nebbiolo2 Summary
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Package: scDiagnostics |
Version: 0.99.3 |
RVersion: 4.4
|
BiocVersion: 3.20
|
BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scDiagnostics |
BuildTime: 2 minutes 20.43 seconds |
CheckCommand: BiocCheckGitClone('scDiagnostics') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3449/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/scDiagnostics.install-out.txt scDiagnostics_0.99.3.tar.gz && BiocCheck('scDiagnostics_0.99.3.tar.gz', `new-package`=TRUE) |
CheckTime: 9 minutes 44.81 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 3194.13 KiB |
BuildID:: scDiagnostics_20240623022004 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scDiagnostics. 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
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===============================
R CMD BUILD
===============================
* 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_0.99.3.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('scDiagnostics')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: scDiagnostics
─ PackageVersion: 0.99.3
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/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')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/scDiagnostics.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDiagnostics’ version ‘0.99.3’
* 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 ... [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 ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [23s/23s] 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 ... [450s/437s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
visualizeCellTypeMDS 59.389 0.487 59.878
boxplotPCA 28.491 1.204 29.697
calculateSampleDistances 26.401 0.576 26.416
calculateSampleDistancesSimilarity 24.912 0.561 24.940
calculateVarImpOverlap 23.015 0.285 16.972
calculateDiscriminantSpace 21.256 0.343 17.262
calculateAveragePairwiseCorrelation 18.330 0.228 18.559
detectAnomaly 18.223 0.248 17.935
plotPairwiseDistancesDensity 17.914 0.356 18.271
calculateNearestNeighborProbabilities 17.634 0.376 18.010
calculateSampleSimilarityPCA 17.188 0.234 17.009
visualizeCellTypePCA 17.206 0.196 17.402
comparePCASubspace 16.318 0.240 16.559
calculateHotellingPValue 16.152 0.328 16.481
compareCCA 16.005 0.332 16.337
comparePCA 16.110 0.224 16.334
projectPCA 16.073 0.100 16.172
regressPC 15.503 0.088 15.591
plotMarkerExpression 15.137 0.176 15.315
plotGeneSetScores 5.603 0.228 5.832
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [6s/6s]
[7s/7s] 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 ... [3s/3s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/scDiagnostics.Rcheck/00check.log’
for details.
===============================
BiocCheck('scDiagnostics_0.99.3.tar.gz')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: scDiagnostics
─ PackageVersion: 0.99.3
─ sourceDir: /tmp/Rtmpy1UaiY/filed8bf33dc40825/scDiagnostics
─ installDir: /tmp/Rtmpy1UaiY/filed8bf338087b76
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/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...
* 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 | 0 WARNINGS | 8 NOTES
See the scDiagnostics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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lconway Summary
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Package: scDiagnostics |
Version: 0.99.3 |
RVersion: 4.4
|
BiocVersion: 3.20
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scDiagnostics |
BuildTime: 1 minutes 35.29 seconds |
CheckCommand: BiocCheckGitClone('scDiagnostics') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3449/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/scDiagnostics.install-out.txt scDiagnostics_0.99.3.tar.gz && BiocCheck('scDiagnostics_0.99.3.tar.gz', `new-package`=TRUE) |
CheckTime: 5 minutes 44.83 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh scDiagnostics_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 15.48 seconds |
PackageFileSize: 3666.14 KiB |
BuildID:: scDiagnostics_20240623022004 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scDiagnostics. 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
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===============================
R CMD BUILD
===============================
* 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_0.99.3.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('scDiagnostics')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: scDiagnostics
─ PackageVersion: 0.99.3
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/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')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/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 ‘0.99.3’
* 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 35.376 0.186 35.562
boxplotPCA 16.860 0.430 17.293
calculateSampleDistances 14.526 0.320 14.881
calculateVarImpOverlap 13.871 0.191 8.126
calculateSampleDistancesSimilarity 13.583 0.197 13.816
calculateDiscriminantSpace 11.895 0.200 8.160
calculateAveragePairwiseCorrelation 9.037 0.186 9.223
plotPairwiseDistancesDensity 8.825 0.172 8.997
detectAnomaly 8.764 0.113 8.914
calculateNearestNeighborProbabilities 8.527 0.080 8.609
calculateSampleSimilarityPCA 8.164 0.078 8.278
visualizeCellTypePCA 8.039 0.066 8.105
comparePCASubspace 7.591 0.053 7.644
projectPCA 7.483 0.072 7.556
calculateHotellingPValue 7.464 0.082 7.546
comparePCA 7.460 0.081 7.542
compareCCA 7.378 0.079 7.458
regressPC 7.059 0.065 7.125
plotMarkerExpression 6.895 0.050 6.944
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/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/e4ddfd6b9de05731c56f89479292851fbbabd45d/scDiagnostics.Rcheck/00check.log’
for details.
===============================
BiocCheck('scDiagnostics_0.99.3.tar.gz')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: scDiagnostics
─ PackageVersion: 0.99.3
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpY4XTMi/file10ebb76d64098/scDiagnostics
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpY4XTMi/file10ebb7906ec17
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3449/e4ddfd6b9de05731c56f89479292851fbbabd45d/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.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir scDiagnostics_0.99.3.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)