Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* preparing ‘scDiagnostics’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘scDiagnostics_0.99.4.tar.gz’

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 BiocCheckGitClone('scDiagnostics')

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─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: scDiagnostics
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3449/81ce49044abd984190b8eb5381e3734f3fff55e1/scDiagnostics
─ 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...
    * NOTE: (Optional) CITATION file not found. Only include a CITATION
      file if there is a preprint or publication for this Bioconductor
      package. Note that Bioconductor packages are not required to have
      a CITATION file but it is useful both for users and for tracking
      Bioconductor project-wide metrics. When including a CITATION
      file, add the publication using the 'doi' argument of
      'bibentry()'.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 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/3449/81ce49044abd984190b8eb5381e3734f3fff55e1/scDiagnostics.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDiagnostics’ version ‘0.99.4’
* 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 ‘scDiagnostics’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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 ... [16s/17s] NOTE
boxplotPCA: no visible binding for global variable ‘cell_type’
boxplotPCA: no visible binding for global variable ‘Value’
boxplotPCA: no visible binding for global variable ‘cell_type_dataset’
histQCvsAnnotation: no visible binding for global variable ‘stats’
histQCvsAnnotation: no visible binding for global variable ‘Metric’
plot.calculateAveragePairwiseCorrelation: no visible binding for global
  variable ‘Var2’
plot.calculateAveragePairwiseCorrelation: no visible binding for global
  variable ‘Var1’
plot.calculateAveragePairwiseCorrelation: no visible binding for global
  variable ‘Freq’
plot.calculateDiscriminantSpace: no visible binding for global variable
  ‘DV1’
plot.calculateDiscriminantSpace: no visible binding for global variable
  ‘DV2’
plot.calculateDiscriminantSpace: no visible binding for global variable
  ‘cell_type_dataset’
plot.calculateDiscriminantSpace: no visible binding for global variable
  ‘cell_type’
plot.calculateDiscriminantSpace: no visible binding for global variable
  ‘value’
plot.calculateNearestNeighborProbabilities: no visible binding for
  global variable ‘probability’
plot.calculateSampleDistances: no visible binding for global variable
  ‘Distance’
plot.calculateSampleDistances: no visible binding for global variable
  ‘Distance_Type’
plot.calculateSampleDistances: no visible binding for global variable
  ‘label_parsed’
plot.calculateSampleSimilarityPCA: no visible binding for global
  variable ‘PC’
plot.calculateSampleSimilarityPCA: no visible binding for global
  variable ‘Sample’
plot.calculateSampleSimilarityPCA: no visible binding for global
  variable ‘CosineSimilarity’
plot.compareCCA: no visible binding for global variable ‘CCA’
plot.compareCCA: no visible binding for global variable ‘Cosine’
plot.compareCCA: no visible binding for global variable ‘Correlation’
plot.comparePCA: no visible binding for global variable ‘Query’
plot.comparePCA: no visible binding for global variable ‘Ref’
plot.comparePCA: no visible binding for global variable ‘value’
plot.comparePCASubspace: no visible binding for global variable ‘PC’
plot.comparePCASubspace: no visible binding for global variable
  ‘Cosine’
plot.comparePCASubspace: no visible binding for global variable
  ‘VarianceExplained’
plot.detectAnomaly: no visible binding for global variable ‘x_value’
plot.detectAnomaly: no visible binding for global variable ‘y_value’
plot.detectAnomaly: no visible binding for global variable ‘y’
plotGeneExpressionDimred: no visible binding for global variable ‘Dim1’
plotGeneExpressionDimred: no visible binding for global variable ‘Dim2’
plotGeneExpressionDimred: no visible binding for global variable
  ‘Expression’
plotGeneExpressionDimred: no visible binding for global variable
  ‘x_value’
plotGeneExpressionDimred: no visible binding for global variable
  ‘y_value’
plotGeneExpressionDimred: no visible binding for global variable ‘y’
plotGeneExpressionDimred: no visible binding for global variable ‘x’
plotGeneSetScores: no visible binding for global variable ‘x_value’
plotGeneSetScores: no visible binding for global variable ‘y_value’
plotGeneSetScores: no visible binding for global variable ‘Scores’
plotGeneSetScores: no visible binding for global variable ‘y’
plotGeneSetScores: no visible binding for global variable ‘x’
plotMarkerExpression: no visible binding for global variable
  ‘GeneExpression’
plotMarkerExpression: no visible binding for global variable ‘Dataset’
plotPCRegression: no visible global function definition for ‘aes’
plotPairwiseDistancesDensity: no visible binding for global variable
  ‘ref_data_subset’
plotPairwiseDistancesDensity: no visible binding for global variable
  ‘Distance’
plotPairwiseDistancesDensity: no visible binding for global variable
  ‘Comparison’
plotQCvsAnnotation: no visible binding for global variable ‘QCStats’
plotQCvsAnnotation: no visible binding for global variable ‘Scores’
plotQCvsAnnotation: no visible binding for global variable ‘CellType’
visualizeCellTypeMDS: no visible global function definition for ‘aes’
visualizeCellTypeMDS: no visible binding for global variable ‘Dim1’
visualizeCellTypeMDS: no visible binding for global variable ‘Dim2’
visualizeCellTypeMDS: no visible binding for global variable
  ‘cell_type_dataset’
visualizeCellTypePCA: no visible binding for global variable ‘x_value’
visualizeCellTypePCA: no visible binding for global variable ‘y_value’
visualizeCellTypePCA: no visible binding for global variable
  ‘cell_type_dataset’
visualizeCellTypePCA: no visible binding for global variable ‘y’
visualizeCellTypePCA: no visible binding for global variable ‘x’
Undefined global functions or variables:
  CCA CellType Comparison Correlation Cosine CosineSimilarity DV1 DV2
  Dataset Dim1 Dim2 Distance Distance_Type Expression Freq
  GeneExpression Metric PC QCStats Query Ref Sample Scores Value Var1
  Var2 VarianceExplained aes cell_type cell_type_dataset label_parsed
  probability ref_data_subset stats value x x_value y y_value
* 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 ... [243s/233s] OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
visualizeCellTypeMDS                  35.335  0.213  35.547
boxplotPCA                            16.855  0.435  17.291
calculateSampleDistances              14.420  0.212  14.667
calculateSampleDistancesSimilarity    14.210  0.198  14.444
calculateVarImpOverlap                13.311  0.164   7.463
calculateDiscriminantSpace            11.917  0.206   8.147
calculateAveragePairwiseCorrelation    9.031  0.185   9.216
plotPairwiseDistancesDensity           8.834  0.164   8.999
detectAnomaly                          8.731  0.101   8.867
calculateNearestNeighborProbabilities  8.553  0.092   8.646
calculateSampleSimilarityPCA           8.164  0.077   8.278
visualizeCellTypePCA                   8.083  0.103   8.188
comparePCASubspace                     7.582  0.074   7.657
comparePCA                             7.557  0.045   7.602
calculateHotellingPValue               7.500  0.066   7.566
projectPCA                             7.451  0.079   7.531
compareCCA                             7.376  0.063   7.440
regressPC                              7.105  0.057   7.164
plotMarkerExpression                   6.887  0.032   6.918
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [5s/5s]
 [5s/5s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/5s] OK
* DONE

Status: 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3449/81ce49044abd984190b8eb5381e3734f3fff55e1/scDiagnostics.Rcheck/00check.log’
for details.





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 BiocCheck('scDiagnostics_0.99.4.tar.gz')

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─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: scDiagnostics
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmpvzr37S/file11abc2d6991e9/scDiagnostics
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmpvzr37S/file11abc3a3059ff
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3449/81ce49044abd984190b8eb5381e3734f3fff55e1/scDiagnostics.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...
    * WARNING: Package files exceed the 5MB size limit.
* 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:
      PrincipalComponent
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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (22%).
* Checking for pinned package versions in DESCRIPTION...
* 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 scDiagnostics...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 25 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 8% of man pages use at least one of these tags.
* 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; 949 lines (17%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 794 lines
      (14%) 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 is in the Support Site Watched Tags.

─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 8 NOTES

See the scDiagnostics.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 scDiagnostics_0.99.4.tar.gz'
>>>>>>> 

* installing *source* package ‘scDiagnostics’ ...
** 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 (scDiagnostics)