Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* preparing ‘HiCExperiment’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘HiCExperiment_0.99.1.tar.gz’

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 BiocCheckGitClone('HiCExperiment')

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─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: HiCExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2879/c2a9f6d31ae8b18543603705bdf6aaf365177909/HiCExperiment
─ 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/2879/c2a9f6d31ae8b18543603705bdf6aaf365177909/HiCExperiment.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 ‘HiCExperiment/DESCRIPTION’ ... OK
* this is package ‘HiCExperiment’ version ‘0.99.1’
* 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 whether package ‘HiCExperiment’ 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 ... [16s/19s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/17s] OK
* checking whether the package can be unloaded cleanly ... [15s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [16s/19s] OK
* checking loading without being on the library search path ... [16s/18s] 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 ... NOTE
Foreign function call to a different package:
  .Call("_H5Fis_hdf5", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [70s/81s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [328s/377s] OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
data                  49.622  6.174  65.014
import-methods        37.612  4.015  45.026
AggrHiCExperiment     33.468  3.166  41.093
parse-other           23.768  3.172  30.014
HiCExperiment-methods 19.901  2.939  26.611
HicproFile-methods    14.332  2.764  20.330
HicproFile-class      12.191  2.164  17.214
CoolFile-class        10.653  2.111  15.172
CoolFile-methods      10.472  2.045  14.824
HicFile-class         10.220  2.067  14.478
HicFile-methods       10.259  2.024  14.413
parse-cool             6.303  1.349   8.999
HiCExperiment          6.332  0.919   8.408
pairsFile-methods      4.083  0.757   5.738
PairsFile-class        4.096  0.711   5.700
parse-hic              3.987  0.720   5.552
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [25s/28s]
 [25s/28s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
   1. └─base::loadNamespace(x) at test-PairsFile.R:2:4
   2.   ├─base::namespaceImport(...)
   3.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   4.     └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.       └─base (local) withOneRestart(expr, restarts[[1L]])
   6.         └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-aggrHicExperiment.R:2'): AggrHiCExperiment methods work ────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'ExperimentHub'
  Backtrace:
      ▆
   1. ├─HiCExperiment::full_contacts_yeast() at test-aggrHicExperiment.R:2:4
   2. └─base::loadNamespace(x)
   3.   ├─base::namespaceImport(...)
   4.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   5.     └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.       └─base (local) withOneRestart(expr, restarts[[1L]])
   7.         └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 9 ]
  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 ... [10s/11s] OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2879/c2a9f6d31ae8b18543603705bdf6aaf365177909/HiCExperiment.Rcheck/00check.log’
for details.

 WARNING: R CMD check exceeded 10 min requirement






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 BiocCheck('HiCExperiment_0.99.1.tar.gz')

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─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: HiCExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp7oaQTn/file41ac4a8ac67c/HiCExperiment
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp7oaQTn/file41ac53130de2
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2879/c2a9f6d31ae8b18543603705bdf6aaf365177909/HiCExperiment.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...
    * NOTE: Update R version dependency from 4.2 to 4.3.0.
* 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...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* 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 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 HiCExperiment...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 143 functions greater than 50 lines.
* Checking man page documentation...
    * WARNING: Add non-empty \value sections to the following man
      pages:
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* 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; 178 lines (4%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 60 lines
      (1%) 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...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      Bioc-Devel mailing list (requires admin credentials). Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/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 ──
1 ERRORS | 1 WARNINGS | 12 NOTES

See the HiCExperiment.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 HiCExperiment_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘HiCExperiment’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (HiCExperiment)