===============================
R CMD BUILD
===============================
* checking for file ‘xCell2/DESCRIPTION’ ... OK
* preparing ‘xCell2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘xCell2’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
** testing if installed package can be loaded from final location
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
Error: package or namespace load failed for ‘xCell2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GSEABase’
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/RtmpaREQrB/Rinst3c8201723e483/xCell2’
-----------------------------------
ERROR: package installation failed
===============================
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_0.99.0.tar.gz’
===============================
BiocCheckGitClone('xCell2')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/xCell2_20240918160917/xCell2
→ BiocVersion: 3.20
→ Package: xCell2
→ PackageVersion: 0.99.0
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/xCell2_20240918160917/xCell2.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/xCell2_20240918160917/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/xCell2_20240918160917/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 ‘0.99.0’
* 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 ... [10s/10s] ERROR
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
Warning messages:
1: In check_forbidden_install("Python packages") :
cannot install Python packages during R CMD check
2: In check_forbidden_install("Python packages") :
cannot install Python packages during R CMD check
It looks like this package has a loading problem: see the messages for
details.
* checking whether the package can be loaded with stated dependencies ... [10s/10s] WARNING
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
Warning messages:
1: In check_forbidden_install("Python packages") :
cannot install Python packages during R CMD check
2: In check_forbidden_install("Python packages") :
cannot install Python packages during R CMD check
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... [11s/11s] WARNING
---- unloading
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] WARNING
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [9s/9s] WARNING
---- unloading
* checking loading without being on the library search path ... [11s/11s] WARNING
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
Warning messages:
1: In check_forbidden_install("Python packages") :
cannot install Python packages during R CMD check
2: In check_forbidden_install("Python packages") :
cannot install Python packages during R CMD check
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
* checking S3 generic/method consistency ... WARNING
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [30s/30s] NOTE
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
* 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 ... WARNING
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
Data with usage in Rd file 'human_mouse_gene_symbols.Rd' but not in code:
‘human_mouse_gene_symbols’
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
Warning in utils::data(list = al, envir = data_env) :
data set ‘human_mouse_gene_symbols’ not found
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
* checking Rd \usage sections ... NOTE
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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] NOTE
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] ERROR
Running examples in ‘xCell2-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xCell2Analysis
> ### Title: xCell2Analysis function
> ### Aliases: xCell2Analysis
>
> ### ** Examples
>
> # For detailed example read xCell2 vignette.
>
> # Load "ready to use" xCell2 reference object or generate a new one using `xCell2Train`
> data(DICE_demo.xCell2Ref, package = "xCell2")
>
> # Load 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)
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 ... [2s/2s] OK
* DONE
Status: 2 ERRORs, 9 WARNINGs, 5 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/xCell2_20240918160917/xCell2.Rcheck/00check.log’
for details.
===============================
BiocCheck('xCell2_0.99.0.tar.gz')
===============================
── Installing xCell2 ───────────────────────────────────────────────────────────
✔ Package installed successfully
── xCell2 session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpurxGGt/file2df11ad019ee/xCell2
→ BiocVersion: 3.20
→ Package: xCell2
→ PackageVersion: 0.99.0
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/xCell2_20240918160917/xCell2.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpurxGGt/file2df11ad019ee/xCell2
→ installDir: /tmp/RtmpurxGGt/file2df1158ac7081
→ 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 4.4.0.
* 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...
i Bioconductor dependencies found in Imports & Depends (29%).
* 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 9
functions greater than 50 lines.
The longest 5 functions are:
• CreateSignatures() (R/xCell2Train.R): 175 lines
• ...
• xCell2Analysis() (R/xCell2Analysis.R): 99 lines
* Checking man page documentation...
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
* 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; 180 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; 383 lines (23%) 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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/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 ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 6 NOTES
i See the xCell2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.