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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellxgenedp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellxgenedp_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/cellxgenedp.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellxgenedp/DESCRIPTION’ ... OK
* this is package ‘cellxgenedp’ version ‘1.0.1’
* 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 ‘cellxgenedp’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ... NOTE
.cxg_sce_validate_software_requirements: no visible global function
  definition for ‘installed.packages’
Undefined global functions or variables:
  installed.packages
Consider adding
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘cellxgenedp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FACETS
> ### Title: Facets available for querying cellxgene data
> ### Aliases: FACETS facets facets_filter
> ### Keywords: datasets
> 
> ### ** Examples
> 
> f <- facets()
Error in `group_by()`:
! Must group by variables found in `.data`.
Column `label` is not found.
Column `ontology_term_id` is not found.
Backtrace:
     ▆
  1. └─cellxgenedp::facets()
  2.   └─base::lapply(facets, .facet, cellxgene_db = cellxgene_db)
  3.     └─cellxgenedp (local) FUN(X[[i]], ...)
  4.       ├─dplyr::bind_cols(...)
  5.       │ └─rlang::list2(...)
  6.       ├─dplyr::ungroup(...)
  7.       ├─dplyr::count(...)
  8.       ├─dplyr::group_by(bind_rows(projection), .data$label, .data$ontology_term_id)
  9.       └─dplyr:::group_by.data.frame(bind_rows(projection), .data$label, .data$ontology_term_id)
 10.         └─dplyr::group_by_prepare(.data, ..., .add = .add, caller_env = caller_env())
 11.           └─rlang::abort(bullets, call = error_call)
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:
    1. └─cellxgenedp::facets() at test-facets.R:5:4
    2.   └─base::lapply(facets, .facet, cellxgene_db = cellxgene_db)
    3.     └─cellxgenedp (local) FUN(X[[i]], ...)
    4.       ├─dplyr::bind_cols(...)
    5.       │ └─rlang::list2(...)
    6.       ├─dplyr::ungroup(...)
    7.       ├─dplyr::count(...)
    8.       ├─dplyr::group_by(bind_rows(projection), .data$label, .data$ontology_term_id)
    9.       └─dplyr:::group_by.data.frame(bind_rows(projection), .data$label, .data$ontology_term_id)
   10.         └─dplyr::group_by_prepare(.data, ..., .add = .add, caller_env = caller_env())
   11.           └─rlang::abort(bullets, call = error_call)
  
  [ FAIL 3 | WARN 0 | SKIP 3 | PASS 36 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/cellxgenedp.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cellxgenedp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘cellxgenedp’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp11.cpp -o cpp11.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c jsoncons_jmespath.cpp -o jsoncons_jmespath.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cellxgenedp.so cpp11.o jsoncons_jmespath.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-cellxgenedp/00new/cellxgenedp/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 (cellxgenedp)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(cellxgenedp)
> 
> test_check("cellxgenedp")
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 36 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)
• files_download() not tested due to mockery limitation (1)

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-datasets.R:21'): datasets() works ────────────────────────────
all(column_names %in% names(datasets)) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Error ('test-datasets.R:22'): datasets() works ──────────────────────────────
<vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
Error in `datasets[column_names]`: Can't subset columns that don't exist.
x Columns `ethnicity` and `x_normalization` don't exist.
Backtrace:
     ▆
  1. ├─base::vapply(datasets[column_names], class, character(1)) at test-datasets.R:22:4
  2. ├─datasets[column_names]
  3. └─tibble:::`[.tbl_df`(datasets, column_names)
  4.   └─tibble:::vectbl_as_col_location(...)
  5.     ├─tibble:::subclass_col_index_errors(...)
  6.     │ └─base::withCallingHandlers(...)
  7.     └─vctrs::vec_as_location(j, n, names, call = call)
  8.       └─vctrs (local) `<fn>`()
  9.         └─vctrs:::stop_subscript_oob(...)
 10.           └─vctrs:::stop_subscript(...)
 11.             └─rlang::abort(...)
── Error ('test-facets.R:5'): facets() works ───────────────────────────────────
Error in `group_by(bind_rows(projection), .data$label, .data$ontology_term_id)`: Must group by variables found in `.data`.
Column `label` is not found.
Column `ontology_term_id` is not found.
Backtrace:
     ▆
  1. └─cellxgenedp::facets() at test-facets.R:5:4
  2.   └─base::lapply(facets, .facet, cellxgene_db = cellxgene_db)
  3.     └─cellxgenedp (local) FUN(X[[i]], ...)
  4.       ├─dplyr::bind_cols(...)
  5.       │ └─rlang::list2(...)
  6.       ├─dplyr::ungroup(...)
  7.       ├─dplyr::count(...)
  8.       ├─dplyr::group_by(bind_rows(projection), .data$label, .data$ontology_term_id)
  9.       └─dplyr:::group_by.data.frame(bind_rows(projection), .data$label, .data$ontology_term_id)
 10.         └─dplyr::group_by_prepare(.data, ..., .add = .add, caller_env = caller_env())
 11.           └─rlang::abort(bullets, call = error_call)

[ FAIL 3 | WARN 0 | SKIP 3 | PASS 36 ]
Error: Test failures
Execution halted