Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘JASPAR2022/DESCRIPTION’ ... OK
* preparing ‘JASPAR2022’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘JASPAR2022_0.99.5.tar.gz’

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 BiocCheckGitClone('JASPAR2022')

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This is BiocCheckGitClone version 1.31.23. 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/2427/4b08d036b467fd2efedf90802df9bfd45ff9d25d/JASPAR2022.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 ‘JASPAR2022/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘JASPAR2022’ version ‘0.99.5’
* 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 ‘JASPAR2022’ can be installed ... [4s/4s] 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 ...Loading required package: methods
Loading required package: BiocFileCache
Loading required package: dbplyr
Error: package or namespace load failed for ‘JASPAR2022’:
 .onLoad failed in loadNamespace() for 'JASPAR2022', details:
  call: read.csv(paste0(path, "/metadata.csv"))
  error: could not find function "read.csv"
Execution halted

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... WARNING
Error: package or namespace load failed for ‘JASPAR2022’:
 .onLoad failed in loadNamespace() for 'JASPAR2022', details:
  call: read.csv(paste0(path, "/metadata.csv"))
  error: could not find function "read.csv"
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Error: .onLoad failed in loadNamespace() for 'JASPAR2022', details:
  call: read.csv(paste0(path, "/metadata.csv"))
  error: could not find function "read.csv"
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... WARNING
Error: .onLoad failed in loadNamespace() for 'JASPAR2022', details:
  call: bfcrpath(BiocFileCache(), url)
  error: could not find function "bfcrpath"
Execution halted
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: package or namespace load failed for ‘JASPAR2022’:
 .onLoad failed in loadNamespace() for 'JASPAR2022', details:
  call: read.csv(paste0(path, "/metadata.csv"))
  error: could not find function "read.csv"
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: lib
Execution halted
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/4s] NOTE
Error: .onLoad failed in loadNamespace() for 'JASPAR2022', details:
  call: read.csv(paste0(path, "/metadata.csv"))
  error: could not find function "read.csv"
Execution halted
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
JASPAR2022-class 11.653  0.426  12.078
* 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: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2427/4b08d036b467fd2efedf90802df9bfd45ff9d25d/JASPAR2022.Rcheck/00check.log’
for details.






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 BiocCheck('JASPAR2022_0.99.5.tar.gz')

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This is BiocCheck version 1.31.23. 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 "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpspt4JO/file2d8053365156/lib/JASPAR2022" 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...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
    * NOTE: Update R version dependency from 3.6.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    AnnotationData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      PackageType
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* 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 JASPAR2022...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 20 lines (10%) are > 80 characters
      long.
    First 6 lines:
      R/AllClasses.R:3 #' @description The JASPAR2022 object class is a thin ...
      man/JASPAR2022-class.Rd:15 \item{\code{db}}{Object of class \code{"char...
      vignettes/JASPAR2022.Rmd:6     affiliation: Imperial College London, Fa...
      vignettes/JASPAR2022.Rmd:30 JASPAR (http://jaspar.genereg.net) is an op...
      vignettes/JASPAR2022.Rmd:31 transcription factor (TF)-binding profiles ...
      vignettes/JASPAR2022.Rmd:32 across multiple species in six taxonomic gr...
    * NOTE: Consider multiples of 4 spaces for line indents, 15
      lines(7%) are not.
    First 6 lines:
      R/AllClasses.R:25          )
      R/zzz.R:3   ns <- asNamespace(pkgname)
      R/zzz.R:4   path <- system.file("extdata", package=pkgname, lib.loc=lib...
      R/zzz.R:5   metaData <- read.csv(paste0(path, "/metadata.csv"))
      R/zzz.R:6   url <- metaData$SourceUrl
      R/zzz.R:7   files <- bfcrpath(BiocFileCache(), url)
    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: 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 JASPAR2022_0.99.5.tar.gz'
>>>>>>> 

* installing *source* package ‘JASPAR2022’ ...
** 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 (JASPAR2022)