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_0.99.19.tar.gz’

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 BiocCheckGitClone('SpatialOmicsOverlay')

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─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: SpatialOmicsOverlay
─ PackageVersion: 0.99.19
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2604/098455610aa8f6f49377c30c80b7c6cdf8ba40c5/SpatialOmicsOverlay
─ 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/2604/098455610aa8f6f49377c30c80b7c6cdf8ba40c5/SpatialOmicsOverlay.Rcheck’
* using R Under development (unstable) (2023-03-15 r83984)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ version ‘0.99.19’
* 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 ‘SpatialOmicsOverlay’ 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 ... 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [28s/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 files in ‘vignettes’ ... OK
* checking examples ... [313s/203s] OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
changeColoringIntensity 27.293  1.146  15.337
add4ChannelImage        24.950  1.519  17.079
recolor                 25.387  0.894  14.594
flipX                   25.313  0.954  14.584
flipY                   24.762  0.926  14.480
cropSamples             24.545  1.029  15.758
cropTissue              22.349  0.944  15.168
readSpatialOverlay      21.443  0.801  17.069
changeImageColoring     20.017  0.872  14.452
addImageOmeTiff         18.790  0.912  14.739
parseOverlayAttrs        9.680  0.421   4.673
xmlExtraction            8.908  0.377   4.501
checkValidRes            8.244  0.463   3.933
parseScanMetadata        7.337  0.281   4.347
createMask               6.924  0.264   7.187
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [169s/148s]
 [170s/149s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  Attaching package: 'S4Vectors'
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  Loading required package: ggplot2
  Extracting XML
  Parsing XML - scan metadata
  Parsing XML - overlay data
  Generating Coordinates
  Extracting XML
  Parsing XML - scan metadata
  Parsing XML - overlay data
  Generating Coordinates
  Calculating and scaling coordinates
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  Error in utils::packageVersion("cli") : there is no package called 'cli'
  Calls: test_check ... style_hyperlink -> .rlang_cli_has_cli -> <Anonymous>
  Execution halted
* checking for unstated dependencies in vignettes ...Error in system2(file.path(R.home("bin"), "R"), c(if (nzchar(arch)) paste0("--arch=",  : 
  error in running command
Execution halted




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 BiocCheck('SpatialOmicsOverlay_0.99.19.tar.gz')

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/bin/sh: 1: /home/biocbuild/bbs-3.17-bioc/R/bin/Rscript: not found