Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘MBECS/DESCRIPTION’ ... OK
* preparing ‘MBECS’:
* 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 ‘MBECS_0.99.6.tar.gz’

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 BiocCheckGitClone('MBECS')

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This is BiocCheckGitClone version 1.31.34. 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/2497/abd4f746957f2597c9cee9ea273a0f67e1a1ae7e/MBECS.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘0.99.6’
* 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 ‘MBECS’ can be installed ... [19s/19s] 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 ... [21s/21s] NOTE
mbecMixedVariance: no visible binding for global variable ‘.’
mbecModelVariancePVCA: no visible binding for global variable ‘.’
mbecMosaic: no visible binding for global variable ‘Freq’
mbecMosaicPlot: no visible binding for global variable ‘Var1’
mbecMosaicPlot: no visible binding for global variable ‘Freq.scaled’
mbecMosaicPlot: no visible binding for global variable ‘Var2’
mbecPVCAStatsPlot: no visible binding for global variable ‘type’
mbecPVCAStatsPlot: no visible binding for global variable ‘covariate’
mbecPVCAStatsPlot: no visible binding for global variable ‘variance’
mbecPVCAStatsPlot: no visible binding for global variable ‘variance.p’
mbecRDAStatsPlot: no visible binding for global variable ‘type’
mbecRDAStatsPlot: no visible binding for global variable ‘variance’
mbecRDAStatsPlot: no visible binding for global variable ‘covariate’
mbecRDAStatsPlot: no visible binding for global variable ‘variance.r’
mbecRLE: no visible binding for global variable ‘.’
mbecRLE: no visible global function definition for ‘everything’
mbecRLE: no visible binding for global variable ‘plot.order’
mbecRLE: no visible binding for global variable ‘specimen’
mbecRLEPlot: no visible binding for global variable ‘specimen’
mbecRLEPlot: no visible binding for global variable ‘values’
mbecSCOEFStatsPlot: no visible binding for global variable ‘variable’
mbecSCOEFStatsPlot: no visible binding for global variable ‘type’
mbecSCOEFStatsPlot: no visible binding for global variable
  ‘sil.coefficient’
mbecSCOEFStatsPlot: no visible binding for global variable ‘cluster’
mbecVarianceStatsLM: no visible binding for global variable ‘.’
mbecVarianceStatsPlot: no visible binding for global variable ‘type’
mbecVarianceStatsPlot: no visible binding for global variable
  ‘variance’
mbecVarianceStatsPlot: no visible binding for global variable
  ‘covariate’
Undefined global functions or variables:
  . Freq Freq.scaled Var1 Var2 cluster covariate everything plot.order
  sil.coefficient specimen type values variable variance variance.p
  variance.r
* 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
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/51s] OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
mbecModelVariance     6.789  0.163   6.951
mbecVarianceStatsPlot 6.073  0.156   6.229
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [304s/304s]
 [304s/304s] 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: 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2497/abd4f746957f2597c9cee9ea273a0f67e1a1ae7e/MBECS.Rcheck/00check.log’
for details.






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 BiocCheck('MBECS_0.99.6.tar.gz')

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This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2497/abd4f746957f2597c9cee9ea273a0f67e1a1ae7e/MBECS_0.99.6.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpzMgMRU/file97aa741c4300/lib" 2>/dev/null' had status 1
* 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 4.1.0 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...
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/mbecs_vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MBECS...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/mbecs_plots.R (line 305, column 18)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        mbecs_analyses.R (line 1033, column 41)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
        suppressMessages() in R/mbecs_analyses.R (line 940, column 3)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 11 functions > 50 lines.
      The longest 5 functions are:
        mbecPCAPlot() (R/mbecs_plots.R, line 343): 147 lines
        MbecData() (R/mbecs_classes.R, line 74): 94 lines
        mbecBoxPlot() (R/mbecs_plots.R, line 82): 91 lines
        mbecMosaicPlot() (R/mbecs_plots.R, line 229): 91 lines
        mbecReportPost() (R/mbecs_reports.R, line 85): 71 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      mbecReportPost.Rd, mbecReportPrelim.Rd, pipe.Rd
* 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; 272 lines (4%) are > 80 characters
      long.
    First 6 lines:
      R/mbecs_analyses.R:714 mbecModelVarianceLM <- function(model.form, mode...
      R/mbecs_classes.R:58 #' @param meta_data A table with covariate informa...
      R/mbecs_classes.R:86       stop("All the values in your count-table nee...
      R/mbecs_classes.R:92     ## check for 'sID' column and set it as row-na...
      R/mbecs_classes.R:96         message("sID column does not match with ro...
      R/mbecs_classes.R:101       # check for rownames and basically make the...
    * NOTE: Consider multiples of 4 spaces for line indents, 1314
      lines(17%) are not.
    First 6 lines:
      R/mbecs_analyses.R:51   tmp <- mbecGetData(input.obj=input.obj, orienta...
      R/mbecs_analyses.R:52                      required.col=eval(model.vars...
      R/mbecs_analyses.R:53                      label=label)
      R/mbecs_analyses.R:54   tmp.cnts <- tmp[[1]]
      R/mbecs_analyses.R:55   tmp.meta <- tmp[[2]] %>% tibble::rownames_to_co...
      R/mbecs_analyses.R:57   if( !(type == "cor") ) {
    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...
    * ERROR: Maintainer must register at the support site; visit
      https://support.bioconductor.org/accounts/signup/ .


Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 11
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
BiocCheck FAILED.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir MBECS_0.99.6.tar.gz'
>>>>>>> 

* installing *source* package ‘MBECS’ ...
** 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 (MBECS)