Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* preparing ‘SpatialOmicsOverlay’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘SpatialOmicsOverlay_0.99.7.tar.gz’

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 BiocCheckGitClone('SpatialOmicsOverlay')

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─ BiocCheckVersion: 1.31.38
─ BiocVersion: 3.15
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.7
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2604/77fecfada2dc3ec132a7fca7b764dcddd8094c63/SpatialOmicsOverlay
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output 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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/2604/77fecfada2dc3ec132a7fca7b764dcddd8094c63/SpatialOmicsOverlay.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ version ‘0.99.7’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpatialOmicsOverlay’ can be installed ... [27s/27s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [27s/27s] NOTE
plotSpatialOverlay: no visible binding for global variable ‘xcoor’
plotSpatialOverlay: no visible binding for global variable ‘ycoor’
plotSpatialOverlay: no visible binding for global variable ‘sampleID’
plotSpatialOverlay: no visible binding for global variable ‘Target’
scaleBarPrinting: no visible binding for global variable ‘X’
scaleBarPrinting: no visible binding for global variable ‘Y’
Undefined global functions or variables:
  Target X Y sampleID xcoor ycoor
* checking Rd files ... [0s/0s] 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [115s/90s] ERROR
Running examples in ‘SpatialOmicsOverlay-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cropSamples
> ### Title: Crop to zoom in on given ROIs
> ### Aliases: cropSamples
> 
> ### ** Examples
> 
> 
> muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
+                                     package = "SpatialOmicsOverlay")))
> 
> image <- downloadMouseBrainImage()
> 
> # muBrain <- addImageOmeTiff(overlay = muBrain, 
> #                           ometiff = image, res = 8)
> 
> # samps <- sampNames(muBrain)
> 
> muBrainCrop <- suppressWarnings(cropSamples(overlay = muBrain, 
+                                             sampleIDs = samps, 
+                                             sampsOnly = TRUE))
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function '%in%': object 'samps' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [326s/301s]
 [326s/302s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  1 PNG      256    256 sRGB       FALSE        0 72x72  
  # A tibble: 1 x 7
    format width height colorspace matte filesize density
    <chr>  <int>  <int> <chr>      <lgl>    <int> <chr>  
  1 PNG      215    143 sRGB       FALSE        0 72x72  
  [ FAIL 1 | WARN 0 | SKIP 12 | PASS 414 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (12)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_all.R:16:9): mouse brain tiff can be downloaded ───────────────
  grepl("/.cache/R/SpatialOmicsOverlay/", tifFile) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 12 | PASS 414 ]
  Deleting unused snapshots:
  • all/cropsamples-all-rois.svg
  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, 4 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2604/77fecfada2dc3ec132a7fca7b764dcddd8094c63/SpatialOmicsOverlay.Rcheck/00check.log’
for details.





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 BiocCheck('SpatialOmicsOverlay_0.99.7.tar.gz')

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─ BiocCheckVersion: 1.31.38
─ BiocVersion: 3.15
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.7
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpwZwmLH/file42adea7fa3/SpatialOmicsOverlay
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpwZwmLH/file42a1ec3b0dd
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2604/77fecfada2dc3ec132a7fca7b764dcddd8094c63/SpatialOmicsOverlay.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 6 object(s) are initialized. Maybe
      they are part of a data set loaded with data(), or perhaps part
      of an object referenced in with() or within().
* 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...
    * NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* 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...
* 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 SpatialOmicsOverlay...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
      times)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.There are 16
      functions > 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      addImageFile.Rd, SpatialOverlay-class.Rd,
  SpatialPosition-class.Rd
* Checking package NEWS...
* 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; 275 lines (5%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 763 lines
      (13%) are not.
    See http://bioconductor.org/developers/how-to/coding-style/
    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 | 12 NOTES

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

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SpatialOmicsOverlay_0.99.7.tar.gz'
>>>>>>> 

* installing *source* package ‘SpatialOmicsOverlay’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘metadata<-’ in package ‘SpatialOmicsOverlay’
** 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 (SpatialOmicsOverlay)