Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file vmrseq/DESCRIPTION ... OK
* preparing vmrseq:
* 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 vmrseq_0.99.0.tar.gz

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 BiocCheckGitClone('vmrseq')

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 sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq
 BiocVersion: 3.20
 Package: vmrseq
 PackageVersion: 0.99.0
 BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq.BiocCheck
 BiocCheckVersion: 1.41.5
 sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq
 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 results 
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file vmrseq/DESCRIPTION ... OK
* checking extension type ... Package
* this is package vmrseq 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package vmrseq 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 stub is invalid DCF.
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [27s/28s] NOTE
.computeProb1Unit : .computeLag: no visible binding for global variable
  chr
.computeProb1Unit : .computeLag: no visible binding for global variable
  state
.computeProb1Unit : .computeLag: no visible binding for global variable
  state_lag
.computeProb1Unit : .computeLag: no visible binding for global variable
  dist_bp
.computeProb1Unit: no visible binding for global variable dist_bp
.computeProb1Unit: no visible binding for global variable N_00
.computeProb1Unit: no visible binding for global variable N_10
.computeProb1Unit: no visible binding for global variable N_01
.computeProb1Unit: no visible binding for global variable N_11
.computeProb1Unit: no visible binding for global variable p_00
.computeProb1Unit: no visible binding for global variable p_01
.estimTransitProbsFromSummary: no visible binding for global variable
  dist_bp
.estimTransitProbsFromSummary: no visible binding for global variable
  p_00
.estimTransitProbsFromSummary: no visible binding for global variable
  p_01
.estimTransitProbsFromSummary: no visible binding for global variable
  p_10
.estimTransitProbsFromSummary: no visible binding for global variable
  p_11
.estimTransitProbsFromSummary : .selectCols: no visible binding for
  global variable dist_bp
HDF5NAdrop2matrix: no visible global function definition for as
computeVar : varByCluster: no visible global function definition for
  as
computeVarCutoff: no visible global function definition for quantile
extractInfo: no visible binding for global variable meth
extractInfo: no visible binding for global variable total
extractInfo: no visible binding for global variable bool
tp.plot: no visible binding for global variable dist_bp
tp.plot: no visible binding for global variable pbar
tp.plot: no visible binding for global variable phat
vmrseq.fit: no visible binding for global variable bpWindow
Undefined global functions or variables:
  N_00 N_01 N_10 N_11 as bool bpWindow chr dist_bp meth p_00 p_01 p_10
  p_11 pbar phat quantile state state_lag total
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'data.pool.Rd':
  \examples lines wider than 100 characters:
     ## Not run: data.pool(cellFiles = your_cell_file_list, sep = ",", chrNames = "chr1", writeDir = "your/write/path")

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 ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in vignettes ... OK
* checking examples ... [65s/46s] OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
vmrseq.fit    19.474  0.940  11.538
vmrseq.smooth 18.495  1.645  11.187
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running testthat.R [9s/9s]
 [9s/9s] 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 ... [4s/4s] OK
* DONE

Status: 4 NOTEs
See
  /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq.Rcheck/00check.log
for details.





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 BiocCheck('vmrseq_0.99.0.tar.gz')

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* Installing package...
 sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZAzTKX/file11c2f64d0a8a3/vmrseq
 BiocVersion: 3.20
 Package: vmrseq
 PackageVersion: 0.99.0
 BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3455/vmrseq_20240716132005/vmrseq.BiocCheck
 BiocCheckVersion: 1.41.5
 sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZAzTKX/file11c2f64d0a8a3/vmrseq
 installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZAzTKX/file11c2f3eef990a
 isTarBall: TRUE
 platform: unix

* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * 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...
    * NOTE: Update R version dependency from 3.5.0 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (50%).
* 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 vmrseq...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 12 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 methods overwritten by 'proxy':
  method               from    
  print.registry_field registry
  print.registry_entry registry
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 9% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 208 lines (9%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 694 lines
      (31%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    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 results 
1 ERRORS | 0 WARNINGS | 13 NOTES

See the vmrseq.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir vmrseq_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package vmrseq ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vmrseq)