===============================
BiocCheckGitClone('DeconvoBuddies')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3503/fe76846132f27838be0577b7ad2ba01a7df1e395/DeconvoBuddies
→ BiocVersion: 3.21
→ Package: DeconvoBuddies
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3503/fe76846132f27838be0577b7ad2ba01a7df1e395/DeconvoBuddies.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3503/fe76846132f27838be0577b7ad2ba01a7df1e395/DeconvoBuddies
→ 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 v1.43.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3503/fe76846132f27838be0577b7ad2ba01a7df1e395/DeconvoBuddies.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeconvoBuddies/DESCRIPTION’ ... OK
* this is package ‘DeconvoBuddies’ version ‘0.99.11’
* 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 ‘DeconvoBuddies’ 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] WARNING
Error: package or namespace load failed for ‘DeconvoBuddies’ in namespaceExport(ns, exports):
undefined exports: create_cell_colors, fetch_deconvo_data, findMarkers_1vAll, get_mean_ratio, make_test_sce, plot_composition_bar, plot_gene_express, plot_marker_express, plot_marker_express_ALL, plot_marker_express_List
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] WARNING
Error in loadNamespace("DeconvoBuddies") :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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 ... [0s/0s] WARNING
Error in loadNamespace("DeconvoBuddies") :
there is no package called ‘DeconvoBuddies’
Calls: suppressMessages ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking loading without being on the library search path ... [0s/0s] WARNING
Error in library(DeconvoBuddies, lib.loc = "/home/pkgbuild/packagebuilder/workers/jobs/3503/R-libs") :
there is no package called ‘DeconvoBuddies’
Execution halted
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
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [2s/2s] NOTE
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
Error in loadNamespace(name) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... NOTE
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd line widths ... NOTE
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: suppressPackageStartupMessages ... withCallingHandlers -> <Anonymous> -> Rd_db -> find.package
Execution halted
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... INFO
Warning in gzfile(file, "rb") :
cannot open compressed file '', probable reason 'No such file or directory'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> readRDS -> gzfile
Execution halted
* checking for missing documentation entries ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> dirname -> find.package
Execution halted
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
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
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 ... NOTE
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> -> find.package
Execution halted
* checking for unstated dependencies in examples ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Execution halted
* checking contents of ‘data’ directory ... WARNING
Output for data("RNAScope_prop", package = "DeconvoBuddies"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("est_prop", package = "DeconvoBuddies"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("marker_test", package = "DeconvoBuddies"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("rse_bulk_test", package = "DeconvoBuddies"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("sce_ab", package = "DeconvoBuddies"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘DeconvoBuddies’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
* checking data for non-ASCII characters ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [0s/0s]
[1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(DeconvoBuddies)
Error in library(DeconvoBuddies) :
there is no package called 'DeconvoBuddies'
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) :
there is no package called ‘DeconvoBuddies’
Execution halted
* 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, 11 WARNINGs, 7 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3503/fe76846132f27838be0577b7ad2ba01a7df1e395/DeconvoBuddies.Rcheck/00check.log’
for details.
===============================
BiocCheck('DeconvoBuddies_0.99.11.tar.gz')
===============================
── Installing DeconvoBuddies ───────────────────────────────────────────────────
✔ Package installed successfully
── DeconvoBuddies session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPLM3O9/file30e3a19a0c6dd/DeconvoBuddies
→ BiocVersion: 3.21
→ Package: DeconvoBuddies
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3503/fe76846132f27838be0577b7ad2ba01a7df1e395/DeconvoBuddies.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /tmp/RtmpPLM3O9/file30e3a19a0c6dd/DeconvoBuddies
→ installDir: /tmp/RtmpPLM3O9/file30e3a1563c1b71
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DeconvoBuddies ─────────────────────────────────────────
* 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 4.4.0 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 (32%).
* 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 DeconvoBuddies...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/plot_marker_express_ALL.R (line 80, column 9)
• print() in R/plot_marker_express_List.R (line 80, column 9)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/create_cell_colors.R (line 108, column 17)
• R/create_cell_colors.R (line 120, column 19)
* 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 6
functions greater than 50 lines.
The longest 5 functions are:
• create_cell_colors() (R/create_cell_colors.R): 102 lines
• ...
• fetch_deconvo_data() (R/fetch_deconvo_data.R): 70 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
Found in files:
• fetch_deconvo_data.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• fetch_deconvo_data.Rd
* 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; 125 lines (4%) are > 80 characters long.
First few lines:
• R/create_cell_colors.R#L113 message(sprintf("Creating %s pallet ...
• ...
• vignettes/Marker_Finding.Rmd#L550 ```{r vignetteBiblio, results = "asis", ...
i NOTE: Consider multiples of 4 spaces for line indents; 58 lines (2%) are not.
First few lines:
• R/create_cell_colors.R#L80 "Micro", ...
• ...
• R/create_cell_colors.R#L187 return(scale_colors) ...
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 v1.43.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the DeconvoBuddies.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.