===============================
R CMD BUILD
===============================
* checking for file ‘CARDspa/DESCRIPTION’ ... OK
* preparing ‘CARDspa’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* 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 ‘CARDspa_0.99.2.tar.gz’
===============================
BiocCheckGitClone('CARDspa')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3470/e9990881633efce702a4753905d52bacd5da49c8/CARDspa
→ BiocVersion: 3.20
→ Package: CARDspa
→ PackageVersion: 0.99.2
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3470/e9990881633efce702a4753905d52bacd5da49c8/CARDspa.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3470/e9990881633efce702a4753905d52bacd5da49c8/CARDspa
→ 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/3470/e9990881633efce702a4753905d52bacd5da49c8/CARDspa.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 ‘CARDspa/DESCRIPTION’ ... OK
* this is package ‘CARDspa’ version ‘0.99.2’
* 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 ‘CARDspa’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 1.5Mb
libs 3.5Mb
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking whether startup messages can be suppressed ... [9s/9s] 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 ... [27s/27s] 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [141s/140s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CARD_refFree 50.412 0.318 50.743
CARD_SCMapping 24.449 3.222 26.885
CARD_visualize_pie 8.600 0.173 8.780
CARD_visualize_gene 5.469 0.176 5.649
CARD_visualize_prop 5.477 0.087 5.567
CARD_deconvolution 5.017 0.188 5.220
CARD_visualize_prop_2CT 5.116 0.087 5.224
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [17s/17s]
[17s/17s] 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 ... [3s/3s] OK
* DONE
Status: 2 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3470/e9990881633efce702a4753905d52bacd5da49c8/CARDspa.Rcheck/00check.log’
for details.
===============================
BiocCheck('CARDspa_0.99.2.tar.gz')
===============================
── Installing CARDspa ──────────────────────────────────────────────────────────
✔ Package installed successfully
── CARDspa session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpeIDAGv/file13b95638168db1/CARDspa
→ BiocVersion: 3.20
→ Package: CARDspa
→ PackageVersion: 0.99.2
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3470/e9990881633efce702a4753905d52bacd5da49c8/CARDspa.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpeIDAGv/file13b95638168db1/CARDspa
→ installDir: /tmp/RtmpeIDAGv/file13b95639c36da1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CARDspa ────────────────────────────────────────────────
* 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 4.3.0 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (11%).
* 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 CARDspa...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/CARD.prop.R (line 105, column 12)
• ...
• R/CARD.SCMapping.R (line 134, column 28)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• CARD.imputation.R (line 23, column 22)
• ...
• CARD.SCMapping.R (line 139, column 38)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
• suppressMessages() in R/visualization.R (line 85, column 10)
• ...
• suppressMessages() in R/visualization.R (line 516, column 10)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
The longest 5 functions are:
• CARD_refFree() (R/CARD.refFree.R): 137 lines
• ...
• CARD_visualize_pie() (R/visualization.R): 90 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; 7 lines (0%) are > 80 characters long.
First few lines:
• R/RcppExports.R#L17 CARDfree <- function(XinputIn, UIn, WIn, ...
• ...
• vignettes/Example_Analysis.Rmd#L166 And `CARDspa` also supports using Single
...
i NOTE: Consider multiples of 4 spaces for line indents; 3 lines (0%) are not.
First few lines:
• R/utilities.R#L151 || is.null(spatial_count) || is.n ...
• vignettes/Example_Analysis.Rmd#L174 spatialCoords ...
• vignettes/Example_Analysis.Rmd#L175 ) ...
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 | • 8 NOTES
i See the CARDspa.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.