Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘peakCombiner/DESCRIPTION’ ... OK
* preparing ‘peakCombiner’:
* 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 ‘peakCombiner_0.99.4.tar.gz’

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 BiocCheckGitClone('peakCombiner')

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─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: peakCombiner
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3188/cfe7cc3ca5a673af855843968cca09ad9b14d096/peakCombiner
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      combpeaksr.Rproj
* 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...
* Checking that provided CITATION file is correctly formatted...
    * NOTE: CITATION file might be not correctly formatted

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 1 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/3188/cfe7cc3ca5a673af855843968cca09ad9b14d096/peakCombiner.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakCombiner/DESCRIPTION’ ... OK
* this is package ‘peakCombiner’ version ‘0.99.4’
* 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 ‘peakCombiner’ 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 ... NOTE
BugReports field should not be empty
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): argument is missing, with no default
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘GenomicRanges’ ‘dplyr’ ‘tidyselect’
Namespaces in Imports field not imported from:
  ‘rlang’ ‘stringr’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/5s] NOTE
center_expand_regions: no visible binding for global variable ‘.data’
check_data_structure: no visible binding for global variable ‘.data’
collapse_summits: no visible binding for global variable ‘.data’
combine_regions: no visible binding for global variable ‘.data’
cr_add_summit: no visible binding for global variable ‘.data’
cr_disjoin_filter: no visible binding for global variable ‘.data’
cr_overlap_with_summits: no visible binding for global variable ‘.data’
cr_reduce: no visible binding for global variable ‘.data’
define_expansion: no visible binding for global variable ‘.data’
filter_by_blacklist: no visible binding for global variable
  ‘blacklist_hg38’
filter_by_blacklist: no visible binding for global variable
  ‘blacklist_mm10’
filter_by_blacklist: no visible binding for global variable ‘.data’
filter_by_chromosome_names: no visible binding for global variable
  ‘.data’
filter_by_significance: no visible binding for global variable ‘.data’
filter_by_top_enriched: no visible binding for global variable ‘.data’
filter_regions: no visible binding for global variable ‘.data’
load_input_regions: no visible binding for global variable ‘.data’
prepare_input_regions: no visible binding for global variable ‘.data’
Undefined global functions or variables:
  .data blacklist_hg38 blacklist_mm10
* checking Rd files ... [0s/0s] WARNING
checkRd: (3) file 'blacklist_hg38.Rd': Empty section ‘list("blacklist_hg38")’
checkRd: (3) file 'blacklist_hg38.Rd': Empty section ‘ A tibble with 910 rows and 3 columns:’
checkRd: (3) blacklist_hg38.Rd:7-10: Empty section \format
checkRd: (3) file 'blacklist_mm10.Rd': Empty section ‘list("blacklist_mm10")’
checkRd: (3) file 'blacklist_mm10.Rd': Empty section ‘ A tibble with 164 rows and 3 columns:’
checkRd: (3) blacklist_mm10.Rd:7-10: Empty section \format
checkRd: (3) file 'syn_blacklist.Rd': Empty section ‘list("syn_blacklist")’
checkRd: (3) file 'syn_blacklist.Rd': Empty section ‘ A tibble with 2 rows and 3 columns:’
checkRd: (3) syn_blacklist.Rd:7-10: Empty section \format
checkRd: (3) file 'syn_control_rep1_narrowPeak.Rd': Empty section ‘list("syn_control_rep1_narrowPeak")’
checkRd: (3) file 'syn_control_rep1_narrowPeak.Rd': Empty section ‘ A tibble with 11 rows and 6 columns:’
checkRd: (3) syn_control_rep1_narrowPeak.Rd:7-10: Empty section \format
checkRd: (3) file 'syn_data_bed.Rd': Empty section ‘list("syn_data_bed")’
checkRd: (3) file 'syn_data_bed.Rd': Empty section ‘ A tibble with 55 rows and 4 columns:’
checkRd: (3) syn_data_bed.Rd:7-10: Empty section \format
checkRd: (3) file 'syn_data_control01.Rd': Empty section ‘list("syn_data_control01")’
checkRd: (3) file 'syn_data_control01.Rd': Empty section ‘ A tibble with 11 rows and 6 columns:’
checkRd: (3) syn_data_control01.Rd:8-11: Empty section \format
checkRd: (3) file 'syn_data_granges.Rd': Empty section ‘list("syn_data_granges")’
checkRd: (3) file 'syn_data_granges.Rd': Empty section ‘ A data frame with 55 rows and 8 columns:’
checkRd: (3) syn_data_granges.Rd:7-10: Empty section \format
checkRd: (3) file 'syn_data_tibble.Rd': Empty section ‘list("syn_data_tibble")’
checkRd: (3) file 'syn_data_tibble.Rd': Empty section ‘ A tibble with 55 rows and 8 columns:’
checkRd: (3) syn_data_tibble.Rd:7-10: Empty section \format
checkRd: (3) file 'syn_data_treatment01.Rd': Empty section ‘list("syn_data_treatment01")’
checkRd: (3) file 'syn_data_treatment01.Rd': Empty section ‘ A tibble with 10 rows and 6 columns:’
checkRd: (3) syn_data_treatment01.Rd:8-11: Empty section \format
checkRd: (3) file 'syn_sample_sheet.Rd': Empty section ‘list("syn_sample_sheet")’
checkRd: (3) file 'syn_sample_sheet.Rd': Empty section ‘ A tibble with 6 rows and 4 columns:’
checkRd: (3) syn_sample_sheet.Rd:7-10: Empty section \format
checkRd: (3) file 'syn_treatment_rep1_narrowPeak.Rd': Empty section ‘list("syn_treatment_rep1_narrowPeak")’
checkRd: (3) file 'syn_treatment_rep1_narrowPeak.Rd': Empty section ‘ A tibble with 11 rows and 6 columns:’
checkRd: (3) syn_treatment_rep1_narrowPeak.Rd:7-10: Empty section \format
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'check_data_structure.Rd':
  ‘peakCombiner’

Missing link or links in documentation object 'cr_add_summit.Rd':
  ‘peakCombiner’

Missing link or links in documentation object 'cr_disjoin_filter.Rd':
  ‘peakCombiner’

Missing link or links in documentation object 'cr_overlap_with_summits.Rd':
  ‘peakCombiner’

Missing link or links in documentation object 'cr_reduce.Rd':
  ‘peakCombiner’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'cr_add_summit'
  ‘combined_center’ ‘annotate_with_input_names’ ‘combined_sample_name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'::' or ':::' imports not declared from:
  ‘dplyr’ ‘here’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘peakCombiner-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: center_expand_regions
> ### Title: Modifies genomic regions by centering and then expanding them
> ### Aliases: center_expand_regions
> 
> ### ** Examples
> 
> # Load in and prepare a an accepted tibble
> sample_sheet <- readr::read_tsv(
+   paste0(infolder, "/lists/synthetic_sample_sheet.tsv"),
+   show_col_types = FALSE
+ )
Error: object 'infolder' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘dplyr’
'library' or 'require' calls not declared from:
  ‘GenomicRanges’ ‘tidyverse’
* checking tests ...
  Running ‘testthat.R’ [0s/1s]
 [1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(combpeaksr)
  Error in library(combpeaksr) : there is no package called 'combpeaksr'
  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 ... [7s/9s] OK
* DONE

Status: 2 ERRORs, 7 WARNINGs, 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3188/cfe7cc3ca5a673af855843968cca09ad9b14d096/peakCombiner.Rcheck/00check.log’
for details.





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 BiocCheck('peakCombiner_0.99.4.tar.gz')

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─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: peakCombiner
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpqcSr9D/file14d5a90136df/peakCombiner
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpqcSr9D/file14d5a102c66f8
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3188/cfe7cc3ca5a673af855843968cca09ad9b14d096/peakCombiner.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...
* 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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import stringr, rlang in NAMESPACE as well as
      DESCRIPTION.
* 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 peakCombiner...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 16 functions greater than 50 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; 192 lines (4%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1407 lines
      (26%) 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 | 1 WARNINGS | 4 NOTES

See the peakCombiner.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 peakCombiner_0.99.4.tar.gz'
>>>>>>> 

* installing *source* package ‘peakCombiner’ ...
** using staged installation
** R
** data
** 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 (peakCombiner)