===============================
R CMD BUILD
===============================
* checking for file ‘xCell2/DESCRIPTION’ ... OK
* preparing ‘xCell2’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘xCell2_0.99.92.tar.gz’
===============================
BiocCheckGitClone('xCell2')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/db1253b409cc0b7a96687e31ad3738f66577c135/xCell2
→ BiocVersion: 3.20
→ Package: xCell2
→ PackageVersion: 0.99.92
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/db1253b409cc0b7a96687e31ad3738f66577c135/xCell2.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/db1253b409cc0b7a96687e31ad3738f66577c135/xCell2
→ 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...
i 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/db1253b409cc0b7a96687e31ad3738f66577c135/xCell2.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 ‘xCell2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘xCell2’ version ‘0.99.92’
* 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 ‘xCell2’ 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 ... 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 ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘quadprog’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [29s/29s] 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 ... WARNING
Data with usage in Rd file 'human_mouse_gene_symbols.Rd' but not in code:
‘human_mouse_gene_symbols’
Warning in utils::data(list = al, envir = data_env) :
data set ‘human_mouse_gene_symbols’ not found
* 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 ... [12s/12s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/29s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
xCell2Train 9.758 0.463 10.440
xCell2GetLineage 4.912 0.275 5.625
* 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/2s] OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/db1253b409cc0b7a96687e31ad3738f66577c135/xCell2.Rcheck/00check.log’
for details.
===============================
BiocCheck('xCell2_0.99.92.tar.gz')
===============================
── Installing xCell2 ───────────────────────────────────────────────────────────
✔ Package installed successfully
── xCell2 session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsUk9vG/file3eaab5202c20/xCell2
→ BiocVersion: 3.20
→ Package: xCell2
→ PackageVersion: 0.99.92
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/db1253b409cc0b7a96687e31ad3738f66577c135/xCell2.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpsUk9vG/file3eaab5202c20/xCell2
→ installDir: /tmp/RtmpsUk9vG/file3eaab55abdb3c1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on xCell2 ─────────────────────────────────────────────────
* 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...
* 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...
i Bioconductor dependencies found in Imports & Depends (27%).
* 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 xCell2...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/xCell2GetLineage.Rd
i Found @ in man/xCell2Train.Rd
i Found @ in vignettes/xCell2-vignette.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
• CreateSignatures() (R/xCell2Train.R): 175 lines
• ...
• xCell2Train() (R/xCell2Train.R): 107 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
i 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...
i NOTE: Consider shorter lines; 192 lines (11%) are > 80 characters long.
First few lines:
• R/data.R#L8 #' @description A table that provides a ...
• ...
• vignettes/xCell2-vignette.Rmd#L324 - Aran, D. (2021). Extracting insights f
...
i NOTE: Consider multiples of 4 spaces for line indents; 490 lines (28%) are
not.
First few lines:
• R/xCell2Analysis.R#L30 xcell2object, ...
• ...
• vignettes/xCell2-vignette.Rmd#L272 xcell2object = DICE_demo.xCell2Ref ...
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 | • 5 NOTES
i See the xCell2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.