===============================
BiocCheckGitClone('tidySpatialExperiment')
===============================
─ BiocCheckVersion: 1.37.14
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3130/tidySpatialExperiment_20230914145710/tidySpatialExperiment
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3130/tidySpatialExperiment_20230914145710/tidySpatialExperiment.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidySpatialExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidySpatialExperiment’ version ‘0.99.0’
* 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 ‘tidySpatialExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘ellipsis’ ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘SpatialExperiment’ ‘tidySingleCellExperiment’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [18s/19s] NOTE
aggregate_cells: no visible binding for global variable ‘feature’
as_tibble.SpatialExperiment: no visible global function definition for
‘spatialCoords’
get_abundance_sc_long : <anonymous>: no visible binding for global
variable ‘.feature’
get_abundance_sc_long : <anonymous>: no visible global function
definition for ‘full_join’
get_abundance_sc_wide: no visible binding for global variable ‘index’
get_special_datasets: no visible global function definition for
‘spatialCoords’
unnest_single_cell_experiment: no visible binding for global variable
‘.’
unnest_single_cell_experiment: no visible global function definition
for ‘is’
cbind,SpatialExperiment: no visible binding for global variable
‘callNextMethod’
cbind,SpatialExperiment: no visible global function definition for
‘imgData’
cbind,SpatialExperiment: no visible binding for global variable
‘imgData’
cbind,SpatialExperiment: no visible global function definition for
‘int_metadata’
cbind,SpatialExperiment: no visible global function definition for
‘int_metadata<-’
join_features,SpatialExperiment: no visible binding for global variable
‘index’
show,SpatialExperiment: no visible global function definition for
‘getMethod’
Undefined global functions or variables:
. .feature callNextMethod feature full_join getMethod imgData index
int_metadata int_metadata<- is spatialCoords
Consider adding
importFrom("methods", "callNextMethod", "getMethod", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [1s/1s] NOTE
prepare_Rd: group_by.Rd:70-72: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/61s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [15s/15s]
[15s/16s] OK
* 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 ... [7s/7s] OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3130/tidySpatialExperiment_20230914145710/tidySpatialExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('tidySpatialExperiment_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.14
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpGfdreR/file8f395173b549/tidySpatialExperiment
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpGfdreR/file8f39abcfd57
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3130/tidySpatialExperiment_20230914145710/tidySpatialExperiment.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Spatial, Transcriptomics, SingleCell, ImmunoOncology, DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import methods, ellipsis, pkgconfig in NAMESPACE as well
as DESCRIPTION.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of tidySpatialExperiment...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 416 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 427 lines
(9%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
2 ERRORS | 2 WARNINGS | 9 NOTES
See the tidySpatialExperiment.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
BiocCheckGitClone('tidySpatialExperiment')
===============================
─ BiocCheckVersion: 1.37.14
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3130/tidySpatialExperiment_20230914145710/tidySpatialExperiment
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3130/tidySpatialExperiment_20230914145710/tidySpatialExperiment.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidySpatialExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidySpatialExperiment’ version ‘0.99.0’
* 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 ‘tidySpatialExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘ellipsis’ ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘SpatialExperiment’ ‘tidySingleCellExperiment’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [26s/26s] NOTE
aggregate_cells: no visible binding for global variable ‘feature’
as_tibble.SpatialExperiment: no visible global function definition for
‘spatialCoords’
get_abundance_sc_long : <anonymous>: no visible binding for global
variable ‘.feature’
get_abundance_sc_long : <anonymous>: no visible global function
definition for ‘full_join’
get_abundance_sc_wide: no visible binding for global variable ‘index’
get_special_datasets: no visible global function definition for
‘spatialCoords’
unnest_single_cell_experiment: no visible binding for global variable
‘.’
unnest_single_cell_experiment: no visible global function definition
for ‘is’
cbind,SpatialExperiment: no visible binding for global variable
‘callNextMethod’
cbind,SpatialExperiment: no visible global function definition for
‘imgData’
cbind,SpatialExperiment: no visible binding for global variable
‘imgData’
cbind,SpatialExperiment: no visible global function definition for
‘int_metadata’
cbind,SpatialExperiment: no visible global function definition for
‘int_metadata<-’
join_features,SpatialExperiment: no visible binding for global variable
‘index’
show,SpatialExperiment: no visible global function definition for
‘getMethod’
Undefined global functions or variables:
. .feature callNextMethod feature full_join getMethod imgData index
int_metadata int_metadata<- is spatialCoords
Consider adding
importFrom("methods", "callNextMethod", "getMethod", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [1s/1s] NOTE
prepare_Rd: group_by.Rd:70-72: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] ERROR
Running examples in ‘tidySpatialExperiment-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aggregate_cells
> ### Title: Aggregate cells
> ### Aliases: aggregate_cells
>
> ### ** Examples
>
> example(read10xVisium)
rd10xV> dir <- system.file(
rd10xV+ file.path("extdata", "10xVisium"),
rd10xV+ package = "SpatialExperiment")
rd10xV> sample_ids <- c("section1", "section2")
rd10xV> samples <- file.path(dir, sample_ids, "outs")
rd10xV> list.files(samples[1])
[1] "raw_feature_bc_matrix" "spatial"
rd10xV> list.files(file.path(samples[1], "spatial"))
[1] "scalefactors_json.json" "tissue_lowres_image.png"
[3] "tissue_positions_list.csv"
rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
[1] "/home/biocbuild/bbs-3.18-bioc/R/site-library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"
rd10xV> (spe <- read10xVisium(samples, sample_ids,
rd10xV+ type = "sparse", data = "raw",
rd10xV+ images = "lowres", load = FALSE))
Warning in read10xVisium(samples, sample_ids, type = "sparse", data = "raw", :
DropletUtils package must be installed to use read10xVisium()
Error in loadNamespace(x) : there is no package called ‘DropletUtils’
Calls: example ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [9s/9s]
[9s/9s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
12. └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test-tidyr_methods.R:3:1'): (code run outside of `test_that()`) ─────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DropletUtils'
Backtrace:
▆
1. ├─utils::example(read10xVisium) at test-tidyr_methods.R:3:0
2. │ └─base::source(...)
3. │ ├─base::withVisible(eval(ei, envir))
4. │ └─base::eval(ei, envir)
5. │ └─base::eval(ei, envir)
6. ├─SpatialExperiment::read10xVisium(...) at tmp/RtmpsJNXSz/Rex7555349af4bbb:18:0
7. │ └─base::lapply(...)
8. │ └─SpatialExperiment (local) FUN(X[[i]], ...)
9. └─base::loadNamespace(x)
10. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11. └─base (local) withOneRestart(expr, restarts[[1L]])
12. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 0 ]
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 ... [4s/4s] OK
* DONE
Status: 2 ERRORs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3130/tidySpatialExperiment_20230914145710/tidySpatialExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('tidySpatialExperiment_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.14
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/RtmpuZMfRn/file758c47b39f51b/tidySpatialExperiment
─ installDir: /tmp/RtmpuZMfRn/file758c443ef7e12
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3130/tidySpatialExperiment_20230914145710/tidySpatialExperiment.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Spatial, Transcriptomics, SingleCell, ImmunoOncology, DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import methods, ellipsis, pkgconfig in NAMESPACE as well
as DESCRIPTION.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of tidySpatialExperiment...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 416 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 427 lines
(9%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
2 ERRORS | 2 WARNINGS | 9 NOTES
See the tidySpatialExperiment.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.