===============================
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_0.99.0.tar.gz’
===============================
BiocCheckGitClone('scDiagnostics')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: scDiagnostics
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/scDiagnostics_20240614135738/scDiagnostics
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
scDiagnostics.Rproj
* 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 ──
1 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3449/scDiagnostics_20240614135738/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 ‘0.99.0’
* 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 ... NOTE
The following files look like leftovers:
‘scDiagnostics/NEWS.rd’
Please remove them from your package.
* 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
‘subspace_comparison’
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 subspace_comparison value x x_value
y y_value
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) regressPC.Rd:55: Lost braces; missing escapes or markup?
55 | Var(C|B) = sum_{i=1}^G Var(C|PC_i) * R^2 (PC_i | B)
| ^
* 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 ... [449s/436s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
visualizeCellTypeMDS 59.461 0.392 59.855
boxplotPCA 27.708 1.000 28.710
calculateSampleDistances 27.332 0.692 27.460
calculateSampleDistancesSimilarity 24.064 0.278 23.806
calculateVarImpOverlap 22.163 0.198 16.092
calculateDiscriminantSpace 21.221 0.322 17.179
calculateAveragePairwiseCorrelation 20.098 0.284 20.383
detectAnomaly 18.236 0.237 17.909
plotPairwiseDistancesDensity 17.959 0.192 18.152
calculateSampleSimilarityPCA 17.247 0.202 17.034
visualizeCellTypePCA 17.186 0.208 17.395
calculateNearestNeighborProbabilities 16.784 0.260 17.045
comparePCASubspace 16.302 0.216 16.519
calculateHotellingPValue 16.160 0.252 16.412
comparePCA 16.140 0.232 16.372
compareCCA 16.013 0.328 16.341
projectPCA 16.110 0.184 16.294
regressPC 15.552 0.096 15.649
plotMarkerExpression 15.181 0.120 15.301
plotGeneSetScores 5.517 0.184 5.702
* 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 ... [4s/4s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ∩ (U+2229)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3449/scDiagnostics_20240614135738/scDiagnostics.Rcheck/00check.log’
for details.
===============================
BiocCheck('scDiagnostics_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: scDiagnostics
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/RtmpakzJ8i/file291bc739e3c1e1/scDiagnostics
─ installDir: /tmp/RtmpakzJ8i/file291bc7399c7492
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/scDiagnostics_20240614135738/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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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...
* 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; 931 lines (16%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 788 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...
Unable to connect to the Bioc-devel mailing list: HTTP 401
Unauthorized.
* Checking for support site registration...
* ERROR: Unable to find your email in the Support Site: HTTP 404
Not Found.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 10 NOTES
See the scDiagnostics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.