lconway Summary
[top]
| Package: tidySpatialExperiment |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tidySpatialExperiment |
| BuildTime: 1 minutes 39.80 seconds |
| CheckCommand: BiocCheckGitClone('tidySpatialExperiment') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3130/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/tidySpatialExperiment.install-out.txt tidySpatialExperiment_0.99.1.tar.gz && BiocCheck('tidySpatialExperiment_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 19.51 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh tidySpatialExperiment_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 19.09 seconds |
| PackageFileSize: 2499.14 KiB |
| BuildID:: tidySpatialExperiment_20230919053504 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: tidySpatialExperiment. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘tidySpatialExperiment/DESCRIPTION’ ... OK
* preparing ‘tidySpatialExperiment’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘tidySpatialExperiment_0.99.1.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('tidySpatialExperiment')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/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/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/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 ‘0.99.1’
* 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 ‘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 ... [5s/5s] 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
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.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [18s/18s] 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 ... [59s/59s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [14s/14s]
[14s/14s] 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 ... [6s/6s] OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/tidySpatialExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('tidySpatialExperiment_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpsvMyYy/filef5482b328351/tidySpatialExperiment
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpsvMyYy/filef54877b29602
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/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...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 7 NOTES
See the tidySpatialExperiment.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir tidySpatialExperiment_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘tidySpatialExperiment’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tidySpatialExperiment)
nebbiolo2 Summary
[top]
| Package: tidySpatialExperiment |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidySpatialExperiment |
| BuildTime: 2 minutes 40.75 seconds |
| CheckCommand: BiocCheckGitClone('tidySpatialExperiment') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3130/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/tidySpatialExperiment.install-out.txt tidySpatialExperiment_0.99.1.tar.gz && BiocCheck('tidySpatialExperiment_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 31.19 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2341.07 KiB |
| BuildID:: tidySpatialExperiment_20230919053504 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: tidySpatialExperiment. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘tidySpatialExperiment/DESCRIPTION’ ... OK
* preparing ‘tidySpatialExperiment’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘tidySpatialExperiment_0.99.1.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('tidySpatialExperiment')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/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/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/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 ‘0.99.1’
* 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 ‘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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
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.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [29s/29s] 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 ... [109s/109s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [25s/25s]
[25s/25s] 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 ... [5s/5s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/tidySpatialExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('tidySpatialExperiment_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/Rtmpx24ayn/file2565569e46cab/tidySpatialExperiment
─ installDir: /tmp/Rtmpx24ayn/file256556500d83ba
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3130/23f040541eae9be46730e92f8dee4e84f01b34d5/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...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 7 NOTES
See the tidySpatialExperiment.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]