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R CMD BUILD
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* checking for file ‘cellmig/DESCRIPTION’ ... OK
* preparing ‘cellmig’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* 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 ‘cellmig_0.99.5.tar.gz’
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BiocCheckGitClone('cellmig')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3919/ccd0ba07a383543610c705c30c8da292e869f0d9/cellmig
→ BiocVersion: 3.22
→ Package: cellmig
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3919/ccd0ba07a383543610c705c30c8da292e869f0d9/cellmig.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3919/ccd0ba07a383543610c705c30c8da292e869f0d9/cellmig
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* 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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3919/ccd0ba07a383543610c705c30c8da292e869f0d9/cellmig.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmig’ version ‘0.99.5’
* 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 ‘cellmig’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 76.6Mb
sub-directories of 1Mb or more:
extdata 3.2Mb
libs 72.9Mb
* 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 ... [4s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/3s] OK
* checking loading without being on the library search path ... [5s/5s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘base’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/12s] NOTE
gen_partial: no visible binding for global variable ‘delta’
get_dose_response_profile: no visible binding for global variable
‘isTip’
get_dose_response_profile: no visible binding for global variable
‘label’
get_dose_response_profile: no visible binding for global variable
‘dose’
get_dose_response_profile: no visible binding for global variable
‘X2.5.’
get_dose_response_profile: no visible binding for global variable
‘X97.5.’
get_pairs: no visible binding for global variable ‘group_x’
get_pairs: no visible binding for global variable ‘group_y’
get_pairs: no visible binding for global variable ‘rho_M’
get_pairs: no visible binding for global variable ‘rho_M_exp’
get_ppc_means: no visible binding for global variable ‘v’
get_ppc_means: no visible binding for global variable ‘X2.5.’
get_ppc_means: no visible binding for global variable ‘X97.5.’
get_ppc_violins: no visible binding for global variable ‘dose’
get_ppc_violins: no visible binding for global variable ‘v’
get_ppc_violins: no visible binding for global variable ‘well’
get_ppc_violins: no visible binding for global variable ‘yhat’
get_treatment_profile: no visible binding for global variable ‘isTip’
get_treatment_profile: no visible binding for global variable ‘label’
get_violins: no visible binding for global variable ‘dose’
get_violins: no visible binding for global variable ‘rho’
Undefined global functions or variables:
X2.5. X97.5. delta dose group_x group_y isTip label rho rho_M
rho_M_exp v well yhat
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [398s/276s] ERROR
Running examples in ‘cellmig-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_violins
> ### Title: Generate violin plots for treatment group comparisons
> ### Aliases: get_violins
>
> ### ** Examples
>
> data(d_mini, package = "cellmig")
> o <- cellmig(x = d_mini,
+ control = list(mcmc_warmup = 200,
+ mcmc_steps = 500,
+ mcmc_chains = 2,
+ mcmc_cores = 2,
+ mcmc_algorithm = "NUTS",
+ adapt_delta = 0.8,
+ max_treedepth = 10))
model fitting...
SAMPLING FOR MODEL 'M' NOW (CHAIN 1).
SAMPLING FOR MODEL 'M' NOW (CHAIN 2).
Chain 1:
Chain 1: Gradient evaluation took 0.000822 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.22 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 500 [ 0%] (Warmup)
Chain 2:
Chain 2: Gradient evaluation took 0.00064 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 6.4 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 500 [ 0%] (Warmup)
Chain 1: Iteration: 200 / 500 [ 40%] (Warmup)
Chain 1: Iteration: 201 / 500 [ 40%] (Sampling)
Chain 2: Iteration: 200 / 500 [ 40%] (Warmup)
Chain 2: Iteration: 201 / 500 [ 40%] (Sampling)
Chain 2: Iteration: 400 / 500 [ 80%] (Sampling)
Chain 2: Iteration: 500 / 500 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 5.236 seconds (Warm-up)
Chain 2: 1.365 seconds (Sampling)
Chain 2: 6.601 seconds (Total)
Chain 2:
Chain 1: Iteration: 400 / 500 [ 80%] (Sampling)
Chain 1: Iteration: 500 / 500 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 4.935 seconds (Warm-up)
Chain 1: 2.608 seconds (Sampling)
Chain 1: 7.543 seconds (Total)
Chain 1:
computing posterior summaries...
>
> str(get_groups(x = o))
'data.frame': 9 obs. of 4 variables:
$ group_id: int 1 2 3 4 5 6 7 8 9
$ group : chr "C2|D3" "C2|D4" "C2|D5" "C3|D3" ...
$ compound: chr "C2" "C2" "C2" "C3" ...
$ dose : chr "D3" "D4" "D5" "D3" ...
> u <- get_violins(x = o,
+ from_groups = c("C2|D1", "C2|D2"),
+ to_group = "C3|D1",
+ exponentiate = FALSE)
Error in get_violins(x = o, from_groups = c("C2|D1", "C2|D2"), to_group = "C3|D1", :
unknown group in from_groups
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cellmig 111.989 1.537 77.618
get_dose_response_profile 101.044 1.369 69.813
get_treatment_profile 99.821 1.151 68.226
get_pairs 24.439 1.015 18.376
get_groups 23.454 0.820 17.222
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [51s/50s]
[51s/51s] 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, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3919/ccd0ba07a383543610c705c30c8da292e869f0d9/cellmig.Rcheck/00check.log’
for details.
===============================
BiocCheck('cellmig_0.99.5.tar.gz')
===============================
── Installing cellmig ──────────────────────────────────────────────────────────
✔ Package installed successfully
── cellmig session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4FYxEZ/file2ebac3c71048f/cellmig
→ BiocVersion: 3.22
→ Package: cellmig
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3919/ccd0ba07a383543610c705c30c8da292e869f0d9/cellmig.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/Rtmp4FYxEZ/file2ebac3c71048f/cellmig
→ installDir: /tmp/Rtmp4FYxEZ/file2ebac73d9b654
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on cellmig ────────────────────────────────────────────────
* 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...
* 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 (7%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• User_manual_analysis.Rmd
• User_manual_simulation.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of cellmig...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/stanmodels.R (line 11, column 15)
* 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 14
functions greater than 50 lines.
The longest 5 functions are:
• check_simulation_control() (R/simulate.R): 185 lines
• ...
• get_pairs() (R/downstream.R): 118 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; 1 lines (0%) are > 80 characters long.
First few lines:
• R/stanmodels.R#L25 mk_cppmodule = function(x ...
i NOTE: Consider multiples of 4 spaces for line indents; 769 lines (33%) are
not.
First few lines:
• R/cellmig.R#L2 ...
• ...
• vignettes/User_manual_simulation.Rmd#L416 theme_bw(base_size = 10) ...
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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 6 NOTES
i See the cellmig.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.