===============================
R CMD BUILD
===============================
* checking for file ‘Polytect/DESCRIPTION’ ... OK
* preparing ‘Polytect’:
* 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 ‘Polytect_0.99.0.tar.gz’
===============================
BiocCheckGitClone('Polytect')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/Polytect_20240917174006/Polytect
→ BiocVersion: 3.20
→ Package: Polytect
→ PackageVersion: 0.99.0
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/Polytect_20240917174006/Polytect.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/Polytect_20240917174006/Polytect
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• data/.DS_Store
• R/.DS_Store
• tests/testthat/.DS_Store
* 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 ──────────────────────────────────────────────────
✖ 1 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/3464/Polytect_20240917174006/Polytect.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 ‘Polytect/DESCRIPTION’ ... OK
* this is package ‘Polytect’ 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 ‘Polytect’ 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 ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘lhs’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] NOTE
GMM_init: no visible global function definition for ‘cov’
cluster_selection: no visible global function definition for ‘combn’
combined_vectors: no visible global function definition for ‘combn’
mstep_cov: no visible global function definition for ‘cov’
polytect_clust: no visible global function definition for ‘setNames’
polytect_merge: no visible binding for global variable ‘cluster’
polytect_merge: no visible global function definition for ‘setNames’
polytect_summary: no visible binding for global variable ‘cluster’
sil_plot: no visible binding for global variable ‘cluster’
sil_plot: no visible binding for global variable ‘width’
silhouette_coef: no visible binding for global variable ‘cluster’
silhouette_coef: no visible binding for global variable ‘width’
silhouette_coef: no visible binding for global variable ‘channel1’
silhouette_coef: no visible binding for global variable ‘channel2’
silhouette_coef: no visible global function definition for ‘png’
silhouette_coef: no visible binding for global variable ‘group’
silhouette_coef: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
channel1 channel2 cluster combn cov dev.off group png setNames width
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("stats", "cov", "setNames")
importFrom("utils", "combn")
to your NAMESPACE file.
* 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 ... WARNING
Documented arguments not in \usage in Rd file 'HMM_merge.Rd':
‘base_cluster’
Documented arguments not in \usage in Rd file 'approxSilhouette.Rd':
‘data’ ‘clustering’
Documented arguments not in \usage in Rd file 'polytect_clust.Rd':
‘type’
Undocumented arguments in Rd file 'polytect_merge.Rd'
‘lambdas’ ‘coefs’
Documented arguments not in \usage in Rd file 'polytect_merge.Rd':
‘type’
Undocumented arguments in Rd file 'polytect_plot.Rd'
‘cluster_num’ ‘cluster_selected’
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.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] ERROR
Running examples in ‘Polytect-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conc_cal
> ### Title: concentration calculation function
> ### Aliases: conc_cal
>
> ### ** Examples
>
> data(HR)
> df_data<-polytect_clust(HR,4)
Starting the flow Peaks analysis...
Task A: compute kmeans...
step 0, set the intial seeds, tot.wss=0.0767292
step 1, do the rough EM, tot.wss=0.0519279 at 0.07363 sec
step 2, do the fine transfer of Hartigan-Wong Algorithm
tot.wss=0.0483346 at 0.139907 sec
...finished summarization at 0.141 sec
Task B: find peaks...
finished at 0.827 sec
[1] 1
[1] 2
[1] 3
[1] 4
> conc_cal(df_data)
Error in conc_cal(df_data) :
argument "cluster_num" is missing, with no default
Calls: conc_cal -> cluster_selection
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [38s/38s]
[38s/38s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
12. └─mlrMBO:::trainModels(...)
13. ├─mlrMBO:::measureTime(...)
14. │ └─base::force(expr)
15. └─mlr::train(learner, tasks[[i]])
16. ├─mlr:::measureTime(...)
17. │ └─base::force(expr)
18. ├─mlr (local) fun1(...)
19. │ ├─utils::capture.output(suppressMessages(x))
20. │ │ └─base::withVisible(...elt(i))
21. │ └─base::suppressMessages(x)
22. │ └─base::withCallingHandlers(...)
23. ├─base (local) fun2(fun3(do.call(trainLearner, pars)))
24. ├─base (local) fun3(do.call(trainLearner, pars))
25. ├─base::do.call(trainLearner, pars)
26. ├─mlr (local) `<fn>`(...)
27. └─mlr:::trainLearner.regr.km(...)
28. └─BBmisc::requirePackages(packs = "rgenoud", why = "fitting 'regr.km' with 'rgenoud' optimization")
29. └─BBmisc::stopf(...)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
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: 2 ERRORs, 2 WARNINGs, 3 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/Polytect_20240917174006/Polytect.Rcheck/00check.log’
for details.
===============================
BiocCheck('Polytect_0.99.0.tar.gz')
===============================
── Installing Polytect ─────────────────────────────────────────────────────────
✔ Package installed successfully
── Polytect session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYHLeAj/file338af161368aa6/Polytect
→ BiocVersion: 3.20
→ Package: Polytect
→ PackageVersion: 0.99.0
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3464/Polytect_20240917174006/Polytect.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpYHLeAj/file338af161368aa6/Polytect
→ installDir: /tmp/RtmpYHLeAj/file338af15d3e4444
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Polytect ───────────────────────────────────────────────
* 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 4.2.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• /tmp/RtmpYHLeAj/file338af161368aa6/Polytect//inst/doc/introduction.pdf
• /tmp/RtmpYHLeAj/file338af161368aa6/Polytect/inst/doc/introduction.pdf
• /tmp/RtmpYHLeAj/file338af161368aa6/Polytect/inst/doc/introduction.pdf
* 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (9%).
* 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 Polytect...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• conc_cal.R (line 28, column 45)
• ...
• polytect_plot.R (line 58, column 78)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/internal_functions.R (line 34, column 9)
• ...
• print() in R/polytect_plot.R (line 59, column 5)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/polytect_clust.R (line 73, column 15)
• ...
• R/polytect_plot.R (line 23, column 14)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/internal_functions.R (line 423, column 21)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 170 lines (15%) are > 80 characters long.
First few lines:
• R/conc_cal.R#L3 #' This function takes a data frame of f ...
• ...
• vignettes/introduction.Rmd#L188 Lun A (2024). bluster: Clustering Algori ...
i NOTE: Consider multiples of 4 spaces for line indents; 66 lines (6%) are not.
First few lines:
• R/conc_cal.R#L25 ...
• ...
• vignettes/introduction.Rmd#L173 ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | • 8 NOTES
i See the Polytect.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.