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R CMD BUILD
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* 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_0.99.98.tar.gz
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BiocCheckGitClone('xCell2')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3540/83342ff6fdcceaaa11c389d0673a6a640973caf5/xCell2
BiocVersion: 3.21
Package: xCell2
PackageVersion: 0.99.98
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3540/83342ff6fdcceaaa11c389d0673a6a640973caf5/xCell2.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3540/83342ff6fdcceaaa11c389d0673a6a640973caf5/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...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.43.2 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3540/83342ff6fdcceaaa11c389d0673a6a640973caf5/xCell2.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* 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 0.99.98
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ... INFO
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 2.6Mb
help 2.8Mb
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [34s/34s] 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 ... [13s/13s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [12s/12s] ERROR
Running examples in xCell2-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xCell2Analysis
> ### Title: Perform Cell Type Enrichment Analysis
> ### Aliases: xCell2Analysis
>
> ### ** Examples
>
> # For detailed example read xCell2 vignette.
>
> library(xCell2)
>
> # Load "ready to use" xCell2 reference object or generate a new one using `xCell2Train`
> data(DICE_demo.xCell2Ref, package = "xCell2")
>
> # Load demo bulk RNA-Seq gene expression mixture
> data(mix_demo, package = "xCell2")
>
> # Run xCell2 cell type enrichment analysis
> xcell2_res <- xCell2::xCell2Analysis(mix = mix_demo, xcell2object = DICE_demo.xCell2Ref)
Starting xCell2 Analysis...
Calculating enrichment scores for all cell types...
Performing spillover correction...
Error: quadprog needed for this function to work. Please install it.
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 ... [3s/3s] OK
* DONE
Status: 1 ERROR
See
/home/pkgbuild/packagebuilder/workers/jobs/3540/83342ff6fdcceaaa11c389d0673a6a640973caf5/xCell2.Rcheck/00check.log
for details.
===============================
BiocCheck('xCell2_0.99.98.tar.gz')
===============================
Installing xCell2
Package installed successfully
xCell2 session metadata
sourceDir: /tmp/Rtmprp4UAJ/file1be503406bd12d/xCell2
BiocVersion: 3.21
Package: xCell2
PackageVersion: 0.99.98
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3540/83342ff6fdcceaaa11c389d0673a6a640973caf5/xCell2.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmprp4UAJ/file1be503406bd12d/xCell2
installDir: /tmp/Rtmprp4UAJ/file1be5036f1195cd
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...
i NOTE: Update R version dependency from 4.0.0 to 4.5.0.
* 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...
i Bioconductor dependencies found in Imports & Depends (31%).
* 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...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
The longest 5 functions are:
xCell2Analysis() (R/xCell2Analysis.R): 178 lines
...
xCell2Train() (R/xCell2Train.R): 107 lines
* Checking man page documentation...
ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
dependencies.Rd
...
spillMat.Rd
* 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; 379 lines (14%) are > 80 characters long.
First few lines:
R/data.R#L3 #' A subset `SummarizedExperiment` objec ...
...
vignettes/xCell2-vignette.Rmd#L907 - Angel, A., Naom, L., Nabet-Levy, S., ...
i NOTE: Consider multiples of 4 spaces for line indents; 618 lines (23%) are
not.
First few lines:
R/xCell2Analysis.R#L83 xcell2object, ...
...
vignettes/xCell2-vignette.Rmd#L882 BPPARAM = BPPARAM ...
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 v1.43.2 results
1 ERRORS | 0 WARNINGS | i 5 NOTES
i See the xCell2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.