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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_0.99.102.tar.gz
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BiocCheckGitClone('xCell2')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3540/84bb77c8ddaa80c8c502da342efc04c4bc0612bf/xCell2
BiocVersion: 3.21
Package: xCell2
PackageVersion: 0.99.102
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3540/84bb77c8ddaa80c8c502da342efc04c4bc0612bf/xCell2.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3540/84bb77c8ddaa80c8c502da342efc04c4bc0612bf/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/3540/84bb77c8ddaa80c8c502da342efc04c4bc0612bf/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 0.99.102
* 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] 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 ... [37s/37s] 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 ... [14s/14s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [58s/53s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
xCell2Train 21.288 4.542 24.256
xCell2GetLineage 7.199 0.998 8.485
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [47s/47s]
[48s/48s] ERROR
Running the tests in tests/testthat.R failed.
Complete output:
> library(testthat)
> library(xCell2)
>
> test_check("xCell2")
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 41 ]
Failed tests
Error ('test-xCell2Train.R:47:3'): xCell2Train works with scRNA-Seq data
Error in `dimnames(x) <- dn`: length of 'dimnames' [2] not equal to array extent
Backtrace:
1. xCell2::xCell2Train(ref = dice_ref, labels = dice_labels, refType = "sc") at test-xCell2Train.R:47:3
2. xCell2:::ScToPseudoBulk(ref, labels, minPbCells, minPbSamples)
3. base::lapply(...)
4. xCell2 (local) FUN(X[[i]], ...)
5. base::`colnames<-`(`*tmp*`, value = as.character(seq_len(tmp)))
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 41 ]
Error: Test failures
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/3540/84bb77c8ddaa80c8c502da342efc04c4bc0612bf/xCell2.Rcheck/00check.log
for details.
===============================
BiocCheck('xCell2_0.99.102.tar.gz')
===============================
Installing xCell2
Package installed successfully
xCell2 session metadata
sourceDir: /tmp/RtmpLQdZZ0/file2cd42549923b91/xCell2
BiocVersion: 3.21
Package: xCell2
PackageVersion: 0.99.102
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3540/84bb77c8ddaa80c8c502da342efc04c4bc0612bf/xCell2.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpLQdZZ0/file2cd42549923b91/xCell2
installDir: /tmp/RtmpLQdZZ0/file2cd4251bb72601
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...
* 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; 382 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; 619 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
0 ERRORS | 0 WARNINGS | i 4 NOTES
i See the xCell2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.