Bioconductor Single Package Builder - Build History

===============================

 R CMD BUILD

===============================

* checking for file ‘MetaboAnnotation/DESCRIPTION’ ... OK
* preparing ‘MetaboAnnotation’:
* 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 ‘MetaboAnnotation_0.99.1.tar.gz’

===============================

 BiocCheckGitClone('MetaboAnnotation')

===============================

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




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2443/5e9acd264ae383d010b635e648c937c38a8a2f27/MetaboAnnotation.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 ‘MetaboAnnotation/DESCRIPTION’ ... OK
* this is package ‘MetaboAnnotation’ version ‘0.99.1’
* 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 ‘MetaboAnnotation’ can be installed ... [40s/41s] 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 ... [39s/41s] 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 ... [22s/25s] OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
CompareSpectraParam 5.594  0.563   6.848
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [40s/43s]
 [41s/43s] 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





===============================

 BiocCheck('MetaboAnnotation_0.99.1.tar.gz')

===============================

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 4.0.0 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 MetaboAnnotation...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/Matched.R (line 765, column 12)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        matchSpectra.R (line 351, column 18)
    * NOTE: Avoid the use of 'paste' in condition signals
      Found in files:
        R/Matched.R (line 809, column 18)
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
      Found in files:
        Matched.R (line 585, column 17)
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in man/Matched.Rd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
* Checking function lengths* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      matchSpectra.Rd
* 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; 155 lines (3%) are > 80 characters
      long.
    First 6 lines:
      R/Matched.R:5 #' @aliases Matched Matched-class [,Matched-method Matche...
      R/Matched.R:231 #' res <- matchedData(mo, columns = c("col1", "col2", "...
      R/Matched.R:297 #' ## Reducing the target elements to only those that m...
      R/Matched.R:407 #' res <- matchedData(mo, columns = c("col1", "col2", "...
      R/Matched.R:413 #' ## rowData of the SummarizedExperiment and all targe...
      R/Matched.R:493         " (", length(unique(object@matches$target_idx))...
    * NOTE: Consider multiples of 4 spaces for line indents, 528
      lines(12%) are not.
    First 6 lines:
      R/AllGenerics.R:5   standardGeneric("addMatches"))
      R/AllGenerics.R:11   standardGeneric("filterMatches"))
      R/Matched.R:446                              target_idx = integer(),
      R/Matched.R:447                              score = numeric()),
      R/Matched.R:457                                          target_idx = i...
      R/Matched.R:458                                          score = numeri...
    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: 1
NOTE count: 8
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

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir MetaboAnnotation_0.99.1.tar.gz'
>>>>>>> 

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