Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘mbOmic/DESCRIPTION’ ... OK
* preparing ‘mbOmic’:
* 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 ‘mbOmic_0.99.4.tar.gz’

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 BiocCheckGitClone('mbOmic')

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This is BiocCheckGitClone version 1.31.21. 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/2234/01855bd149cf8504b69356eb4181469a9d770b01/mbOmic.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 ‘mbOmic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mbOmic’ version ‘0.99.4’
* 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 ‘mbOmic’ can be installed ... [38s/38s] 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 ... [36s/37s] OK
* checking Rd files ... [1s/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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [64s/68s] OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plot_network   14.176  0.392  14.600
coExpress      12.675  0.450  13.149
plot_coExpress  7.776  0.016   7.822
corr            5.797  0.589   6.886
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/11s]
 [12s/12s] 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('mbOmic_0.99.4.tar.gz')

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This is BiocCheck version 1.31.21. 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 mbOmic...
* Checking coding practice...
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/plot.R (line 20, column 30)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 4 times)
        <<- in R/enterotype.R (line 104, column 32)
        <<- in R/enterotype.R (line 105, column 30)
        <<- in R/enterotype.R (line 106, column 36)
        <<- in R/enterotype.R (line 107, column 36)
* 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...
    * NOTE: Consider shorter lines; 105 lines (5%) are > 80 characters
      long.
    First 6 lines:
      R/AllClasses.R:30                          msg <- c(msg, "Samples and F...
      R/AllClasses.R:34                          msg <- c(msg, "Dimension of ...
      R/AllClasses.R:56 #' m.path <- system.file("extdata", "metabolites_and_...
      R/AllClasses.R:79 #' b.path <- system.file("extdata", "metabolites_and_...
      R/enterotype.R:5 #'       \sqrt{0.5 \times KLD (P||\frac{P + Q}{2}) + 0...
      R/enterotype.R:24                         sqrt(0.5 * KLD(x, (x + y) / 2...
    * NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
      tabs.
    First 1 lines:
      R/m-corr.R:73 			  registerDoParallel(cores = ncore)
    * NOTE: Consider multiples of 4 spaces for line indents, 150
      lines(8%) are not.
    First 6 lines:
      R/AllClasses.R:16          representation = representation(Samples = 'c...
      R/AllClasses.R:17                                          Features = "...
      R/AllClasses.R:18                                          dt = "data.t...
      R/AllClasses.R:19                                          'VIRTUAL'),
      R/AllClasses.R:20          validity = function (object) {
      R/AllClasses.R:21                  Sam <- unique(object@Samples)
    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 mbOmic_0.99.4.tar.gz'
>>>>>>> 

* installing *source* package ‘mbOmic’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘mbOmic’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘mbOmic’
** 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 (mbOmic)