You are viewing a plain text version of this content. The canonical link for it is here.
Posted to github@arrow.apache.org by "paleolimbot (via GitHub)" <gi...@apache.org> on 2023/03/02 01:28:01 UTC
[GitHub] [arrow-nanoarrow] paleolimbot opened a new issue, #141: [R] Test failure on 0.1-RC1 verification
paleolimbot opened a new issue, #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141
Kindly reported by @kou (thank you!)
```
── Error ('test-as-array.R:466'): as_nanoarrow_array() works for blob::blob() -> na_large_binary() ──
── Error ('test-convert-array.R:757'): convert to vector works for data frames nested inside lists ──
── Error ('test-convert-array.R:775'): convert to vector works for lists nested in data frames ──
── Error ('test-infer-ptype.R:104'): infer_nanoarrow_ptype() infers ptypes for nested types ──
```
These seem like real errors...they all involve nested lists and `vctrs::list_of()` in some way and I recall that was a rather difficult conversion to get right.
I would be interested to see what the output of `sessioninfo::session_info()` is for the nanoarrow dependencies. Here is what it looks like for me:
``` r
sessioninfo::session_info(c("blob", "hms", "rlang", "tibble", "vctrs", "withr"))
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 (2022-10-31)
#> os macOS Monterey 12.5
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Halifax
#> date 2023-03-01
#> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
#> cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0)
#> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
#> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
#> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
#> hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
#> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
#> vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
#>
#> [1] /Users/deweydunnington/Library/R/arm64/4.2/library
#> [2] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
```
I will try to replicate in Docker as well.
Detailed output:
<details>
```
R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting"
Copyright (C) 2022 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.
> # Licensed to the Apache Software Foundation (ASF) under one
> # or more contributor license agreements. See the NOTICE file
> # distributed with this work for additional information
> # regarding copyright ownership. The ASF licenses this file
> # to you under the Apache License, Version 2.0 (the
> # "License"); you may not use this file except in compliance
> # with the License. You may obtain a copy of the License at
> #
> # http://www.apache.org/licenses/LICENSE-2.0
> #
> # Unless required by applicable law or agreed to in writing,
> # software distributed under the License is distributed on an
> # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
> # KIND, either express or implied. See the License for the
> # specific language governing permissions and limitations
> # under the License.
>
> library(testthat)
> library(nanoarrow)
>
> verbose_test_output <- identical(tolower(Sys.getenv("ARROW_R_DEV", "false")), "true") ||
+ identical(tolower(Sys.getenv("ARROW_R_VERBOSE_TEST", "false")), "true")
>
> if (verbose_test_output) {
+ reporter <- MultiReporter$new(list(CheckReporter$new(), LocationReporter$new()))
+ } else {
+ reporter <- check_reporter()
+ }
>
> test_check("nanoarrow", reporter = reporter)
[ FAIL 4 | WARN 0 | SKIP 4 | PASS 963 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (4)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-as-array.R:466'): as_nanoarrow_array() works for blob::blob() -> na_large_binary() ──
Error: Invalid: invalid R type to convert to binary
Backtrace:
▆
1. ├─nanoarrow::as_nanoarrow_array(...) at test-as-array.R:466:2
2. ├─nanoarrow:::as_nanoarrow_array.blob(...)
3. │ ├─nanoarrow::as_nanoarrow_array(unclass(x), schema = schema)
4. │ └─nanoarrow:::as_nanoarrow_array.default(unclass(x), schema = schema)
5. └─nanoarrow:::as_nanoarrow_array_from_c(`<list>`, `<nnrrw_sc>`)
6. ├─nanoarrow::as_nanoarrow_array(x, schema = schema, .from_c = TRUE)
7. └─nanoarrow:::as_nanoarrow_array.default(x, schema = schema, .from_c = TRUE)
8. ├─nanoarrow::as_nanoarrow_array(arrow::as_arrow_array(x, type = arrow::as_data_type(schema)))
9. ├─arrow::as_arrow_array(x, type = arrow::as_data_type(schema))
10. └─arrow:::as_arrow_array.default(x, type = arrow::as_data_type(schema))
11. └─arrow:::vec_to_Array(x, type)
── Error ('test-convert-array.R:757'): convert to vector works for data frames nested inside lists ──
Error in `(function (x, ..., type = NULL)
{
UseMethod("as_arrow_array")
})(structure(list(structure(list(x = 1:5), class = "data.frame", row.names = c(NA,
-5L)), structure(list(x = 6:10), class = "data.frame", row.names = c(NA,
-5L)), structure(list(x = 11:15), class = "data.frame", row.names = c(NA,
-5L))), ptype = structure(list(x = integer(0)), class = "data.frame", row.names = integer(0)), class = c("vctrs_list_of",
"vctrs_vctr", "list")), type = <environment>, from_vec_to_array = TRUE)`: Can't create Array<list_of(struct(x = int32()))> from object of type vctrs_list_of / vctrs_vctr / list
Backtrace:
▆
1. ├─nanoarrow::as_nanoarrow_array(df_in_list) at test-convert-array.R:757:2
2. ├─nanoarrow:::as_nanoarrow_array.default(df_in_list)
3. ├─nanoarrow:::as_nanoarrow_array_from_c(`<list<df[,1]>>`, `<nnrrw_sc>`)
4. │ ├─nanoarrow::as_nanoarrow_array(x, schema = schema, .from_c = TRUE)
5. │ └─nanoarrow:::as_nanoarrow_array.default(x, schema = schema, .from_c = TRUE)
6. │ ├─nanoarrow::as_nanoarrow_array(arrow::as_arrow_array(x, type = arrow::as_data_type(schema)))
7. │ ├─arrow::as_arrow_array(x, type = arrow::as_data_type(schema))
8. │ └─arrow:::as_arrow_array.default(x, type = arrow::as_data_type(schema))
9. │ └─arrow:::vec_to_Array(x, type)
10. ├─arrow (local) `<fn>`(`<list<df[,1]>>`, type = `<ListType>`, from_vec_to_array = TRUE)
11. └─arrow:::as_arrow_array.default(`<list<df[,1]>>`, type = `<ListType>`, from_vec_to_array = TRUE)
12. └─arrow:::stop_cant_convert_array(x, type)
13. └─rlang::abort(...)
── Error ('test-convert-array.R:775'): convert to vector works for lists nested in data frames ──
Error in `(function (x, ..., type = NULL)
{
UseMethod("as_arrow_array")
})(structure(list(structure(list(x = 1:5), class = "data.frame", row.names = c(NA,
-5L)), structure(list(x = 6:10), class = "data.frame", row.names = c(NA,
-5L)), structure(list(x = 11:15), class = "data.frame", row.names = c(NA,
-5L))), ptype = structure(list(x = integer(0)), class = "data.frame", row.names = integer(0)), class = c("vctrs_list_of",
"vctrs_vctr", "list")), type = <environment>, from_vec_to_array = TRUE)`: Can't create Array<list_of(struct(x = int32()))> from object of type vctrs_list_of / vctrs_vctr / list
Backtrace:
▆
1. ├─nanoarrow::as_nanoarrow_array(df_in_list_in_df) at test-convert-array.R:775:2
2. ├─nanoarrow:::as_nanoarrow_array.default(df_in_list_in_df)
3. ├─nanoarrow:::as_nanoarrow_array_from_c(`<list<df[,1]>>`, `<nnrrw_sc>`)
4. │ ├─nanoarrow::as_nanoarrow_array(x, schema = schema, .from_c = TRUE)
5. │ └─nanoarrow:::as_nanoarrow_array.default(x, schema = schema, .from_c = TRUE)
6. │ ├─nanoarrow::as_nanoarrow_array(arrow::as_arrow_array(x, type = arrow::as_data_type(schema)))
7. │ ├─arrow::as_arrow_array(x, type = arrow::as_data_type(schema))
8. │ └─arrow:::as_arrow_array.default(x, type = arrow::as_data_type(schema))
9. │ └─arrow:::vec_to_Array(x, type)
10. ├─arrow (local) `<fn>`(`<list<df[,1]>>`, type = `<ListType>`, from_vec_to_array = TRUE)
11. └─arrow:::as_arrow_array.default(`<list<df[,1]>>`, type = `<ListType>`, from_vec_to_array = TRUE)
12. └─arrow:::stop_cant_convert_array(x, type)
13. └─rlang::abort(...)
── Error ('test-infer-ptype.R:104'): infer_nanoarrow_ptype() infers ptypes for nested types ──
Error in `(function (x, ..., type = NULL)
{
UseMethod("as_arrow_array")
})(structure(list(integer(0)), ptype = integer(0), class = c("vctrs_list_of",
"vctrs_vctr", "list")), type = <environment>, from_vec_to_array = TRUE)`: Can't create Array<list_of(int32())> from object of type vctrs_list_of / vctrs_vctr / list
Backtrace:
▆
1. ├─nanoarrow::as_nanoarrow_array(vctrs::list_of(integer())) at test-infer-ptype.R:104:2
2. ├─nanoarrow:::as_nanoarrow_array.default(vctrs::list_of(integer()))
3. ├─nanoarrow:::as_nanoarrow_array_from_c(`<list<int>>`, `<nnrrw_sc>`)
4. │ ├─nanoarrow::as_nanoarrow_array(x, schema = schema, .from_c = TRUE)
5. │ └─nanoarrow:::as_nanoarrow_array.default(x, schema = schema, .from_c = TRUE)
6. │ ├─nanoarrow::as_nanoarrow_array(arrow::as_arrow_array(x, type = arrow::as_data_type(schema)))
7. │ ├─arrow::as_arrow_array(x, type = arrow::as_data_type(schema))
8. │ └─arrow:::as_arrow_array.default(x, type = arrow::as_data_type(schema))
9. │ └─arrow:::vec_to_Array(x, type)
10. ├─arrow (local) `<fn>`(`<list<int>>`, type = `<ListType>`, from_vec_to_array = TRUE)
11. └─arrow:::as_arrow_array.default(`<list<int>>`, type = `<ListType>`, from_vec_to_array = TRUE)
12. └─arrow:::stop_cant_convert_array(x, type)
13. └─rlang::abort(...)
[ FAIL 4 | WARN 0 | SKIP 4 | PASS 963 ]
Error: Test failures
Execution halted
```
...with full gist at https://gist.github.com/kou/1194cf28cb8e70fe309d0f07e6f49b3b#file-testthat-rout-fail
</details>
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] kou commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1451232330
Passed. Is this expected? Or should I install `"arrow"` package manually?
```text
========================
Build and test R package
========================
└ Install nanoarrow test dependencies
R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting"
Copyright (C) 2022 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.
> for (pkg in c("blob", "hms", "tibble", "rlang", "testthat", "tibble", "vctrs", "withr")) if (!requireNamespace(pkg, quietly = TRUE)) install.packages(pkg, repos = "https://cloud.r-project.org/")
>
>
└ Build the R package source tarball
* installing *source* package 'nanoarrow' ...
** using staged installation
cmake version 3.25.1
CMake suite maintained and supported by Kitware (kitware.com/cmake).
[0] 'cmake' --version
-- Building using CMake version: 3.25.1
-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/RtmpIp5kap/filec44dc24dc148c/build
[0] 'cmake' /tmp/nanoarrow-0.1.0.fvxJK0/apache-arrow-nanoarrow-0.1.0 -DNANOARROW_BUNDLE=ON -DNANOARROW_NAMESPACE=RPkg
[0] 'cmake' --build '/tmp/RtmpIp5kap/filec44dc24dc148c/build'
-- Install configuration: ""
-- Installing: /tmp/RtmpIp5kap/filec44dc24dc148c/dist/./nanoarrow.h
-- Installing: /tmp/RtmpIp5kap/filec44dc24dc148c/dist/./nanoarrow.c
-- Installing: /tmp/RtmpIp5kap/filec44dc24dc148c/dist/./nanoarrow.hpp
[0] 'cmake' --install '/tmp/RtmpIp5kap/filec44dc24dc148c/build' --prefix='/tmp/RtmpIp5kap/filec44dc24dc148c/dist'
[1] TRUE
Vendoring files from arrow-nanoarrow to src/:
- /tmp/RtmpIp5kap/filec44dc24dc148c/dist/nanoarrow.c
- /tmp/RtmpIp5kap/filec44dc24dc148c/dist/nanoarrow.h
All files successfully copied to src/
Found vendored nanoarrow
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep.c -o altrep.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c array.c -o array.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c array_stream.c -o array_stream.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c array_view.c -o array_view.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c as_array.c -o as_array.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c buffer.c -o buffer.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c convert.c -o convert.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c convert_array.c -o convert_array.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c convert_array_stream.c -o convert_array_stream.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c infer_ptype.c -o infer_ptype.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c materialize.c -o materialize.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nanoarrow.c -o nanoarrow.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nanoarrow_cpp.cc -o nanoarrow_cpp.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pointers.c -o pointers.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c schema.c -o schema.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c util.c -o util.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-z,relro -o nanoarrow.so altrep.o array.o array_stream.o array_view.o as_array.o buffer.o convert.o convert_array.o convert_array_stream.o infer_ptype.o init.o materialize.o nanoarrow.o nanoarrow_cpp.o pointers.o schema.o util.o version.o -L/usr/lib/R/lib -lR
installing to /tmp/nanoarrow-0.1.0.fvxJK0/tmplib/00LOCK-r/00new/nanoarrow/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nanoarrow)
/tmp/nanoarrow-0.1.0.fvxJK0 /tmp/nanoarrow-0.1.0.fvxJK0/apache-arrow-nanoarrow-0.1.0 ~/work/c/arrow-nanoarrow
* checking for file '/tmp/nanoarrow-0.1.0.fvxJK0/apache-arrow-nanoarrow-0.1.0/r/DESCRIPTION' ... OK
* preparing 'nanoarrow':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'nanoarrow_0.1.0.tar.gz'
└ Run R CMD check
* using log directory '/tmp/nanoarrow-0.1.0.fvxJK0/nanoarrow.Rcheck'
* using R version 4.2.2 Patched (2022-11-10 r83330)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ASCII
* using option '--no-manual'
* checking for file 'nanoarrow/DESCRIPTION' ... OK
* this is package 'nanoarrow' version '0.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'arrow'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'nanoarrow' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... WARNING
Warning in Sys.setlocale("LC_CTYPE", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
* 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 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 cross-references ... NOTE
Package unavailable to check Rd xrefs: 'arrow'
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
'/tmp/nanoarrow-0.1.0.fvxJK0/nanoarrow.Rcheck/00check.log'
for details.
```
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] kou closed issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou closed issue #141: [R] Test failure on 0.1-RC1 verification
URL: https://github.com/apache/arrow-nanoarrow/issues/141
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] paleolimbot commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "paleolimbot (via GitHub)" <gi...@apache.org>.
paleolimbot commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1451181625
Recreating in Docker now and I'm realizing that all of those tests have `skip_if_not_installed("arrow")` and that we added `blob` and `list_of` support in version 10.0.0.
Does `packageVersion("arrow")` give you something before 10.0.0?
```bash
# docker run --rm -it debian:sid
# packages for debian: https://github.com/apache/arrow-nanoarrow/tree/main/dev/release#debianubuntu
git clone https://github.com/apache/arrow-nanoarrow.git arrow-nanoarrow
cd arrow-nanoarrow/dev/release
# Works with no arrow
./verify-release-candidate.sh 0.1.0 1
# Works with Arrow 11.0.0
R -e 'install.packages("arrow")'
./verify-release-candidate.sh 0.1.0 1
# Fails for Arrow 9.0.0
NOT_CRAN=true ARROW_USE_PKG_CONFIG=false R -e 'remotes::install_github("cran/arrow@9.0.0")'
./verify-release-candidate.sh 0.1.0 1
```
...either way I should update the verification script to output some of that information and check the version constraints in the R package DESCRIPTION.
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] kou commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1451220266
How can I remove the `"arrow"` package? `remove.packages("arrow")`?
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] kou commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1452767830
Thanks.
I also tried after `install.package("arrow")` again and it also passed.
Sorry. This was my environment problem.
> Strange that a previous version required `sudo` to remove!
I don't remember but I think that I used `sudo R -e ...` when I install the arrow package because I use system R (installed by `apt`) and it installs packages into `/usr/local/...`.
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] eddelbuettel commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "eddelbuettel (via GitHub)" <gi...@apache.org>.
eddelbuettel commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1455122944
FYI If this is on a Debian/Ubuntu we had this scheme for a decade+ where _if you add the users you want to be able to do this_ to the appropriate group everything works without sudo:
```sh
edd@rob:~/git$ ls -ld /usr/local/lib/R/site-library/
drwxrwsr-x 1093 root staff 36864 Mar 5 09:26 /usr/local/lib/R/site-library/
edd@rob:~/git$ touch /usr/local/lib/R/site-library/foobarbiz
edd@rob:~/git$ ls -l /usr/local/lib/R/site-library/foobarbiz
-rw-rw-r-- 1 edd staff 0 Mar 5 09:27 /usr/local/lib/R/site-library/foobarbiz
edd@rob:~/git$ id
uid=1000(edd) gid=1000(edd) groups=1000(edd),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),50(staff),110(lxd),114(lpadmin),115(sambashare),998(docker)
edd@rob:~/git$ rm /usr/local/lib/R/site-library/foobarbiz
edd@rob:~/git$
```
No `sudo` needed here as the system user (me) add my normal account to `staff`.
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] kou commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1451225557
Sorry. I needed `sudo` to remove `"arrow"` package:
```text
> packageVersion("arrow")
Error in packageVersion("arrow") : there is no package called 'arrow'
```
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] kou commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1451222988
Hmm... `remove.packages("arrow")` doesn't uninstall `"arrow"` package...
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] paleolimbot commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "paleolimbot (via GitHub)" <gi...@apache.org>.
paleolimbot commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1451864660
Yes, it's expected that verification passes without the 'arrow' R package (although some extra tests will run if it is installed and those should pass as well). If you did want to install the latest arrow R package version you could probably do so with `NOT_CRAN=true ARROW_USE_PKG_CONFIG=false R -e 'install.packages("arrow")'`.
Strange that a previous version required `sudo` to remove!
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] kou commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1451217360
`session_info`:
```text
> sessioninfo::session_info(c("blob", "hms", "rlang", "tibble", "vctrs", "withr"))
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.2 Patched (2022-11-10 r83330)
os Debian GNU/Linux bookworm/sid
system x86_64, linux-gnu
ui X11
language (EN)
collate ja_JP.UTF-8
ctype ja_JP.UTF-8
tz Asia/Tokyo
date 2023-03-02
pandoc 2.17.1.1 @ /bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.2)
cli 3.5.0 2022-12-20 [1] CRAN (R 4.2.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.2)
hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.2)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.2)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.2)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.2)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2)
vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.2)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.2)
[1] /usr/local/lib/R/site-library
[2] /usr/lib/R/site-library
[3] /usr/lib/R/library
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
```
`packageVersion("arrow")`:
```text
> packageVersion("arrow")
[1] ‘8.0.0.20220529’
```
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org
[GitHub] [arrow-nanoarrow] kou commented on issue #141: [R] Test failure on 0.1-RC1 verification
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #141:
URL: https://github.com/apache/arrow-nanoarrow/issues/141#issuecomment-1455200967
Thanks for the info!
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: github-unsubscribe@arrow.apache.org
For queries about this service, please contact Infrastructure at:
users@infra.apache.org