Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* 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 ‘gemma.R_0.99.0.tar.gz’

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 BiocCheckGitClone('gemma.R')

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This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
    * ERROR: System Files found that should not be git tracked:
        gemma.R.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...


Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.




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 R CMD CHECK

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2533/gemma.R_20220225134143/gemma.R.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘0.99.0’
* 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 ‘gemma.R’ can be installed ... [2s/2s] 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 ... [3s/3s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/67s] OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
getDataset           4.464  0.315  20.457
getDatasetTidy       1.275  0.125   9.238
getDatasetExpression 0.838  0.066   8.731
searchAnnotations    0.008  0.000   8.448
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [13s/116s]
 [13s/116s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
   6. │   └─... %>% ...
   7. ├─base::paste0(., collapse = "\n")
   8. └─base::readLines(.)
  ── Error (testDatasetEndpoints.R:80:5): getDatasetExpression queries work ──────
  Error in `.body(memoised, fname, validators, endpoint, environment(), isFile, 
      header, raw, overwrite, file, match.call())`: 429
  Backtrace:
      ▆
   1. ├─testthat::expect_gt(...) at testDatasetEndpoints.R:80:4
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─getDatasetExpression(1, filter = TRUE) %>% nrow()
   5. ├─base::nrow(.)
   6. └─gemma.R::getDatasetExpression(1, filter = TRUE)
   7.   └─gemma.R:::.body(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 76 ]
  Error: Test failures
  In addition: Warning message:
  In for (i in seq_along(cols)) { :
    closing unused connection 4 (/tmp/RtmpP4M2ot/file3c1a8be1cd85)
  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 ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2533/gemma.R_20220225134143/gemma.R.Rcheck/00check.log’
for details.





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 BiocCheck('gemma.R_0.99.0.tar.gz')

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This is BiocCheck version 1.31.34. 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 '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2533/gemma.R_20220225134143/gemma.R_0.99.0.tar.gz" "/tmp/RtmpHEJPdx/file3c274e2abc986d/lib" 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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    ExperimentData
* 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:
      ENCODE
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...
* 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 'Apache License (>= 2)' unknown; licenses cannot
      restrict 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 gemma.R...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 4 functions > 50 lines.
      The longest 5 functions are:
        processDEA() (R/processors.R, line 214): 81 lines
        .body() (R/processors.R, line 18): 75 lines
        getDataset() (R/convenience.R, line 113): 63 lines
        getPlatformAnnotation() (R/convenience.R, line 31): 62 lines
        getDatasetDE() (R/convenience.R, line 222): 31 lines
* 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; 272 lines (6%) are > 80 characters
      long.
    First 6 lines:
      R/allEndpoints.R:15 #' @param limit Optional, defaults to 20. Limits th...
      R/allEndpoints.R:32 #' @param memoised Whether or not to cache results ...
      R/allEndpoints.R:37 #' @param overwrite Whether or not to overwrite if ...
      R/allEndpoints.R:45 #' in Gemma. You can [read more about the geeq prop...
      R/allEndpoints.R:69     endpoint <- "datasets/{encode(datasets)}?&offse...
      R/allEndpoints.R:85 #' @param resultSet Optional, defaults to empty. A ...
    * NOTE: Consider multiples of 4 spaces for line indents, 138
      lines(3%) are not.
    First 6 lines:
      man/dot-getResultSetFactors.Rd:8   resultSet = NA_character_,
      man/dot-getResultSetFactors.Rd:9   dataset = NA_character_,
      man/dot-getResultSetFactors.Rd:10   offset = 0L,
      man/dot-getResultSetFactors.Rd:11   limit = 20L,
      man/dot-getResultSetFactors.Rd:12   sort = "+id",
      man/dot-getResultSetFactors.Rd:13   excludeResults = TRUE,
    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.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.


Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 5
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
BiocCheck FAILED.