Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘alabaster.bumpy/DESCRIPTION’ ... OK
* preparing ‘alabaster.bumpy’:
* 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 ‘alabaster.bumpy_0.99.0.tar.gz’

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 BiocCheckGitClone('alabaster.bumpy')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.bumpy
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.bumpy_20230131153206/alabaster.bumpy
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.bumpy_20230131153206/alabaster.bumpy.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.bumpy/DESCRIPTION’ ... OK
* this is package ‘alabaster.bumpy’ version ‘0.99.0’
* 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 serialization versions ... OK
* checking whether package ‘alabaster.bumpy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [11s/12s] OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] ERROR
Running examples in ‘alabaster.bumpy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadBumpyDataFrameMatrix
> ### Title: Load a BumpyDataFrameMatrix object
> ### Aliases: loadBumpyDataFrameMatrix
> 
> ### ** Examples
> 
> # Mocking up a BumpyMatrix.
> library(BumpyMatrix)
> library(S4Vectors)
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

> df <- DataFrame(x=runif(100), y=runif(100))
> f <- factor(sample(letters[1:20], nrow(df), replace=TRUE), letters[1:20])
> out <- S4Vectors::split(df, f)
> mat <- BumpyMatrix(out, c(5, 4))
> 
> # Staging it:
> tmp <- tempfile()
> dir.create(tmp)
> meta <- stageObject(mat, tmp, "BUMPY")
Error in value[[3L]](cond) : 
  failed to stage the underlying DataFrame in a BumpyDataFrameMatrix
  - there is no package called ‘jsonvalidate’
Calls: stageObject ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [4s/4s]
 [5s/5s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
   2. └─alabaster.bumpy::stageObject(smat, tmp, "bumpy")
   3.   └─alabaster.bumpy (local) .local(x, dir, path, child, ...)
   4.     └─base::tryCatch(...)
   5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.           └─value[[3L]](cond)
  ── Error ('test-hdf5.R:17'): staging and loading works with a HDF5 backend ─────
  Error in `value[[3L]](cond)`: failed to stage the underlying DataFrame in a BumpyDataFrameMatrix
    - there is no package called 'jsonvalidate'
  Backtrace:
      ▆
   1. ├─alabaster.base::stageObject(mat, tmp, "bumpy") at test-hdf5.R:17:4
   2. └─alabaster.bumpy::stageObject(mat, tmp, "bumpy")
   3.   └─alabaster.bumpy (local) .local(x, dir, path, child, ...)
   4.     └─base::tryCatch(...)
   5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.           └─value[[3L]](cond)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* 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 ... [4s/4s] OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.bumpy_20230131153206/alabaster.bumpy.Rcheck/00check.log’
for details.





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 BiocCheck('alabaster.bumpy_0.99.0.tar.gz')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.bumpy
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpgvCk3V/file11c8e5c27b30d/alabaster.bumpy
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpgvCk3V/file11c8e48edb46d
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.bumpy_20230131153206/alabaster.bumpy.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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...
* 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of alabaster.bumpy...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 6 functions greater than 50 lines.
* 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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 30 lines (8%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1 lines
      (0%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES

See the alabaster.bumpy.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir alabaster.bumpy_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘alabaster.bumpy’ ...
** 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 (alabaster.bumpy)