===============================
R CMD BUILD
===============================
* checking for file ‘DeconvoBuddies/DESCRIPTION’ ... OK
* preparing ‘DeconvoBuddies’:
* 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
* building ‘DeconvoBuddies_0.99.4.tar.gz’
===============================
BiocCheckGitClone('DeconvoBuddies')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3503/d10a2af1a8f11960573f935e6262c31642112a61/DeconvoBuddies
→ BiocVersion: 3.20
→ Package: DeconvoBuddies
→ PackageVersion: 0.99.4
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3503/d10a2af1a8f11960573f935e6262c31642112a61/DeconvoBuddies.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3503/d10a2af1a8f11960573f935e6262c31642112a61/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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3503/d10a2af1a8f11960573f935e6262c31642112a61/DeconvoBuddies.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 ‘DeconvoBuddies/DESCRIPTION’ ... OK
* this is package ‘DeconvoBuddies’ version ‘0.99.4’
* 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 serialization versions ... 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/15s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [13s/13s] 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/38s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'plot_gene_express.Rd':
\examples lines wider than 100 characters:
plot_gene_express(sce = sce_DLPFC_example, category = "cellType_broad_hc", genes = c("GAD2", "CD22"))
plot_gene_express(sce = sce_DLPFC_example, category = "cellType_broad_hc", genes = c("GAD2", "CD22"), plot_points = TRUE)
plot_gene_express(sce = sce_DLPFC_example, category = "cellType_broad_hc", genes = c("GAD2", "CD22"), title = "My Genes")
These lines will be truncated in the PDF manual.
* 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 ... [6s/6s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] ERROR
Running examples in ‘DeconvoBuddies-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: est_prop
> ### Title: Test Estimated Cell Type Proportions
> ### Aliases: est_prop
> ### Keywords: datasets
>
> ### ** Examples
>
> ## R Note that the `rowSums(est_prop)` is equal to 1,
> ## with a small error tolerance.
> summary(rowSums(est_prop) - 1)
Min. 1st Qu. Median Mean 3rd Qu. Max.
-1.11e-16 0.00e+00 0.00e+00 -1.11e-18 0.00e+00 0.00e+00
>
> ## You can check this yourself with:
> testthat::expect_equal(rowSums(est_prop), rep(1, 100), ignore_attr = TRUE)
Error: rowSums(est_prop) not equal to rep(1, 100).
names for target but not for current
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [20s/21s]
[20s/21s] OK
* 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, 1 NOTE
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3503/d10a2af1a8f11960573f935e6262c31642112a61/DeconvoBuddies.Rcheck/00check.log’
for details.
===============================
BiocCheck('DeconvoBuddies_0.99.4.tar.gz')
===============================
── Installing DeconvoBuddies ───────────────────────────────────────────────────
✔ Package installed successfully
── DeconvoBuddies session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmpV60f06/file78ebb42aaebfe/DeconvoBuddies
→ BiocVersion: 3.20
→ Package: DeconvoBuddies
→ PackageVersion: 0.99.4
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3503/d10a2af1a8f11960573f935e6262c31642112a61/DeconvoBuddies.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpV60f06/file78ebb42aaebfe/DeconvoBuddies
→ installDir: /tmp/RtmpV60f06/file78ebb4ed8ff92
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DeconvoBuddies ─────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 2.10 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 (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 78, column 9)
• print() in R/plot_marker_express_List.R (line 79, column 9)
* 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:
• get_mean_ratio() (R/get_mean_ratio.R): 74 lines
• ...
• findMarkers_1vAll() (R/findMarkers_1vAll.R): 71 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 6% 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; 144 lines (5%) are > 80 characters long.
First few lines:
• R/data.R#L23 #' @source <https://github.com/LieberIns ...
• ...
• vignettes/Marker_Finding.Rmd#L550 ```{r vignetteBiblio, results = "asis", ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 7 NOTES
i See the DeconvoBuddies.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.