Bioconductor Single Package Builder - Build History

===============================

 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_0.99.4.tar.gz’

===============================

 BiocCheckGitClone('SplineDV')

===============================

→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/84a3898d9699ac17571ccdc997c5f3fe402128be/SplineDV
→ BiocVersion: 3.20
→ Package: SplineDV
→ PackageVersion: 0.99.4
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/84a3898d9699ac17571ccdc997c5f3fe402128be/SplineDV.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/84a3898d9699ac17571ccdc997c5f3fe402128be/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/3489/84a3898d9699ac17571ccdc997c5f3fe402128be/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 ‘0.99.4’
* 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 ... [8s/8s] 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 ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [24s/24s] NOTE
DV_plot: no visible binding for global variable ‘drop1’
DV_plot: no visible binding for global variable ‘drop2’
DV_splinefit: no visible binding for global variable ‘X_dvecx’
DV_splinefit: no visible binding for global variable ‘X_dvecy’
DV_splinefit: no visible binding for global variable ‘X_dvecz’
DV_splinefit: no visible binding for global variable ‘Y_dvecx’
DV_splinefit: no visible binding for global variable ‘Y_dvecy’
DV_splinefit: no visible binding for global variable ‘Y_dvecz’
DV_splinefit: no visible binding for global variable ‘dist1’
DV_splinefit: no visible binding for global variable ‘dist2’
DV_splinefit: no visible binding for global variable ‘Vector_Dist’
DV_splinefit: no visible binding for global variable ‘Z’
DV_splinefit: no visible binding for global variable ‘Pval’
DV_splinefit: no visible binding for global variable ‘genes’
DV_splinefit: no visible binding for global variable ‘mu1’
DV_splinefit: no visible binding for global variable ‘mu2’
DV_splinefit: no visible binding for global variable ‘CV1’
DV_splinefit: no visible binding for global variable ‘CV2’
DV_splinefit: no visible binding for global variable ‘drop1’
DV_splinefit: no visible binding for global variable ‘drop2’
DV_splinefit: no visible binding for global variable ‘X_splinex’
DV_splinefit: no visible binding for global variable ‘X_spliney’
DV_splinefit: no visible binding for global variable ‘X_splinez’
DV_splinefit: no visible binding for global variable ‘Y_splinex’
DV_splinefit: no visible binding for global variable ‘Y_spliney’
DV_splinefit: no visible binding for global variable ‘Y_splinez’
DV_splinefit: no visible binding for global variable ‘Direction’
HVG_plot: no visible binding for global variable ‘Dropout’
HVG_splinefit: no visible binding for global variable ‘logMean’
HVG_splinefit: no visible binding for global variable ‘logCV’
HVG_splinefit: no visible binding for global variable ‘Distance’
HVG_splinefit: no visible binding for global variable ‘nearidx’
Undefined global functions or variables:
  CV1 CV2 Direction Distance Dropout Pval Vector_Dist 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
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 ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [14s/14s]
 [14s/14s] 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/3489/84a3898d9699ac17571ccdc997c5f3fe402128be/SplineDV.Rcheck/00check.log’
for details.





===============================

 BiocCheck('SplineDV_0.99.4.tar.gz')

===============================

── Installing SplineDV ─────────────────────────────────────────────────────────
✔ Package installed successfully
── SplineDV session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvWetkS/file3e196f60188bbb/SplineDV
→ BiocVersion: 3.20
→ Package: SplineDV
→ PackageVersion: 0.99.4
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3489/84a3898d9699ac17571ccdc997c5f3fe402128be/SplineDV.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpvWetkS/file3e196f60188bbb/SplineDV
→ installDir: /tmp/RtmpvWetkS/file3e196f17632d5f
→ 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...
* 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:
• HVG_splinefit() (R/main.R): 114 lines
• DV_splinefit() (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; 40 lines (7%) are > 80 characters long.
First few lines:
• R/main.R#L16 #' @param QC A Boolean value (TRUE/FALSE ...
• ...
• vignettes/SplineDV.Rmd#L110 This is the output of `sessionInfo()` on ...
i NOTE: Consider multiples of 4 spaces for line indents; 190 lines (34%) are
not.
First few lines:
• R/main.R#L31 ncounts=500, n ...
• ...
• vignettes/SplineDV.Rmd#L76 ...
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 Unable to connect to the Bioc-devel mailing list: Failed to perform HTTP
request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached:
[stat.ethz.ch] SSL connection timeout
* 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 | • 6 NOTES
i See the SplineDV.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.