===============================
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_0.99.3.tar.gz’
===============================
BiocCheckGitClone('SplineDV')
===============================
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3489/f2e82bd68dffe331fcfcaa424391b346a462322a/SplineDV
─ BiocVersion: 3.20
─ Package: SplineDV
─ PackageVersion: 0.99.3
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3489/f2e82bd68dffe331fcfcaa424391b346a462322a/SplineDV.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3489/f2e82bd68dffe331fcfcaa424391b346a462322a/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...
* 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 ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3489/f2e82bd68dffe331fcfcaa424391b346a462322a/SplineDV.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SplineDV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SplineDV’ version ‘0.99.3’
* 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 ... [28s/31s] NOTE
DV_splinefit: no visible binding for global variable ‘x’
DV_splinefit: no visible binding for global variable ‘y’
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 ‘Direction’
HVG_QC: no visible binding for global variable ‘x’
HVG_splinefit: no visible binding for global variable ‘x’
HVG_splinefit: no visible binding for global variable ‘logMean’
HVG_splinefit: no visible binding for global variable ‘logCV’
HVG_splinefit: no visible global function definition for ‘predict’
HVG_splinefit: no visible binding for global variable ‘Distance’
Undefined global functions or variables:
CV1 CV2 Direction Distance Pval Vector_Dist X_dvecx X_dvecy X_dvecz
Y_dvecx Y_dvecy Y_dvecz Z dist1 dist2 drop1 drop2 genes logCV logMean
mu1 mu2 predict x y
Consider adding
importFrom("stats", "drop1", "predict")
to your NAMESPACE file.
* checking Rd files ... [0s/1s] 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 ... [14s/16s] 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 ... [7s/8s] OK
* DONE
Status: 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3489/f2e82bd68dffe331fcfcaa424391b346a462322a/SplineDV.Rcheck/00check.log’
for details.
===============================
BiocCheck('SplineDV_0.99.3.tar.gz')
===============================
* Installing package...
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmppF9YVa/file4c454bd1998b/SplineDV
─ BiocVersion: 3.20
─ Package: SplineDV
─ PackageVersion: 0.99.3
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3489/f2e82bd68dffe331fcfcaa424391b346a462322a/SplineDV.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmppF9YVa/file4c454bd1998b/SplineDV
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmppF9YVa/file4c452db79b90
─ isTarBall: TRUE
─ platform: unix
* 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...
* 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...
* 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...
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...
* 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 2 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 40 lines (8%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 173 lines
(36%) 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 7 NOTES
See the SplineDV.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SplineDV_0.99.3.tar.gz'
>>>>>>>
* installing *source* package ‘SplineDV’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SplineDV)