CRAN Issues Fix. CRAN archived.
Opened this issue · 19 comments
bedantaguru commented
Got it archived. Devlopment cycle need to fix urgently.
bedantaguru commented
Make an intermediate silent release.
Target May 14 noon.
Most of the things can be kept as it is.
- DT plot option to be kept silent (all shiny modules to be in ggplot2 for this time)
- exploration finding can be kept silent
- if the initial deadline fail - try a full-scale release
bedantaguru commented
I think at this point the only option is to perform quick fix in the main repo.
Taken a fork here for future reference.
Need to fix things in the main repo and release a patch.
bedantaguru commented
I think last error was coming in
bedantaguru commented
Just checked it is mostly happening for dplyr 1.0.0
tidyverse/dplyr#5211
As suggested by Hadley
mydev::beta_lib_loc()
library(dplyr, warn.conflicts = F)
packageVersion("dplyr")
#> [1] '0.8.99.9002'
packageVersion("vctrs")
#> [1] '0.3.0'
dat <- iris %>% head()
# class(dat) <- c(class(dat),"test")
class(dat) <- c("test", class(dat))
iris %>% head() %>% select(Species, Sepal.Length)
#> Species Sepal.Length
#> 1 setosa 5.1
#> 2 setosa 4.9
#> 3 setosa 4.7
#> 4 setosa 4.6
#> 5 setosa 5.0
#> 6 setosa 5.4
dat %>% select(Species, Sepal.Length)
#> Species Sepal.Length
#> 1 setosa 5.1
#> 2 setosa 4.9
#> 3 setosa 4.7
#> 4 setosa 4.6
#> 5 setosa 5.0
#> 6 setosa 5.4
iris %>% vctrs::vec_assert()
dat %>% vctrs::vec_assert()Created on 2020-05-11 by the reprex package (v0.3.0)
bedantaguru commented
My bad all mails filtered in junk folder god knows how..
bedantaguru commented
as_cell_df is quite slow and hoping a lot in S3 method dispatch.. need to fix it..
See #40
bedantaguru commented
RHub Console Output 1
* using log directory 'C:/Users/USERCBPbIvzeHV/tidycells.Rcheck'
* using R Under development (unstable) (2020-04-22 r78281)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'tidycells/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tidycells' version '0.2.2.9000'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Indranil Gayen <nil.gayen@gmail.com>'
New submission
Package was archived on CRAN
Version contains large components (0.2.2.9000)
Found the following (possibly) invalid URLs:
URL: https://cran.r-project.org/web/checks/check_results_tidycells.html
From: README.md
Status: 404
Message: Not Found
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'tidycells' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'tidycells-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_cell_df
> ### Title: Transform data into Cell-DF Structure
> ### Aliases: as_cell_df
>
> ### ** Examples
>
>
> as_cell_df(iris)
A Cell Data Frame
= To see cell stats, call summary()
= To see cell structure, call plot()
= Content:
Error in loadNamespace(name) : there is no package called 'utf8'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
Running 'testthat.R' [123s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
43. base::asNamespace(ns)
44. base::getNamespace(ns)
45. base::loadNamespace(name)
46. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
47. base:::withOneRestart(expr, restarts[[1L]])
48. base:::doWithOneRestart(return(expr), restart)
== testthat results ===========================================================
[ OK: 151 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 3 ]
1. Error: numeric_values_classifier works (@test-VA_classifier.R#19)
2. Error: read_cells for NULL works (@test-read_cells.R#4)
3. Error: read_cells for external packages works (@test-read_cells.R#22)
Error: testthat unit tests failed
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
...
--- re-building 'tidycells-intro.Rmd' using rmarkdown
Quitting from lines 298-314 (tidycells-intro.Rmd)
Error: processing vignette 'tidycells-intro.Rmd' failed with diagnostics:
there is no package called 'utf8'
--- failed re-building 'tidycells-intro.Rmd'
SUMMARY: processing the following file failed:
'tidycells-intro.Rmd'
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTERHub Console Output 2
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
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.
> library(testthat)
> library(tidycells)
>
>
> test_check("tidycells")
── 1. Failure: read_cells: csv works (@test-read_cells.R#75) ──────────────────
`dc0` not equal to `expct_d2`.
2/20 mismatches
x[1]: "12"
y[1]: "1.5"
x[2]: "1.5"
y[2]: "12"
Support present for following type of files: csv, xls, xlsx, docx, pdf, html
Note:
☰ LibreOffice may be required for doc files
☰ Support is enabled for content type (means it will work even if the extension is wrong)
☰ Support not present for following type of files: doc
Details:
┌──────────────────────────────────────────────�
│ │
│ type package present support │
│ 1 csv{utils} utils ✔ ✔ │
│ 2 csv readr ✔ ✔ │
│ 3 xls{readxl} readxl ✔ ✔ │
│ 4 xls xlsx ✔ ✔ │
│ 5 xlsx tidyxl ✔ ✔ │
│ 6 doc docxtractr ✔ ✖ │
│ 7 docx docxtractr ✔ ✔ │
│ 8 pdf tabulizer ✔ ✔ │
│ 9 html XML ✔ ✔ │
│ │
└──────────────────────────────────────────────┘
Support present for following type of files: csv, xls, xlsx, docx, pdf, html
Note:
☰ LibreOffice may be required for doc files
☰ Support is enabled for content type (means it will work even if the extension is wrong)
☰ Support not present for following type of files: doc
Details:
┌──────────────────────────────────────────────�
│ │
│ type package present support │
│ 1 csv{utils} utils ✔ ✔ │
│ 2 csv readr ✔ ✔ │
│ 3 xls{readxl} readxl ✔ ✔ │
│ 4 xls xlsx ✔ ✔ │
│ 5 xlsx tidyxl ✔ ✔ │
│ 6 doc docxtractr ✔ ✖ │
│ 7 docx docxtractr ✔ ✔ │
│ 8 pdf tabulizer ✔ ✔ │
│ 9 html XML ✔ ✔ │
│ │
└──────────────────────────────────────────────┘
�� testthat results �����������������������������������������������������������
[ OK: 182 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: read_cells: csv works (@test-read_cells.R#75)
Error: testthat unit tests failed
Execution haltedRHub Console Output 3
R Under development (unstable) (2020-05-07 r78381) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
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.
> library(testthat)
> library(tidycells)
>
>
> test_check("tidycells")
── 1. Error: etc works ────────────────────────────────────────────────────────
Java Exception <no description because toString() failed>.jcall(cell, "Lorg/apache/poi/ss/usermodel/RichTextString;", "getRichStringCellValue")new("jobjRef", jobj = <pointer: 0x559c1b285030>, jclass = "java/lang/Throwable")
Backtrace:
1. tidycells:::read_xls_from_xlsx(dex)
6. tidycells:::read_xls_for_tidycells(fn)
11. purrr::map(., for_a_sheet)
16. tidycells:::.f(.x[[i]], ...)
13. purrr::map(., xlsx::getCellValue)
26. xlsx:::.f(.x[[i]], ...)
28. rJava::.jcall(...)
29. rJava::.jcheck(silent = FALSE)
── 2. Failure: optional_package dependency test (@test-optional_package.R#25) ─
`d1` not equal to `d2`.
target is NULL, current is tbl_df
Support present for following type of files: csv, xls, xlsx, docx, html
Note:
☰ LibreOffice may be required for doc files
☰ Support is enabled for content type (means it will work even if the extension is wrong)
☰ Support not present for following type of files: doc, pdf
Note:
☰ These packages are required: tabulizer
Details:
┌──────────────────────────────────────────────�
│ │
│ type package present support │
│ 1 csv{utils} utils ✔ ✔ │
│ 2 csv readr ✔ ✔ │
│ 3 xls{readxl} readxl ✔ ✔ │
│ 4 xls xlsx ✔ ✔ │
│ 5 xlsx tidyxl ✔ ✔ │
│ 6 doc docxtractr ✔ ✖ │
│ 7 docx docxtractr ✔ ✔ │
│ 8 pdf tabulizer ✖ ✖ │
│ 9 html XML ✔ ✔ │
│ │
└──────────────────────────────────────────────┘
Error in .jcall("java/lang/Class", "Ljava/lang/Class;", "forName", cl, :
RcallMethod: cannot determine object class
�� testthat results �����������������������������������������������������������
[ OK: 171 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 2 ]
1. Error: etc works
2. Failure: optional_package dependency test (@test-optional_package.R#25)
Error: testthat unit tests failed
Execution haltedRHub Console Output 4
R Under development (unstable) (2020-05-07 r78381) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
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.
> library(testthat)
> library(tidycells)
>
>
> test_check("tidycells")
── 1. Error: etc works ────────────────────────────────────────────────────────
Java Exception <no description because toString() failed>.jcall(cell, "Lorg/apache/poi/ss/usermodel/RichTextString;", "getRichStringCellValue")new("jobjRef", jobj = <pointer: 0x559c1b285030>, jclass = "java/lang/Throwable")
Backtrace:
1. tidycells:::read_xls_from_xlsx(dex)
6. tidycells:::read_xls_for_tidycells(fn)
11. purrr::map(., for_a_sheet)
16. tidycells:::.f(.x[[i]], ...)
13. purrr::map(., xlsx::getCellValue)
26. xlsx:::.f(.x[[i]], ...)
28. rJava::.jcall(...)
29. rJava::.jcheck(silent = FALSE)
── 2. Failure: optional_package dependency test (@test-optional_package.R#25) ─
`d1` not equal to `d2`.
target is NULL, current is tbl_df
Support present for following type of files: csv, xls, xlsx, docx, html
Note:
☰ LibreOffice may be required for doc files
☰ Support is enabled for content type (means it will work even if the extension is wrong)
☰ Support not present for following type of files: doc, pdf
Note:
☰ These packages are required: tabulizer
Details:
┌──────────────────────────────────────────────�
│ │
│ type package present support │
│ 1 csv{utils} utils ✔ ✔ │
│ 2 csv readr ✔ ✔ │
│ 3 xls{readxl} readxl ✔ ✔ │
│ 4 xls xlsx ✔ ✔ │
│ 5 xlsx tidyxl ✔ ✔ │
│ 6 doc docxtractr ✔ ✖ │
│ 7 docx docxtractr ✔ ✔ │
│ 8 pdf tabulizer ✖ ✖ │
│ 9 html XML ✔ ✔ │
│ │
└──────────────────────────────────────────────┘
Error in .jcall("java/lang/Class", "Ljava/lang/Class;", "forName", cl, :
RcallMethod: cannot determine object class
�� testthat results �����������������������������������������������������������
[ OK: 171 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 2 ]
1. Error: etc works
2. Failure: optional_package dependency test (@test-optional_package.R#25)
Error: testthat unit tests failed
Execution halted bedantaguru commented
AppVeyor Console Output
packages 'utf8', 'data.table', 'pingr' are available as source packages but not as binaries
Error: (converted from warning) packages 'utf8', 'data.table', 'pingr' are not available (as a binary package for R Under development)
Execution halted
Command exited with code 1
7z a failure.zip *.Rcheck\*
packages 'utf8', 'data.table', 'pingr' are available as source packages but not as binaries
Error: (converted from warning) packages 'utf8', 'data.table', 'pingr' are not available (as a binary package for R Under development)
Execution halted
Command exited with code 1
7z a failure.zip *.Rcheck\*
This is CI issue I think is possible to fix (see this)
bedantaguru commented
Travis Console Output
* installing *source* package ‘pkgbuild’ ...
** package ‘pkgbuild’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'processx', details:
call: loadNamespace(name)
error: there is no package called ‘ps’
Execution halted
ERROR: lazy loading failed for package ‘pkgbuild’
* removing ‘/Users/travis/R/Library/pkgbuild’
Error in i.p(...) :
(converted from warning) installation of package ‘pkgbuild’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
The command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .This is CI issue I think is possible to fix (see this)
bedantaguru commented
RHub Console Output (vignette) 1
--- re-building ‘tidycells-intro.Rmd’ using rmarkdown
Quitting from lines 446-457 (tidycells-intro.Rmd)
Error: processing vignette 'tidycells-intro.Rmd' failed with diagnostics:
no applicable method for 'select_' applied to an object of class "NULL"
--- failed re-building ‘tidycells-intro.Rmd’
SUMMARY: processing the following file failed:
‘tidycells-intro.Rmd’
Error: Vignette re-building failed.
Execution halted
RHub Console Output (vignette) 2
--- re-building 'tidycells-intro.Rmd' using rmarkdown
Quitting from lines 298-314 (tidycells-intro.Rmd)
Error: processing vignette 'tidycells-intro.Rmd' failed with diagnostics:
there is no package called 'utf8'
--- failed re-building 'tidycells-intro.Rmd'
SUMMARY: processing the following file failed:
'tidycells-intro.Rmd'
Error: Vignette re-building failed.
Execution halted)bedantaguru commented
All winbuilder builds are successful
bedantaguru commented
Issue 'utf8'
Line 25 in 429b9c9
Vignette Issue
This possibly by {utf8}
tidycells/vignettes/tidycells-intro.Rmd
Line 298 in bcecc73
This may be avoided by safe dependency
tidycells/vignettes/tidycells-intro.Rmd
Line 446 in bcecc73
Tests
This may be avoided by safe dependency
tidycells/tests/testthat/test-etc.R
Line 79 in bcecc73
This may be avoided by safe dependency
bedantaguru commented
For {dplyr} S3 class needs to be fixed (ordering)
see #40
bedantaguru commented
Tests 1st Case : Console Output
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
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.
> library(testthat)
> library(tidycells)
>
>
> test_check("tidycells")
── 1. Failure: read_cells: csv works (@test-read_cells.R#75) ──────────────────
`dc0` not equal to `expct_d2`.
2/20 mismatches
x[1]: "12"
y[1]: "1.5"
x[2]: "1.5"
y[2]: "12"
Support present for following type of files: csv, xls, xlsx, docx, pdf, html
Note:
☰ LibreOffice may be required for doc files
☰ Support is enabled for content type (means it will work even if the extension is wrong)
☰ Support not present for following type of files: doc
Details:
┌──────────────────────────────────────────────�
│ │
│ type package present support │
│ 1 csv{utils} utils ✔ ✔ │
│ 2 csv readr ✔ ✔ │
│ 3 xls{readxl} readxl ✔ ✔ │
│ 4 xls xlsx ✔ ✔ │
│ 5 xlsx tidyxl ✔ ✔ │
│ 6 doc docxtractr ✔ ✖ │
│ 7 docx docxtractr ✔ ✔ │
│ 8 pdf tabulizer ✔ ✔ │
│ 9 html XML ✔ ✔ │
│ │
└──────────────────────────────────────────────┘
Support present for following type of files: csv, xls, xlsx, docx, pdf, html
Note:
☰ LibreOffice may be required for doc files
☰ Support is enabled for content type (means it will work even if the extension is wrong)
☰ Support not present for following type of files: doc
Details:
┌──────────────────────────────────────────────�
│ │
│ type package present support │
│ 1 csv{utils} utils ✔ ✔ │
│ 2 csv readr ✔ ✔ │
│ 3 xls{readxl} readxl ✔ ✔ │
│ 4 xls xlsx ✔ ✔ │
│ 5 xlsx tidyxl ✔ ✔ │
│ 6 doc docxtractr ✔ ✖ │
│ 7 docx docxtractr ✔ ✔ │
│ 8 pdf tabulizer ✔ ✔ │
│ 9 html XML ✔ ✔ │
│ │
└──────────────────────────────────────────────┘
�� testthat results �����������������������������������������������������������
[ OK: 182 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: read_cells: csv works (@test-read_cells.R#75)
Error: testthat unit tests failed
Execution haltedThat can happen for
testthat::expect_equal(c("12","1.5"), c("1.5","12"))
I don't know how that happened at max base::sort can be added in
bedantaguru commented
safe dependency framework needs to be implemented
See #41
bedantaguru commented
I don't know how to solve: Issue 'utf8'
It's may need to see it again what exactly happening here (RHub)
bedantaguru commented
dplyr 1.0.0 is quite strict .. that's good I think
But it is less fun to code in R then .. I think R's biggest advantage is that R is really flexible. It can understand you.
-
ifelsehas to be replaced withdplyr::if_else -
NAtoNA_things -
bind_rowis strict and some function is changing the order of columns - why don't you use {strict}
bedantaguru commented
For this ropensci/tabulapdf#106 Vignette Issue, 2 is occurring
in
tidycells/vignettes/tidycells-intro.Rmd
Line 446 in bcecc73
This is tracked using cloud_picker framework in CITestR
Ref this Circle CI build
bedantaguru commented
dependency framework for {tabulizer} is also required