Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* 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_0.99.6.tar.gz’

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 BiocCheckGitClone('tidySpatialExperiment')

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─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3130/7ff283cb7a703cdd732624529e7361d34c24f024/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')




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 R CMD CHECK

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3130/7ff283cb7a703cdd732624529e7361d34c24f024/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 ‘0.99.6’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘tidySingleCellExperiment::plot_ly’ by ‘ttservice::plot_ly’ when loading ‘tidySpatialExperiment’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3130/7ff283cb7a703cdd732624529e7361d34c24f024/tidySpatialExperiment.Rcheck/00install.out’ for details.
* 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 ... [10s/10s] 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
Package in Depends field not imported from: ‘tidySummarizedExperiment’
  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 ... [29s/29s] NOTE
join_features,SpatialExperiment: no visible binding for global variable
  ‘index’
Undefined global functions or variables:
  index
* checking Rd files ... [1s/1s] OK
* 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 ... WARNING
Error: package or namespace load failed for ‘tidySpatialExperiment’ in loadNamespace(package, lib.loc):
 there is no package called ‘tidySpatialExperiment’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TR
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘tidySpatialExperiment’
Calls: <Anonymous> -> find.package
Execution halted
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in find.package(package, lib.loc) : 
  there is no package called ‘tidySpatialExperiment’
Calls: <Anonymous> -> find.package
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘tidySpatialExperiment’
Calls: <Anonymous> -> find.package
Execution halted
* checking for unstated dependencies in examples ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘tidySpatialExperiment’
Execution halted
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [0s/0s]
 [1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidySpatialExperiment)
  Error in library(tidySpatialExperiment) : 
    there is no package called 'tidySpatialExperiment'
  Execution halted
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘tidySpatialExperiment’
Execution halted
* 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: 1 ERROR, 5 WARNINGs, 3 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3130/7ff283cb7a703cdd732624529e7361d34c24f024/tidySpatialExperiment.Rcheck/00check.log’
for details.





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 BiocCheck('tidySpatialExperiment_0.99.6.tar.gz')

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─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: tidySpatialExperiment
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmpP8QlC2/file2522ef3cacf2aa/tidySpatialExperiment
─ installDir: /tmp/RtmpP8QlC2/file2522ef7134ee09
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3130/7ff283cb7a703cdd732624529e7361d34c24f024/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:
      Transcription, Normalization, Clustering, ImmunoOncology,
      DifferentialExpression, QualityControl, 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...
Warning: replacing previous import ‘tidySingleCellExperiment::plot_ly’ by ‘ttservice::plot_ly’ when loading ‘tidySpatialExperiment’
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* 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...
* 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: replacing previous import ‘tidySingleCellExperiment::plot_ly’ by ‘ttservice::plot_ly’ when loading ‘tidySpatialExperiment’
* 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; 396 lines (8%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 371 lines
      (8%) 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 | 0 WARNINGS | 5 NOTES

See the tidySpatialExperiment.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.