===============================
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_0.99.5.tar.gz’
===============================
BiocCheckGitClone('SplineDV')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/8d11e2662a8021931a6cd69d68a902e99091a811/SplineDV
→ BiocVersion: 3.20
→ Package: SplineDV
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/8d11e2662a8021931a6cd69d68a902e99091a811/SplineDV.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/8d11e2662a8021931a6cd69d68a902e99091a811/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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/8d11e2662a8021931a6cd69d68a902e99091a811/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 ‘0.99.5’
* 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 ... [7s/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 ... [7s/7s] 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 ‘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’
splineHVG: no visible binding for global variable ‘nearidx’
Undefined global functions or variables:
CV1 CV2 Direction Distance 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
nearidx 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] ERROR
Running examples in ‘SplineDV-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DVPlot
> ### Title: Plot 3D scatter plot in two conditions
> ### Aliases: DVPlot
>
> ### ** Examples
>
> # example code
> ## Load Data
> load(system.file("extdata", "WT_count.rda", package="SplineDV")) # WT Sample
Warning in readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '', probable reason 'No such file or directory'
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/7s]
[8s/8s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(SplineDV)
>
> test_check("SplineDV")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_DV.R:6:3'): DV works with matrix ───────────────────────────────
Error in `DV_splinefit(X, Y)`: could not find function "DV_splinefit"
── Error ('test_HVG.R:4:3'): HVG works with matrix ─────────────────────────────
Error in `HVG_splinefit(X)`: could not find function "HVG_splinefit"
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
* 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 ERRORs, 2 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/8d11e2662a8021931a6cd69d68a902e99091a811/SplineDV.Rcheck/00check.log’
for details.
===============================
BiocCheck('SplineDV_0.99.5.tar.gz')
===============================
── Installing SplineDV ─────────────────────────────────────────────────────────
✔ Package installed successfully
── SplineDV session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpe8jTGY/file22f4044f9aa093/SplineDV
→ BiocVersion: 3.20
→ Package: SplineDV
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/8d11e2662a8021931a6cd69d68a902e99091a811/SplineDV.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmpe8jTGY/file22f4044f9aa093/SplineDV
→ installDir: /tmp/Rtmpe8jTGY/file22f4041818f8f0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SplineDV ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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...
* 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 (50%).
* 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 100, column 28)
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
• splineHVG() (R/main.R): 114 lines
• splineDV() (R/main.R): 74 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; 49 lines (8%) are > 80 characters long.
First few lines:
• R/main.R#L16 #' @param QC A Boolean value (TRUE/FALSE ...
• ...
• vignettes/SplineDV.Rmd#L146 This is the output of `sessionInfo()` on ...
i NOTE: Consider multiples of 4 spaces for line indents; 190 lines (31%) are
not.
First few lines:
• R/main.R#L31 ncounts=500, n ...
• ...
• vignettes/SplineDV.Rmd#L96 ...
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 | • 7 NOTES
i See the SplineDV.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.