Aaron Lun
| Snapshot Date: 2025-01-20 13:40 -0500 (Mon, 20 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/alabaster.base |
| git_branch: devel |
| git_last_commit: 735fbdd |
| git_last_commit_date: 2025-01-19 21:53:52 -0500 (Sun, 19 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-21 11:46 -0500 (Tue, 21 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4502 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4467 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4422 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4406 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 41/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| alabaster.base 1.7.3 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the alabaster.base package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.base.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: alabaster.base |
| Version: 1.7.3 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.base_1.7.3.tar.gz |
| StartedAt: 2025-01-21 03:43:50 -0000 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 03:45:10 -0000 (Tue, 21 Jan 2025) |
| EllapsedTime: 79.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: alabaster.base.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.base_1.7.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.base.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.base/DESCRIPTION’ ... OK
* this is package ‘alabaster.base’ version ‘1.7.3’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘alabaster.base’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 34.1Mb
sub-directories of 1Mb or more:
libs 33.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘assorthead’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/alabaster.base/libs/alabaster.base.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Found ‘sprintf’, possibly from ‘sprintf’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘alabaster.base-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: acquireFile
> ### Title: Acquire file or metadata
> ### Aliases: acquireFile acquireMetadata acquireFile,character-method
> ### acquireMetadata,character-method
>
> ### ** Examples
>
> # Staging an example DataFrame:
> library(S4Vectors)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
> df <- DataFrame(A=1:10, B=LETTERS[1:10])
> tmp <- tempfile()
> dir.create(tmp)
> info <- stageObject(df, tmp, path="coldata")
> writeMetadata(info, tmp)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Calls: writeMetadata ... jsonvalidate_js -> loadNamespace -> library.dynam -> dyn.load
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "./whee") at test-writeMetadata.R:57:5
2. └─alabaster.base::stageObject(df, tmp, "./whee")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
[ FAIL 50 | WARN 0 | SKIP 0 | PASS 313 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.base.Rcheck/00check.log’
for details.
alabaster.base.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘alabaster.base’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c check_csv.cpp -o check_csv.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c check_list.cpp -o check_list.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/uzuki2.hpp:17,
from check_list.cpp:3:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:450:44: required from ‘uzuki2::ParsedList uzuki2::json::parse(byteme::Reader&, Externals, Options) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals]’
450 | auto output = parse_object<Provisioner>(contents.get(), etrack, "", version);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:578:28: required from here
578 | parse<DummyProvisioner>(reader, std::move(ext), std::move(options));
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:236:21: warning: possibly dangling reference to a temporary [-Wdangling-reference]
236 | const auto& lvals = extract_array(map, "levels", path);
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:236:42: note: the temporary was destroyed at the end of the full expression ‘uzuki2::json::extract_array((* & map), std::__cxx11::basic_string<char>(((const char*)"levels"), std::allocator<char>()), (* & path))’
236 | const auto& lvals = extract_array(map, "levels", path);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:367:21: warning: possibly dangling reference to a temporary [-Wdangling-reference]
367 | const auto& vals = extract_array(map, "values", path);
| ^~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:367:41: note: the temporary was destroyed at the end of the full expression ‘uzuki2::json::extract_array((* & map), std::__cxx11::basic_string<char>(((const char*)"values"), std::allocator<char>()), (* & path))’
367 | const auto& vals = extract_array(map, "values", path);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c is_rfc3339.cpp -o is_rfc3339.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c load_csv.cpp -o load_csv.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c load_list.cpp -o load_list.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/uzuki2.hpp:17,
from load_list.cpp:3:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:450:44: required from ‘uzuki2::ParsedList uzuki2::json::parse(byteme::Reader&, Externals, Options) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals]’
450 | auto output = parse_object<Provisioner>(contents.get(), etrack, "", version);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:578:28: required from here
578 | parse<DummyProvisioner>(reader, std::move(ext), std::move(options));
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:236:21: warning: possibly dangling reference to a temporary [-Wdangling-reference]
236 | const auto& lvals = extract_array(map, "levels", path);
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:236:42: note: the temporary was destroyed at the end of the full expression ‘uzuki2::json::extract_array((* & map), std::__cxx11::basic_string<char>(((const char*)"levels"), std::allocator<char>()), (* & path))’
236 | const auto& lvals = extract_array(map, "levels", path);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:367:21: warning: possibly dangling reference to a temporary [-Wdangling-reference]
367 | const auto& vals = extract_array(map, "values", path);
| ^~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:367:41: note: the temporary was destroyed at the end of the full expression ‘uzuki2::json::extract_array((* & map), std::__cxx11::basic_string<char>(((const char*)"values"), std::allocator<char>()), (* & path))’
367 | const auto& vals = extract_array(map, "values", path);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = RProvisioner; Externals = uzuki2::ExternalTracker<RExternals>; std::string = std::__cxx11::basic_string<char>]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:450:44: required from ‘uzuki2::ParsedList uzuki2::json::parse(byteme::Reader&, Externals, Options) [with Provisioner = RProvisioner; Externals = RExternals]’
450 | auto output = parse_object<Provisioner>(contents.get(), etrack, "", version);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:500:30: required from ‘uzuki2::ParsedList uzuki2::json::parse_file(const std::string&, Externals, Options) [with Provisioner = RProvisioner; Externals = RExternals; std::string = std::__cxx11::basic_string<char>]’
500 | return parse<Provisioner>(reader, std::move(ext), std::move(options));
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
load_list.cpp:413:54: required from here
413 | auto ptr = uzuki2::json::parse_file<RProvisioner>(file, std::move(others));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:236:21: warning: possibly dangling reference to a temporary [-Wdangling-reference]
236 | const auto& lvals = extract_array(map, "levels", path);
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:236:42: note: the temporary was destroyed at the end of the full expression ‘uzuki2::json::extract_array((* & map), std::__cxx11::basic_string<char>(((const char*)"levels"), std::allocator<char>()), (* & path))’
236 | const auto& lvals = extract_array(map, "levels", path);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:367:21: warning: possibly dangling reference to a temporary [-Wdangling-reference]
367 | const auto& vals = extract_array(map, "values", path);
| ^~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:367:41: note: the temporary was destroyed at the end of the full expression ‘uzuki2::json::extract_array((* & map), std::__cxx11::basic_string<char>(((const char*)"values"), std::allocator<char>()), (* & path))’
367 | const auto& vals = extract_array(map, "values", path);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c validate.cpp -o validate.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:10,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/takane.hpp:4,
from validate.cpp:2:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/atomic_vector.hpp: In function ‘void takane::atomic_vector::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/atomic_vector.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
33 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "atomic_vector");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/atomic_vector.hpp:33:66: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"atomic_vector"), std::allocator<char>()))’
33 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "atomic_vector");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:12:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp: In function ‘void takane::simple_list::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp:75:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
75 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp:75:76: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"simple_list"), std::allocator<char>()))’
75 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp:77:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
77 | const std::string& vstring = internal_json::extract_string_from_typed_object(metamap, "version", "simple_list");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp:77:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & metamap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"simple_list"), std::allocator<char>()))’
77 | const std::string& vstring = internal_json::extract_string_from_typed_object(metamap, "version", "simple_list");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp: In function ‘size_t takane::simple_list::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp:143:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
143 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp:143:76: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"simple_list"), std::allocator<char>()))’
143 | const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:13:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/data_frame.hpp: In function ‘void takane::data_frame::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/data_frame.hpp:161:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
161 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/data_frame.hpp:161:66: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"data_frame"), std::allocator<char>()))’
161 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:14:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/data_frame_factor.hpp: In function ‘void takane::data_frame_factor::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/data_frame_factor.hpp:48:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
48 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame_factor");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/data_frame_factor.hpp:48:66: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"data_frame_factor"), std::allocator<char>()))’
48 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "data_frame_factor");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:16:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/genomic_ranges.hpp: In function ‘void takane::genomic_ranges::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/genomic_ranges.hpp:96:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
96 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "genomic_ranges");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/genomic_ranges.hpp:96:66: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"genomic_ranges"), std::allocator<char>()))’
96 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "genomic_ranges");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:21:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/compressed_sparse_matrix.hpp: In function ‘void takane::compressed_sparse_matrix::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/compressed_sparse_matrix.hpp:169:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
169 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "compressed_sparse_matrix");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/compressed_sparse_matrix.hpp:169:66: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"compressed_sparse_matrix"), std::allocator<char>()))’
169 | const auto& vstring = internal_json::extract_version_for_type(metadata.other, "compressed_sparse_matrix");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:22:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp: In function ‘void takane::summarized_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp:45:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
45 | const auto& semap = internal_json::extract_typed_object_from_metadata(metadata.other, "summarized_experiment");
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp:45:74: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"summarized_experiment"), std::allocator<char>()))’
45 | const auto& semap = internal_json::extract_typed_object_from_metadata(metadata.other, "summarized_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp:47:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
47 | const std::string& vstring = internal_json::extract_string_from_typed_object(semap, "version", "summarized_experiment");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp:47:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & semap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"summarized_experiment"), std::allocator<char>()))’
47 | const std::string& vstring = internal_json::extract_string_from_typed_object(semap, "version", "summarized_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp: In function ‘size_t takane::summarized_experiment::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp:122:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
122 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp:122:54: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_object(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"summarized_experiment"), std::allocator<char>()))’
122 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp: In function ‘std::vector<long unsigned int> takane::summarized_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp:135:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
135 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/summarized_experiment.hpp:135:54: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_object(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"summarized_experiment"), std::allocator<char>()))’
135 | const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:23:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/ranged_summarized_experiment.hpp: In function ‘void takane::ranged_summarized_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/ranged_summarized_experiment.hpp:44:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
44 | const auto& rsemap = internal_json::extract_typed_object_from_metadata(metadata.other, "ranged_summarized_experiment");
| ^~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/ranged_summarized_experiment.hpp:44:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"ranged_summarized_experiment"), std::allocator<char>()))’
44 | const auto& rsemap = internal_json::extract_typed_object_from_metadata(metadata.other, "ranged_summarized_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/ranged_summarized_experiment.hpp:46:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
46 | const std::string& vstring = internal_json::extract_string_from_typed_object(rsemap, "version", "ranged_summarized_experiment");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/ranged_summarized_experiment.hpp:46:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & rsemap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"ranged_summarized_experiment"), std::allocator<char>()))’
46 | const std::string& vstring = internal_json::extract_string_from_typed_object(rsemap, "version", "ranged_summarized_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:24:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/single_cell_experiment.hpp: In function ‘void takane::single_cell_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/single_cell_experiment.hpp:49:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
49 | const auto& scemap = internal_json::extract_typed_object_from_metadata(metadata.other, "single_cell_experiment");
| ^~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/single_cell_experiment.hpp:49:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"single_cell_experiment"), std::allocator<char>()))’
49 | const auto& scemap = internal_json::extract_typed_object_from_metadata(metadata.other, "single_cell_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/single_cell_experiment.hpp:51:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
51 | const std::string& vstring = internal_json::extract_string_from_typed_object(scemap, "version", "single_cell_experiment");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/single_cell_experiment.hpp:51:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & scemap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"single_cell_experiment"), std::allocator<char>()))’
51 | const std::string& vstring = internal_json::extract_string_from_typed_object(scemap, "version", "single_cell_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:25:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/spatial_experiment.hpp: In function ‘void takane::spatial_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/spatial_experiment.hpp:237:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
237 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "spatial_experiment");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/spatial_experiment.hpp:237:73: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"spatial_experiment"), std::allocator<char>()))’
237 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "spatial_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:26:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/multi_sample_dataset.hpp: In function ‘void takane::multi_sample_dataset::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/multi_sample_dataset.hpp:42:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
42 | const auto& dmap = internal_json::extract_typed_object_from_metadata(metadata.other, "multi_sample_dataset");
| ^~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/multi_sample_dataset.hpp:42:73: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"multi_sample_dataset"), std::allocator<char>()))’
42 | const auto& dmap = internal_json::extract_typed_object_from_metadata(metadata.other, "multi_sample_dataset");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/multi_sample_dataset.hpp:44:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
44 | const std::string& vstring = internal_json::extract_string_from_typed_object(dmap, "version", "multi_sample_dataset");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/multi_sample_dataset.hpp:44:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & dmap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"multi_sample_dataset"), std::allocator<char>()))’
44 | const std::string& vstring = internal_json::extract_string_from_typed_object(dmap, "version", "multi_sample_dataset");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:27:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp: In function ‘void takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp:215:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
215 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set");
| ^~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp:215:72: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"sequence_string_set"), std::allocator<char>()))’
215 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp:216:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
216 | const auto& vstring = internal_json::extract_string_from_typed_object(obj, "version", "sequence_string_set");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp:216:74: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & obj), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"sequence_string_set"), std::allocator<char>()))’
216 | const auto& vstring = internal_json::extract_string_from_typed_object(obj, "version", "sequence_string_set");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp:245:28: warning: possibly dangling reference to a temporary [-Wdangling-reference]
245 | const std::string& stype = internal_json::extract_string(obj, "sequence_type", [&](std::exception& e) -> void {
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp:245:65: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string<takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)> >((* & obj), std::__cxx11::basic_string<char>(((const char*)"sequence_type"), std::allocator<char>()), (<lambda closure object>takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)>(), takane::sequence_string_set::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)>()))’
245 | const std::string& stype = internal_json::extract_string(obj, "sequence_type", [&](std::exception& e) -> void {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
246 | throw std::runtime_error("failed to extract 'sequence_string_set.sequence_type' from the object metadata; " + std::string(e.what()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
247 | });
| ~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp: In function ‘size_t takane::sequence_string_set::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp:362:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
362 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set");
| ^~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/sequence_string_set.hpp:362:72: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"sequence_string_set"), std::allocator<char>()))’
362 | const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:28:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bam_file.hpp: In function ‘void takane::bam_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bam_file.hpp:34:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bam_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bam_file.hpp:34:73: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"bam_file"), std::allocator<char>()))’
34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bam_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:29:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bcf_file.hpp: In function ‘void takane::bcf_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bcf_file.hpp:34:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bcf_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bcf_file.hpp:34:73: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"bcf_file"), std::allocator<char>()))’
34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bcf_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:30:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bigwig_file.hpp: In function ‘void takane::bigwig_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bigwig_file.hpp:34:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bigwig_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bigwig_file.hpp:34:73: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"bigwig_file"), std::allocator<char>()))’
34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bigwig_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:31:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bigbed_file.hpp: In function ‘void takane::bigbed_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bigbed_file.hpp:34:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bigbed_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bigbed_file.hpp:34:73: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"bigbed_file"), std::allocator<char>()))’
34 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bigbed_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:32:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fasta_file.hpp: In function ‘void takane::fasta_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fasta_file.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
33 | const auto& famap = internal_json::extract_typed_object_from_metadata(metadata.other, "fasta_file");
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fasta_file.hpp:33:74: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"fasta_file"), std::allocator<char>()))’
33 | const auto& famap = internal_json::extract_typed_object_from_metadata(metadata.other, "fasta_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fasta_file.hpp:35:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
35 | const std::string& vstring = internal_json::extract_string_from_typed_object(famap, "version", "fasta_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fasta_file.hpp:35:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & famap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"fasta_file"), std::allocator<char>()))’
35 | const std::string& vstring = internal_json::extract_string_from_typed_object(famap, "version", "fasta_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:33:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fastq_file.hpp: In function ‘void takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fastq_file.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
33 | const auto& fqmap = internal_json::extract_typed_object_from_metadata(metadata.other, "fastq_file");
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fastq_file.hpp:33:74: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"fastq_file"), std::allocator<char>()))’
33 | const auto& fqmap = internal_json::extract_typed_object_from_metadata(metadata.other, "fastq_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fastq_file.hpp:35:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
35 | const std::string& vstring = internal_json::extract_string_from_typed_object(fqmap, "version", "fastq_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fastq_file.hpp:35:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & fqmap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"fastq_file"), std::allocator<char>()))’
35 | const std::string& vstring = internal_json::extract_string_from_typed_object(fqmap, "version", "fastq_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fastq_file.hpp:45:28: warning: possibly dangling reference to a temporary [-Wdangling-reference]
45 | const std::string& qtype = internal_json::extract_string(fqmap, "quality_type", [&](std::exception& e) -> void {
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/fastq_file.hpp:45:65: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string<takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)> >((* & fqmap), std::__cxx11::basic_string<char>(((const char*)"quality_type"), std::allocator<char>()), (<lambda closure object>takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)>(), takane::fastq_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)::<lambda(std::exception&)>()))’
45 | const std::string& qtype = internal_json::extract_string(fqmap, "quality_type", [&](std::exception& e) -> void {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
46 | throw std::runtime_error("failed to extract 'fastq_file.quality_type' from the object metadata; " + std::string(e.what()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
47 | });
| ~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:34:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bed_file.hpp: In function ‘void takane::bed_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bed_file.hpp:34:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
34 | const auto& bedmap = internal_json::extract_typed_object_from_metadata(metadata.other, "bed_file");
| ^~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bed_file.hpp:34:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"bed_file"), std::allocator<char>()))’
34 | const auto& bedmap = internal_json::extract_typed_object_from_metadata(metadata.other, "bed_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bed_file.hpp:36:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
36 | const std::string& vstring = internal_json::extract_string_from_typed_object(bedmap, "version", "bed_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/bed_file.hpp:36:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & bedmap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"bed_file"), std::allocator<char>()))’
36 | const std::string& vstring = internal_json::extract_string_from_typed_object(bedmap, "version", "bed_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:35:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gmt_file.hpp: In function ‘void takane::gmt_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gmt_file.hpp:33:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
33 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "gmt_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gmt_file.hpp:33:73: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_version_for_type(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"gmt_file"), std::allocator<char>()))’
33 | const std::string& vstring = internal_json::extract_version_for_type(metadata.other, "gmt_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:36:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gff_file.hpp: In function ‘void takane::gff_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gff_file.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
33 | const auto& gffmap = internal_json::extract_typed_object_from_metadata(metadata.other, "gff_file");
| ^~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gff_file.hpp:33:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"gff_file"), std::allocator<char>()))’
33 | const auto& gffmap = internal_json::extract_typed_object_from_metadata(metadata.other, "gff_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gff_file.hpp:35:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
35 | const std::string& vstring = internal_json::extract_string_from_typed_object(gffmap, "version", "gff_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gff_file.hpp:35:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & gffmap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"gff_file"), std::allocator<char>()))’
35 | const std::string& vstring = internal_json::extract_string_from_typed_object(gffmap, "version", "gff_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gff_file.hpp:43:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
43 | const std::string& fstring = internal_json::extract_string_from_typed_object(gffmap, "format", "gff_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/gff_file.hpp:43:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & gffmap), std::__cxx11::basic_string<char>(((const char*)"format"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"gff_file"), std::allocator<char>()))’
43 | const std::string& fstring = internal_json::extract_string_from_typed_object(gffmap, "format", "gff_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:37:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/rds_file.hpp: In function ‘void takane::rds_file::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/rds_file.hpp:33:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
33 | const auto& rdsmap = internal_json::extract_typed_object_from_metadata(metadata.other, "rds_file");
| ^~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/rds_file.hpp:33:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"rds_file"), std::allocator<char>()))’
33 | const auto& rdsmap = internal_json::extract_typed_object_from_metadata(metadata.other, "rds_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/rds_file.hpp:35:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
35 | const std::string& vstring = internal_json::extract_string_from_typed_object(rdsmap, "version", "rds_file");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/rds_file.hpp:35:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & rdsmap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"rds_file"), std::allocator<char>()))’
35 | const std::string& vstring = internal_json::extract_string_from_typed_object(rdsmap, "version", "rds_file");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:40:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp: In function ‘void takane::vcf_experiment::validate(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp:188:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
188 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
| ^~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp:188:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"vcf_experiment"), std::allocator<char>()))’
188 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp:190:24: warning: possibly dangling reference to a temporary [-Wdangling-reference]
190 | const std::string& vstring = internal_json::extract_string_from_typed_object(vcfmap, "version", "vcf_experiment");
| ^~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp:190:81: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_string_from_typed_object((* & vcfmap), std::__cxx11::basic_string<char>(((const char*)"version"), std::allocator<char>()), std::__cxx11::basic_string<char>(((const char*)"vcf_experiment"), std::allocator<char>()))’
190 | const std::string& vstring = internal_json::extract_string_from_typed_object(vcfmap, "version", "vcf_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp: In function ‘size_t takane::vcf_experiment::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp:239:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
239 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
| ^~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp:239:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"vcf_experiment"), std::allocator<char>()))’
239 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp: In function ‘std::vector<long unsigned int> takane::vcf_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp:251:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
251 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
| ^~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/vcf_experiment.hpp:251:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"vcf_experiment"), std::allocator<char>()))’
251 | const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/uzuki2.hpp:17,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/simple_list.hpp:8:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::json::parse_object(const millijson::Base*, Externals&, const std::string&, const uzuki2::Version&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:450:44: required from ‘uzuki2::ParsedList uzuki2::json::parse(byteme::Reader&, Externals, Options) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals]’
450 | auto output = parse_object<Provisioner>(contents.get(), etrack, "", version);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:578:28: required from here
578 | parse<DummyProvisioner>(reader, std::move(ext), std::move(options));
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:236:21: warning: possibly dangling reference to a temporary [-Wdangling-reference]
236 | const auto& lvals = extract_array(map, "levels", path);
| ^~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:236:42: note: the temporary was destroyed at the end of the full expression ‘uzuki2::json::extract_array((* & map), std::__cxx11::basic_string<char>(((const char*)"levels"), std::allocator<char>()), (* & path))’
236 | const auto& lvals = extract_array(map, "levels", path);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:367:21: warning: possibly dangling reference to a temporary [-Wdangling-reference]
367 | const auto& vals = extract_array(map, "values", path);
| ^~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/uzuki2/parse_json.hpp:367:41: note: the temporary was destroyed at the end of the full expression ‘uzuki2::json::extract_array((* & map), std::__cxx11::basic_string<char>(((const char*)"values"), std::allocator<char>()), (* & path))’
367 | const auto& vals = extract_array(map, "values", path);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/validate.hpp:13,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/chihaya.hpp:10,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/utils_public.hpp:13,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/takane/_validate.hpp:9:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = int]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized]
51 | if (x > start && i <= previous) {
| ~~^~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here
45 | Index_ previous;
| ^~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = long unsigned int]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized]
51 | if (x > start && i <= previous) {
| ~~^~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here
45 | Index_ previous;
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-alabaster.base/00new/alabaster.base/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (alabaster.base)
alabaster.base.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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Platform: aarch64-unknown-linux-gnu
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> library(testthat)
> library(alabaster.base)
> test_check("alabaster.base")
[ FAIL 50 | WARN 0 | SKIP 0 | PASS 313 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-DataFrame.R:24:9'): DFs handle their column types correctly ────
Error in `value[[3L]](cond)`: failed to stage levels of factor column 'blah'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(...) at test-DataFrame.R:24:9
2. └─alabaster.base::stageObject(...)
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-DataFrame.R:100:5'): staging of weird objects within DFs works correctly ──
Error in `value[[3L]](cond)`: failed to stage column 'X'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(input, tmp, path = "WHEE") at test-DataFrame.R:100:5
2. └─alabaster.base::stageObject(input, tmp, path = "WHEE")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-DataFrame.R:154:5'): staging of uncompressed Gzip works correctly ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(meta2, tmp) at test-DataFrame.R:154:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-DataFrame.R:249:5'): handling of NAs works correctly ───────────
Error in `value[[3L]](cond)`: failed to stage levels of factor column 'c'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, path = "WHEE") at test-DataFrame.R:249:5
2. └─alabaster.base::stageObject(df, tmp, path = "WHEE")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-DataFrame.R:479:5'): stageObject works with extra mcols ────────
Error in `value[[3L]](cond)`: failed to stage 'mcols(<DFrame>)'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "thing") at test-DataFrame.R:479:5
2. └─alabaster.base::stageObject(df, tmp, "thing")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base::.processMcols(x, dir, path, mcols.name)
5. └─alabaster.base::processMcols(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
── Error ('test-DataFrame.R:524:5'): DF staging preserves odd colnames ─────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(meta, tmp) at test-DataFrame.R:524:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-DataFrame.R:638:5'): staging of arrays within DFs works correctly ──
Error in `value[[3L]](cond)`: failed to stage column 'Y'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(input, tmp, path = "WHEE") at test-DataFrame.R:638:5
2. └─alabaster.base::stageObject(input, tmp, path = "WHEE")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-DataFrame.R:664:5'): staging of arrays continues to work with character matrices ──
Error in `value[[3L]](cond)`: failed to stage column 'Y'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(input, tmp, path = "WHEE") at test-DataFrame.R:664:5
2. └─alabaster.base::stageObject(input, tmp, path = "WHEE")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-DataFrameFactor.R:12:5'): staging and loading of data frame factors work as expected ──
Error in `value[[3L]](cond)`: failed to stage underlying DataFrame in a DataFrameFactor
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(X, tmp, path = "test1") at test-DataFrameFactor.R:12:5
2. └─alabaster.base::stageObject(X, tmp, path = "test1")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
── Error ('test-acquireMetadata.R:11:5'): acquireMetadata works correctly in simple cases ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-acquireMetadata.R:11:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-acquireMetadata.R:27:5'): acquireMetadata correctly redirects to other things ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-acquireMetadata.R:27:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-factor.R:9:5'): factors work correctly without names ───────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(input, tmp, path = "foo") at test-factor.R:9:5
2. ├─alabaster.base::stageObject(input, tmp, path = "foo")
3. │ └─alabaster.base::writeMetadata(level_meta, dir)
4. │ └─jsonvalidate::json_validate(...)
5. │ └─jsonvalidate::json_validator(...)
6. │ └─jsonvalidate:::jsonvalidate_js()
7. └─base::loadNamespace(x)
8. └─base::library.dynam(lib, package, package.lib)
9. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-factor.R:55:5'): factors work correctly with names ─────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(vals, tmp, path = "bar") at test-factor.R:55:5
2. ├─alabaster.base::stageObject(vals, tmp, path = "bar")
3. │ └─alabaster.base::writeMetadata(level_meta, dir)
4. │ └─jsonvalidate::json_validate(...)
5. │ └─jsonvalidate::json_validator(...)
6. │ └─jsonvalidate:::jsonvalidate_js()
7. └─base::loadNamespace(x)
8. └─base::library.dynam(lib, package, package.lib)
9. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:23:5'): lists handle complex types correctly ────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:23:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:69:5'): lists work in HDF5 mode ─────────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:69:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:123:5'): names are properly supported ───────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:123:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:159:5'): data.frames cause dispatch to external objects ──
Error in `value[[3L]](cond)`: failed to stage list element 'X'
- failed to stage 'DFrame' entry inside a list
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff") at test-list.R:159:5
2. └─alabaster.base::stageObject(vals, tmp, path = "stuff")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.transform_list_json(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-list.R:209:5'): unnamed lists are properly supported ───────────
Error in `value[[3L]](cond)`: failed to stage list element 4
- failed to stage list element 2
- failed to stage list element 1
- failed to stage 'DFrame' entry inside a list
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff") at test-list.R:209:5
2. └─alabaster.base::stageObject(vals, tmp, path = "stuff")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.transform_list_json(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-list.R:260:5'): external references work correctly ─────────────
Error in `value[[3L]](cond)`: failed to stage list element 'B'
- failed to stage list element 'C'
- failed to stage 'DFrame' entry inside a list
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff") at test-list.R:260:5
2. └─alabaster.base::stageObject(vals, tmp, path = "stuff")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.transform_list_json(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-list.R:323:5'): we handle lists with NAs ───────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:323:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:445:5'): loaders work correctly from HDF5 with non-default placeholders ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:445:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:470:5'): we handle the various float specials ───────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:470:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:504:5'): we handle lists with NULLs ─────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:504:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:560:5'): we handle lists with times ─────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:560:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:658:5'): lists work correctly in legacy mode (JSON) ─────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:658:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-list.R:671:5'): lists work correctly in legacy mode (HDF5) ─────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(info, tmp) at test-list.R:671:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-listDirectory.R:10:1'): (code run outside of `test_that()`) ────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(meta, tmp) at test-listDirectory.R:10:1
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-removeObject.R:25:5'): removeObject works correctly for direct calls ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base (local) populate() at test-removeObject.R:25:5
2. │ └─alabaster.base::writeMetadata(meta, tmp) at test-removeObject.R:13:5
3. │ └─jsonvalidate::json_validate(...)
4. │ └─jsonvalidate::json_validator(...)
5. │ └─jsonvalidate:::jsonvalidate_js()
6. └─base::loadNamespace(x)
7. └─base::library.dynam(lib, package, package.lib)
8. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-removeObject.R:39:5'): removeObject works correctly for redirected calls ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base (local) populate() at test-removeObject.R:39:5
2. │ └─alabaster.base::writeMetadata(meta, tmp) at test-removeObject.R:13:5
3. │ └─jsonvalidate::json_validate(...)
4. │ └─jsonvalidate::json_validator(...)
5. │ └─jsonvalidate:::jsonvalidate_js()
6. └─base::loadNamespace(x)
7. └─base::library.dynam(lib, package, package.lib)
8. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-removeObject.R:53:5'): moveObject works correctly for children ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base (local) populate() at test-removeObject.R:53:5
2. │ └─alabaster.base::writeMetadata(meta, tmp) at test-removeObject.R:13:5
3. │ └─jsonvalidate::json_validate(...)
4. │ └─jsonvalidate::json_validator(...)
5. │ └─jsonvalidate:::jsonvalidate_js()
6. └─base::loadNamespace(x)
7. └─base::library.dynam(lib, package, package.lib)
8. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-removeObject.R:69:5'): moveObject works correctly for direct calls ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base (local) populate() at test-removeObject.R:69:5
2. │ └─alabaster.base::writeMetadata(meta, tmp) at test-removeObject.R:13:5
3. │ └─jsonvalidate::json_validate(...)
4. │ └─jsonvalidate::json_validator(...)
5. │ └─jsonvalidate:::jsonvalidate_js()
6. └─base::loadNamespace(x)
7. └─base::library.dynam(lib, package, package.lib)
8. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-removeObject.R:90:5'): moveObject works correctly for redirected calls ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base (local) populate() at test-removeObject.R:90:5
2. │ └─alabaster.base::writeMetadata(meta, tmp) at test-removeObject.R:13:5
3. │ └─jsonvalidate::json_validate(...)
4. │ └─jsonvalidate::json_validator(...)
5. │ └─jsonvalidate:::jsonvalidate_js()
6. └─base::loadNamespace(x)
7. └─base::library.dynam(lib, package, package.lib)
8. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-stageANY.R:68:5'): stageObject fails for saving non-child objects in other object's subdirectories ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(meta, tmp) at test-stageANY.R:68:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-validateDirectory.R:17:5'): validateDirectory works as expected ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(stageObject(df, tmp, "foo"), tmp) at test-validateDirectory.R:17:5
2. │ └─alabaster.base:::.strip_null_from_list(meta)
3. │ └─base::logical(length(x))
4. ├─alabaster.base::stageObject(df, tmp, "foo")
5. └─alabaster.base::stageObject(df, tmp, "foo")
6. └─alabaster.base (local) .local(x, dir, path, child, ...)
7. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:41:5'): validateDirectory throws with invalid metadata ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:41:5
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:54:5'): validateDirectory throws with invalid objects ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:54:5
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:80:9'): validateDirectory throws with inconsistent paths ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(stageObject(df, tmp, "foo"), tmp) at test-validateDirectory.R:80:9
2. │ └─alabaster.base:::.strip_null_from_list(meta)
3. │ └─base::logical(length(x))
4. ├─alabaster.base::stageObject(df, tmp, "foo")
5. └─alabaster.base::stageObject(df, tmp, "foo")
6. └─alabaster.base (local) .local(x, dir, path, child, ...)
7. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:103:9'): validateDirectory throws with non-nested children ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:103:9
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:138:5'): validateDirectory throws with non-child references ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:138:5
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:152:5'): validateDirectory throws with multiple child references ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:152:5
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:163:5'): validateDirectory throws with missing child object ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:163:5
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:174:5'): validateDirectory throws with extra child object ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:174:5
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:185:5'): validateDirectory throws with nested non-child object ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:185:5
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:201:5'): validateDirectory throws with random extra objects ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:201:5
2. └─alabaster.base::stageObject(df, tmp, "foo")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-validateDirectory.R:214:9'): validateDirectory handles redirects correctly ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(stageObject(df, tmp, "foo"), tmp) at test-validateDirectory.R:214:9
2. │ └─alabaster.base:::.strip_null_from_list(meta)
3. │ └─base::logical(length(x))
4. ├─alabaster.base::stageObject(df, tmp, "foo")
5. └─alabaster.base::stageObject(df, tmp, "foo")
6. └─alabaster.base (local) .local(x, dir, path, child, ...)
7. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
── Error ('test-vector.R:11:5'): vectors work correctly without names ──────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(meta, tmp) at test-vector.R:11:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-vector.R:79:5'): vectors work correctly with names ─────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::writeMetadata(meta, tmp) at test-vector.R:79:5
2. │ └─jsonvalidate::json_validate(...)
3. │ └─jsonvalidate::json_validator(...)
4. │ └─jsonvalidate:::jsonvalidate_js()
5. └─base::loadNamespace(x)
6. └─base::library.dynam(lib, package, package.lib)
7. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-writeMetadata.R:22:5'): writing saves the MD5 sums ─────────────
Error in `value[[3L]](cond)`: failed to stage levels of factor column 'blah'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "rnaseq") at test-writeMetadata.R:22:5
2. └─alabaster.base::stageObject(df, tmp, "rnaseq")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-writeMetadata.R:40:5'): writing strips the dots ────────────────
Error in `value[[3L]](cond)`: failed to stage levels of factor column 'blah'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "./whee") at test-writeMetadata.R:40:5
2. └─alabaster.base::stageObject(df, tmp, "./whee")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
── Error ('test-writeMetadata.R:57:5'): writing respects the package attribute ──
Error in `value[[3L]](cond)`: failed to stage levels of factor column 'blah'
- unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─alabaster.base::stageObject(df, tmp, "./whee") at test-writeMetadata.R:57:5
2. └─alabaster.base::stageObject(df, tmp, "./whee")
3. └─alabaster.base (local) .local(x, dir, path, child, ...)
4. └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
[ FAIL 50 | WARN 0 | SKIP 0 | PASS 313 ]
Error: Test failures
Execution halted
alabaster.base.Rcheck/alabaster.base-Ex.timings
| name | user | system | elapsed | |
| Rfc3339 | 0.003 | 0.000 | 0.004 | |
| absolutizePath | 0.000 | 0.000 | 0.001 | |