===============================
R CMD BUILD
===============================
* checking for file ‘SplineDV/DESCRIPTION’ ... OK
* preparing ‘SplineDV’:
* 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 ‘SplineDV_0.99.8.tar.gz’
===============================
BiocCheckGitClone('SplineDV')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/a1dde707496b82bb502c0a325b7c3d32b2e50e8b/SplineDV
→ BiocVersion: 3.20
→ Package: SplineDV
→ PackageVersion: 0.99.8
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/a1dde707496b82bb502c0a325b7c3d32b2e50e8b/SplineDV.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/a1dde707496b82bb502c0a325b7c3d32b2e50e8b/SplineDV
→ 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/a1dde707496b82bb502c0a325b7c3d32b2e50e8b/SplineDV.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 ‘SplineDV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SplineDV’ version ‘0.99.8’
* 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 ‘SplineDV’ 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 ... 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 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 ... [6s/7s] 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 ... [8s/8s] OK
* checking loading without being on the library search path ... [7s/7s] 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
DVPlot: no visible binding for global variable ‘mu1’
DVPlot: no visible binding for global variable ‘mu2’
HVGPlot: no visible binding for global variable ‘logMean’
splineDV: no visible binding for global variable ‘X_dvecx’
splineDV: no visible binding for global variable ‘X_dvecy’
splineDV: no visible binding for global variable ‘X_dvecz’
splineDV: no visible binding for global variable ‘Y_dvecx’
splineDV: no visible binding for global variable ‘Y_dvecy’
splineDV: no visible binding for global variable ‘Y_dvecz’
splineDV: no visible binding for global variable ‘dist1’
splineDV: no visible binding for global variable ‘dist2’
splineDV: no visible binding for global variable ‘vectorDist’
splineDV: no visible binding for global variable ‘Z’
splineDV: no visible binding for global variable ‘Pval’
splineDV: no visible binding for global variable ‘FDR’
splineDV: no visible binding for global variable ‘genes’
splineDV: no visible binding for global variable ‘mu1’
splineDV: no visible binding for global variable ‘mu2’
splineDV: no visible binding for global variable ‘CV1’
splineDV: no visible binding for global variable ‘CV2’
splineDV: no visible binding for global variable ‘drop1’
splineDV: no visible binding for global variable ‘drop2’
splineDV: no visible binding for global variable ‘X_splinex’
splineDV: no visible binding for global variable ‘X_spliney’
splineDV: no visible binding for global variable ‘X_splinez’
splineDV: no visible binding for global variable ‘Y_splinex’
splineDV: no visible binding for global variable ‘Y_spliney’
splineDV: no visible binding for global variable ‘Y_splinez’
splineDV: no visible binding for global variable ‘Direction’
splineHVG: no visible binding for global variable ‘logMean’
splineHVG: no visible binding for global variable ‘logCV’
splineHVG: no visible binding for global variable ‘Distance’
Undefined global functions or variables:
CV1 CV2 Direction Distance FDR Pval X_dvecx X_dvecy X_dvecz X_splinex
X_spliney X_splinez Y_dvecx Y_dvecy Y_dvecz Y_splinex Y_spliney
Y_splinez Z dist1 dist2 drop1 drop2 genes logCV logMean mu1 mu2
vectorDist
Consider adding
importFrom("stats", "drop1")
to your NAMESPACE file.
* 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 ... [20s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/13s]
[13s/13s] 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 ... [2s/2s] OK
* DONE
Status: 2 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/a1dde707496b82bb502c0a325b7c3d32b2e50e8b/SplineDV.Rcheck/00check.log’
for details.
===============================
BiocCheck('SplineDV_0.99.8.tar.gz')
===============================
── Installing SplineDV ─────────────────────────────────────────────────────────
✔ Package installed successfully
── SplineDV session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpT0yp2Y/file368fd07bc0fffd/SplineDV
→ BiocVersion: 3.20
→ Package: SplineDV
→ PackageVersion: 0.99.8
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/a1dde707496b82bb502c0a325b7c3d32b2e50e8b/SplineDV.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpT0yp2Y/file368fd07bc0fffd/SplineDV
→ installDir: /tmp/RtmpT0yp2Y/file368fd040437786
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SplineDV ───────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 3.5.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• /tmp/RtmpT0yp2Y/file368fd07bc0fffd/SplineDV//inst/doc/SplineDV.html
• /tmp/RtmpT0yp2Y/file368fd07bc0fffd/SplineDV/inst/doc/SplineDV.html
• /tmp/RtmpT0yp2Y/file368fd07bc0fffd/SplineDV/inst/doc/SplineDV.html
* 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: GeneTarget
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 (58%).
* 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 SplineDV...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• main.R (line 109, column 28)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/main.R (line 145, column 71)
* 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 3
functions greater than 50 lines.
The longest 5 functions are:
• splineHVG() (R/main.R): 124 lines
• splineDV() (R/main.R): 78 lines
• DVPlot() (R/main.R): 53 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; 55 lines (8%) are > 80 characters long.
First few lines:
• R/main.R#L2 #' @description Compute Highly Variable ...
• ...
• vignettes/SplineDV.Rmd#L170 This is the output of `sessionInfo()` on ...
i NOTE: Consider multiples of 4 spaces for line indents; 201 lines (31%) are
not.
First few lines:
• R/main.R#L35 ncounts=500, n ...
• ...
• R/main.R#L456 return(resOut) ...
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 v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 7 NOTES
i See the SplineDV.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.