" for " pft_id, created_at, stat, trait "

updated insert.format.vars.R

baa49dd

fixed tidyverse notes "no visible binding for global variable" for "id, name, collect"

updated query.pft.R

b7045e9

ixed tidyverse notes "no visible binding for global variable" for "name, pft_type, name.mt, cultivar_id, specie_id, genus, species, scientificname, name.cv"

updated query.format.vars.R

63f11b0

updated query.traits.R

9fee618

fixed tidyverse notes "no visible binding for global variable" for "name"

updated search_references.R

bbcf0b1

fixed tidyverse notes "no visible binding for global variable" for "score, author, author_family, author_given, issued"

updated Rcheck_reference.log

84be22e

removed relevant "no visible binding for global variable" lines from the file .