Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘CDI/DESCRIPTION’ ... OK
* preparing ‘CDI’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘CDI_0.99.2.tar.gz’

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 BiocCheckGitClone('CDI')

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This is BiocCheckGitClone version 1.31.14. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2297/821426a5613f5569af14d39d0ef4c3c4f3961ba2/CDI.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CDI/DESCRIPTION’ ... OK
* this is package ‘CDI’ version ‘0.99.2’
* 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 ‘CDI’ can be installed ... [52s/53s] 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [47s/48s] OK
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* ch* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [19s/19s]
 [19s/19s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK





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 BiocCheck('CDI_0.99.2.tar.gz')

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This is BiocCheck version 1.31.14. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1 to 4.2.0.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CDI...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths    * NOTE: Recommended function length <= 50 lines.
      There are 3 functions > 50 lines.
      The longest 5 functions are:
        calculate_CDI_oneset() (R/CalculateCDI.R, line 110): 77 lines
        CDI_lineplot() (R/PlotFunctions.R, line 51): 76 lines
        calculate_CDI() (R/CalculateCDI.R, line 318): 71 lines
        contingency_heatmap() (R/PlotFunctions.R, line 183): 49 lines
        feature_gene_selection() (R/FeatureGeneSelection.R, line 102):
      48 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...
    * NOTE: Consider shorter lines; 130 lines (8%) are > 80 characters
      long.
    First 6 lines:
      R/CalculateCDI.R:1 ## -------------------------------------------------...
      R/CalculateCDI.R:3 ## -------------------------------------------------...
      R/CalculateCDI.R:100       total_nllk <- total_nllk + ifelse(lrt_test_p...
      R/CalculateCDI.R:104   return(list(NegLLK = total_nllk, nReject = sum(l...
      R/CalculateCDI.R:123       sub_indx <- c(seq_len(length(candidate_label...
      R/CalculateCDI.R:154       sub_indx <- c(seq_len(length(combine_label))...
    * NOTE: Consider 4 spaces instead of tabs; 249 lines (14%) contain
      tabs.
    First 6 lines:
      R/CalculateCDI.R:46 	candidate_label, 
      R/CalculateCDI.R:47 	ncluster, 
      R/CalculateCDI.R:48 	cell_size_factor){
      R/CalculateCDI.R:66 	candidate_label, 
      R/CalculateCDI.R:67 	ncluster,
      R/CalculateCDI.R:68 	size_ct_list,
    * NOTE: Consider multiples of 4 spaces for line indents, 243
      lines(14%) are not.
    First 6 lines:
      R/CalculateCDI.R:12   mu <- input_parameter[1]
      R/CalculateCDI.R:13   r <- input_parameter[2]
      R/CalculateCDI.R:14   s_mu <- sc_vec * mu
      R/CalculateCDI.R:15   return(-sum(dnbinom(x_vec, size = r, mu = s_mu , ...
      R/CalculateCDI.R:22   if(sum(x_vec) == 0){
      R/CalculateCDI.R:25   }
    See http://bioconductor.org/developers/how-to/coding-style/
    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.
    Package name is in support site watched tags.


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 6
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir CDI_0.99.2.tar.gz'
>>>>>>> 

* installing *source* package ‘CDI’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (CDI)