Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘comapr/DESCRIPTION’ ... OK
* preparing ‘comapr’:
* 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 ‘comapr_0.99.399.tar.gz’

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 BiocCheckGitClone('comapr')

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This is BiocCheckGitClone version 1.31.15. 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/2335/e3f0650fda18f9676f05c1c457026f90efff9825/comapr.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 ‘comapr/DESCRIPTION’ ... OK
* this is package ‘comapr’ version ‘0.99.399’
* 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 ‘comapr’ 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 ... [53s/53s] OK
* checking Rd files ... [0s/1s] 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 data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [47s/47s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [47s/44s]
 [47s/44s] 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('comapr_0.99.399.tar.gz')

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This is BiocCheck version 1.31.15. 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...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
    * NOTE: Update R version dependency from 4.1.0 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 for pinned package versions...
* 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 comapr...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
      times)
        suppressMessages() in R/diagnostic-qc-checks.R (line 141,
      column 14)
        suppressMessages() in R/plot-count.R (line 191, column 7)
        suppressMessages() in R/plot-count.R (line 206, column 7)
        suppressWarnings() in R/read-hap-state.R (line 99, column 3)
        suppressMessages() in R/read-hap-state.R (line 165, column 3)
* Checking function lengths    * NOTE: Recommended function length <= 50 lines.
      There are 10 functions > 50 lines.
      The longest 5 functions are:
        readColMM() (R/read-col-mm.R, line 23): 146 lines
        .filterCOsExtra() (R/read-hap-state.R, line 150): 94 lines
        plotGeneticDist() (R/plot-genetic-dist.R, line 37): 73 lines
        cal_bin_dist() (R/cal-genetic-dist.R, line 137): 65 lines
        plot_count() (R/plot-count.R, line 165): 64 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; 86 lines (2%) are > 80 characters
      long.
    First 6 lines:
      R/count-gt.R:6 #' helps identify poor samples or poor markers for filte...
      R/count-gt.R:18 #' @param interactive, it determines whether an interac...
      R/find-dup-samples.R:11 #' are duplicated, defaults to \code{0.99}. NAs...
      R/get-af-tracks.R:13 #' cell's alternative allele frequency DataTrack a...
      R/get-distorted-markers.R:9 #' @param p the expected geneotype ratio in...
      R/get-distorted-markers.R:10 #' @param adj.method Methods to adjust for...
    * NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
      tabs.
    First 1 lines:
      R/read-col-mm.R:56       stop("readMM(): row	 values 'i' are not in 1:n...
    * NOTE: Consider multiples of 4 spaces for line indents, 1332
      lines(24%) are not.
    First 6 lines:
      R/bootstrap.R:31   .check_mapping_fun(mapping_fun)
      R/bootstrap.R:32   count_m_idex <- .get_count_matrix(co_gr_rse = co_gr,...
      R/bootstrap.R:33   group_idx <- count_m_idex$gi
      R/bootstrap.R:34   count_matrix <- count_m_idex$c
      R/bootstrap.R:36   #group_size <- sapply(group_idx, length)
      R/bootstrap.R:37   result_fun <- function(){
    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 comapr_0.99.399.tar.gz'
>>>>>>> 

* installing *source* package ‘comapr’ ...
** using staged installation
** R
** data
** 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 (comapr)