nebbiolo2 Summary
[top]
| Package: scDiagnostics |
| Version: 0.99.10 |
| 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 33.11 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/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.install-out.txt scDiagnostics_0.99.10.tar.gz && BiocCheck('scDiagnostics_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 52.66 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4626.30 KiB |
| BuildID:: scDiagnostics_20240920210917 |
| 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
[top]
===============================
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
* looking to see if a ‘data/datalist’ file should be added
* building ‘scDiagnostics_0.99.10.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('scDiagnostics')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics
→ BiocVersion: 3.20
→ Package: scDiagnostics
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 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 ‘0.99.10’
* 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] OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking LazyData ... NOTE
'LazyDataCompression' is specified without 'LazyData'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [107s/98s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCellTypeMDS 16.383 0.267 16.667
calculateCellDistances 12.953 0.347 12.852
calculateCramerPValue 5.865 0.015 5.880
calculateCellDistancesSimilarity 4.839 0.203 4.595
calculateDiscriminantSpace 4.907 0.099 1.740
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [125s/108s]
[125s/109s] 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] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.Rcheck/00check.log’
for details.
===============================
BiocCheck('scDiagnostics_0.99.10.tar.gz')
===============================
── Installing scDiagnostics ────────────────────────────────────────────────────
✔ Package installed successfully
── scDiagnostics session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics
→ BiocVersion: 3.20
→ Package: scDiagnostics
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics
→ installDir: /tmp/Rtmpw2WePQ/filebfd4336db763
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scDiagnostics ──────────────────────────────────────────
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
PrincipalComponent, Regression
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics/vignettes/AnnotationAnomalies.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics/vignettes/CellDistancesDiagnostics.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics/vignettes/DatasetMarkerGeneAlignment.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics/vignettes/QCandAnnotationScores.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics/vignettes/scDiagnostics.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics/vignettes/StatisticalMeasures.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw2WePQ/filebfd436556f8b0/scDiagnostics/vignettes/VisualizationTools.Rmd
* 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...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• boxplotPCA.R (line 50, column 36)
• ...
• regressPC.R (line 89, column 35)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 35
functions greater than 50 lines.
The longest 5 functions are:
• plot.calculateSIRSpaceObject() (R/plot.calculateSIRSpaceObject.R): 222 lines
• ...
• calculateVarImpOverlap() (R/calculateVarImpOverlap.R): 141 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 1257 lines (15%) are > 80 characters long.
First few lines:
• R/argumentCheck.R#L4 #' This function validates the input arg ...
• ...
• vignettes/VisualizationTools.Rmd#L314 ```{r SessionInfo, echo=FALSE,
message=F ...
i NOTE: Consider multiples of 4 spaces for line indents; 863 lines (10%) are
not.
First few lines:
• R/argumentCheck.R#L48 reference_data ...
• ...
• vignettes/VisualizationTools.Rmd#L282 cell_type = "B_and_plasma" ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 5 NOTES
i See the scDiagnostics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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teran2 Summary
[top]
| Package: scDiagnostics |
| Version: 0.99.10 |
| 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 26.77 seconds |
| CheckCommand: BiocCheckGitClone('scDiagnostics') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3449/R-libs --install=check:/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.install-out.txt scDiagnostics_0.99.10.tar.gz && BiocCheck('scDiagnostics_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 6 minutes 28.61 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4626.40 KiB |
| BuildID:: scDiagnostics_20240920210917 |
| 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. |
teran2 BUILD SRC output
[top]
===============================
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
* looking to see if a ‘data/datalist’ file should be added
* building ‘scDiagnostics_0.99.10.tar.gz’
teran2 CHECK output
[top]
===============================
BiocCheckGitClone('scDiagnostics')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics
→ BiocVersion: 3.20
→ Package: scDiagnostics
→ PackageVersion: 0.99.10
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 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 ‘0.99.10’
* 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 ... [7s/7s] 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 ... [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 ... [25s/25s] OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [7s/7s] OK
* checking LazyData ... NOTE
'LazyDataCompression' is specified without 'LazyData'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [123s/111s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculateCellDistances 17.108 0.454 17.091
plotCellTypeMDS 14.525 0.115 14.641
calculateVarImpOverlap 9.876 0.064 2.040
calculateCellDistancesSimilarity 4.848 0.881 5.300
calculateCramerPValue 5.549 0.005 5.558
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [123s/111s]
[123s/111s] 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] OK
* DONE
Status: 1 NOTE
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.Rcheck/00check.log’
for details.
===============================
BiocCheck('scDiagnostics_0.99.10.tar.gz')
===============================
── Installing scDiagnostics ────────────────────────────────────────────────────
✔ Package installed successfully
── scDiagnostics session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics
→ BiocVersion: 3.20
→ Package: scDiagnostics
→ PackageVersion: 0.99.10
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3449/5ffd2515308308d63c1044337760c4470e2e363d/scDiagnostics.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics
→ installDir: /tmp/Rtmpw3av28/file1ab442665f5135
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scDiagnostics ──────────────────────────────────────────
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
PrincipalComponent, Regression
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics/vignettes/AnnotationAnomalies.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics/vignettes/CellDistancesDiagnostics.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics/vignettes/DatasetMarkerGeneAlignment.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics/vignettes/QCandAnnotationScores.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics/vignettes/scDiagnostics.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics/vignettes/StatisticalMeasures.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmpw3av28/file1ab4427fd4bb2b/scDiagnostics/vignettes/VisualizationTools.Rmd
* 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...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• boxplotPCA.R (line 50, column 36)
• ...
• regressPC.R (line 89, column 35)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 35
functions greater than 50 lines.
The longest 5 functions are:
• plot.calculateSIRSpaceObject() (R/plot.calculateSIRSpaceObject.R): 222 lines
• ...
• calculateVarImpOverlap() (R/calculateVarImpOverlap.R): 141 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 1257 lines (15%) are > 80 characters long.
First few lines:
• R/argumentCheck.R#L4 #' This function validates the input arg ...
• ...
• vignettes/VisualizationTools.Rmd#L314 ```{r SessionInfo, echo=FALSE,
message=F ...
i NOTE: Consider multiples of 4 spaces for line indents; 863 lines (10%) are
not.
First few lines:
• R/argumentCheck.R#L48 reference_data ...
• ...
• vignettes/VisualizationTools.Rmd#L282 cell_type = "B_and_plasma" ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 5 NOTES
i See the scDiagnostics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
teran2 BUILD BIN output
[top]