Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* preparing ‘ReUseData’:
* 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 ‘ReUseData_0.99.14.tar.gz’

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 BiocCheckGitClone('ReUseData')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.14
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2868/851394882a1877df915b450c23f3635ec9982775/ReUseData
─ 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/2868/851394882a1877df915b450c23f3635ec9982775/ReUseData.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘0.99.14’
* 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 serialization versions ... OK
* checking whether package ‘ReUseData’ can be installed ... 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘Rcwl:::env_Rcwl’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] 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 ... [17s/17s] ERROR
Running examples in ‘ReUseData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataUpdate
> ### Title: dataUpdate
> ### Aliases: dataUpdate
> 
> ### ** Examples
> 
> ## Generate data 
> library(Rcwl)
Loading required package: yaml
Loading required package: 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

> recipeLoad("ensembl_liftover", return = TRUE)
Data recipe 'ensembl_liftover' loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)

> Rcwl::inputs(ensembl_liftover)
inputs:
  species (species)  (string):  
  from (from)  (string):  
  to (to)  (string):  
> ensembl_liftover$species <- "human"
> ensembl_liftover$from <- "GRCh37"
> ensembl_liftover$to <- "GRCh38"
> outdir <- file.path(tempdir(), "SharedData")
> res <- getData(ensembl_liftover,
+         outdir = outdir, 
+         notes = c("ensembl", "liftover", "human", "GRCh37", "GRCh38"),
+         showLog = TRUE)
INFO /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/Rcwl/1.15.5/env_Rcwl/bin/cwltool 3.1.20221201130942
INFO Resolved '/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpeC4UqO/SharedData/ensembl_liftover_human_GRCh37_GRCh38.cwl' to 'file:///var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpeC4UqO/SharedData/ensembl_liftover_human_GRCh37_GRCh38.cwl'
INFO [job ensembl_liftover_human_GRCh37_GRCh38.cwl] /private/tmp/docker_tmpoxkqh8de$ bash \
    script.sh \
    human \
    GRCh37 \
    GRCh38
script.sh: line 12: wget: command not found
gzip: can't stat: GRCh37_to_GRCh38.chain.gz (GRCh37_to_GRCh38.chain.gz.gz): No such file or directory
WARNING [job ensembl_liftover_human_GRCh37_GRCh38.cwl] exited with status: 1
WARNING [job ensembl_liftover_human_GRCh37_GRCh38.cwl] completed permanentFail
WARNING Final process status is permanentFail
Warning in system2(cwlRunner, args = paste0("--outdir ", outdir, " ", cwlArgs,  :
  running command ''cwltool' --outdir /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpeC4UqO/SharedData  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpeC4UqO/SharedData/ensembl_liftover_human_GRCh37_GRCh38.cwl /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpeC4UqO/SharedData/ensembl_liftover_human_GRCh37_GRCh38.yml' had status 1
}
Error in getData(ensembl_liftover, outdir = outdir, notes = c("ensembl",  : 
  HINT: The output file was not successfully generated. Please check the recipe (output globbing pattern, input parameters, parameter types, etc.)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [17s/23s]
 [17s/24s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
  for user instructions (e.g., eligible input values, data source, etc.)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 17 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_data.R:6'): (code run outside of `test_that()`) ────────────────
  Error in `getData(rcp, outdir = outdir, notes = c("ensembl", "liftover", 
      "NCBIM37", "GRCm38"))`: HINT: The output file was not successfully generated. Please check the recipe (output globbing pattern, input parameters, parameter types, etc.)
  
  Backtrace:
      ▆
   1. └─ReUseData::getData(...) at test_data.R:6:0
  ── Failure ('test_recipes.R:31'): recipe evaluation works ──────────────────────
  dirname(res$output) (`actual`) not equal to tempdir() (`expected`).
  
  `actual`:   "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpKW0BQL" 
  `expected`: "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpKW0BQL"
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 17 ]
  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 ... [5s/5s] OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2868/851394882a1877df915b450c23f3635ec9982775/ReUseData.Rcheck/00check.log’
for details.





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 BiocCheck('ReUseData_0.99.14.tar.gz')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.14
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpFL9zyF/file141a12a4eccb/ReUseData
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpFL9zyF/file141a17cf3f3a7
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2868/851394882a1877df915b450c23f3635ec9982775/ReUseData.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...
    * NOTE: Consider adding these automatically suggested biocViews:
      WorkflowManagement
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
    * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict 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 ReUseData...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
    * ERROR: Avoid references to external hosting platforms
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 41 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 18% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* 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; 43 lines (2%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 119 lines
      (5%) 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.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.

─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 15 NOTES

See the ReUseData.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 ReUseData_0.99.14.tar.gz'
>>>>>>> 

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