Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/EnrichDO
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
lconway macOS 12.7.1 Monterey/x86_64   OK     ERROR     OK     OK  
nebbiolo2 Linux (Ubuntu 22.04.3 LTS)/x86_64   OK     ERROR     skipped     OK  

lconway Summary

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Package: EnrichDO
Version: 0.99.3
RVersion: 4.4
BiocVersion: 3.20
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data EnrichDO
BuildTime: 0 minutes 41.19 seconds
CheckCommand: BiocCheckGitClone('EnrichDO') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3468/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO.install-out.txt EnrichDO_0.99.3.tar.gz && BiocCheck('EnrichDO_0.99.3.tar.gz', `new-package`=TRUE)
CheckTime: 3 minutes 47.81 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh EnrichDO_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 17.65 seconds
PackageFileSize: 3952.68 KiB
BuildID:: EnrichDO_20240706091115
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: EnrichDO. Starting Build package. Starting Check package. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0.

lconway BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘EnrichDO/DESCRIPTION’ ... OK
* preparing ‘EnrichDO’:
* 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 ‘EnrichDO_0.99.3.tar.gz’


lconway CHECK output

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===============================

 BiocCheckGitClone('EnrichDO')

===============================

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: EnrichDO
─ PackageVersion: 0.99.3
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO
─ 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...
    * NOTE: (Optional) CITATION file not found. Only include a CITATION
      file if there is a preprint or publication for this Bioconductor
      package. Note that Bioconductor packages are not required to have
      a CITATION file but it is useful both for users and for tracking
      Bioconductor project-wide metrics. When including a CITATION
      file, add the publication using the 'doi' argument of
      'bibentry()'.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES

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




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichDO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnrichDO’ version ‘0.99.3’
* 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 ‘EnrichDO’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    extdata   5.2Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [5s/5s] 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 ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] 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 ... [15s/16s] NOTE
TermStruct: no visible binding for global variable ‘doterms’
TermStruct: no visible binding for global variable ‘DOID’
TermStruct: no visible binding for global variable ‘parent.arr’
TermStruct: no visible binding for global variable ‘gene.len’
TermStruct: no visible binding for global variable ‘geneRatio’
TermStruct: no visible binding for global variable ‘p’
binomTest: no visible binding for global variable ‘dotermgenes’
chisqTest: no visible binding for global variable ‘dotermgenes’
computeTermSig: no visible binding for '<<-' assignment to ‘enrich’
computeTermSig: no visible binding for global variable ‘enrich’
computeTermSig : <anonymous>: no visible binding for global variable
  ‘enrich’
computeTermSig : <anonymous>: no visible binding for '<<-' assignment
  to ‘enrich’
computeTermSig : <anonymous>: no visible binding for global variable
  ‘DOID_C’
computeTermSig : <anonymous> : <anonymous>: no visible binding for
  global variable ‘enrich’
computeTermSig : <anonymous> : <anonymous>: no visible binding for
  '<<-' assignment to ‘enrich’
doEnrich: no visible binding for global variable ‘dotermgenes’
doEnrich: no visible binding for '<<-' assignment to ‘enrich’
doEnrich: no visible binding for global variable ‘enrich’
doEnrich: no visible binding for global variable ‘gene.arr’
doEnrich: no visible binding for global variable ‘cg.arr’
doEnrich: no visible binding for global variable ‘cg.len’
doEnrich: no visible binding for global variable ‘gene.len’
doEnrich: no visible binding for '<<-' assignment to ‘DOID_C’
doEnrich : <anonymous>: no visible binding for '<<-' assignment to
  ‘enrich’
doEnrich : <anonymous>: no visible binding for global variable ‘enrich’
doEnrich : <anonymous>: no visible binding for global variable ‘DOID_C’
doEnrich: no visible binding for global variable ‘level’
doEnrich: no visible binding for global variable ‘DOID’
doEnrich: no visible binding for global variable ‘DOID_C’
doEnrich: no visible binding for global variable ‘p’
drawBarGraph: no visible binding for global variable ‘p’
drawBarGraph: no visible binding for global variable ‘DOID’
drawBarGraph: no visible binding for global variable ‘DOTerm’
drawBarGraph: no visible binding for global variable ‘cg.len’
drawBarGraph: no visible binding for global variable ‘ig.len’
drawBarGraph: no visible global function definition for ‘na.omit’
drawBarGraph: no visible global function definition for ‘reorder’
drawBarGraph: no visible binding for global variable ‘DO’
drawBarGraph: no visible binding for global variable ‘log10p’
drawBarGraph: no visible binding for global variable ‘geneRatio’
drawGraphViz: no visible binding for global variable ‘enrich’
drawGraphViz: no visible binding for global variable ‘p’
drawGraphViz: no visible binding for global variable ‘DOID’
drawGraphViz: no visible binding for global variable ‘DOTerm’
drawGraphViz: no visible binding for global variable ‘parent.arr’
drawGraphViz: no visible binding for global variable ‘cg.len’
drawGraphViz: no visible binding for global variable ‘log10p’
drawGraphViz: no visible global function definition for ‘text’
drawHeatmap: no visible binding for '<<-' assignment to ‘weight_matrix’
drawHeatmap : <anonymous>: no visible binding for '<<-' assignment to
  ‘weight_matrix’
drawHeatmap : <anonymous>: no visible binding for global variable
  ‘weight_matrix’
drawHeatmap: no visible binding for global variable ‘weight_matrix’
drawPointGraph: no visible binding for global variable ‘p’
drawPointGraph: no visible binding for global variable ‘DOID’
drawPointGraph: no visible binding for global variable ‘DOTerm’
drawPointGraph: no visible binding for global variable ‘cg.len’
drawPointGraph: no visible binding for global variable ‘gene.len’
drawPointGraph: no visible binding for global variable ‘ig.len’
drawPointGraph: no visible global function definition for ‘na.omit’
drawPointGraph: no visible binding for global variable ‘geneRatio’
drawPointGraph: no visible global function definition for ‘reorder’
drawPointGraph: no visible binding for global variable ‘DO’
drawPointGraph: no visible binding for global variable ‘log10p’
fisherTest: no visible binding for global variable ‘dotermgenes’
getAncestors: no visible binding for global variable ‘enrich’
getAncestors: no visible global function definition for ‘str’
hypergeomTest: no visible binding for global variable ‘dotermgenes’
init: no visible binding for global variable ‘doterms’
init: no visible binding for '<<-' assignment to ‘enrich’
init: no visible binding for global variable ‘gene.len’
init: no visible binding for global variable ‘gene.arr’
init: no visible binding for global variable ‘weight.arr’
logoddTest: no visible binding for global variable ‘dotermgenes’
writeDoTerms: no visible binding for global variable ‘gene.arr’
writeDoTerms: no visible binding for global variable ‘parent.arr’
writeDoTerms: no visible binding for global variable ‘child.arr’
writeDoTerms: no visible binding for global variable ‘DOID’
writeDoTerms: no visible binding for global variable ‘DOTerm’
writeDoTerms: no visible binding for global variable ‘level’
writeDoTerms: no visible binding for global variable ‘genes’
writeDoTerms: no visible binding for global variable ‘parents’
writeDoTerms: no visible binding for global variable ‘children’
writeDoTerms: no visible binding for global variable ‘gene.len’
writeDoTerms: no visible binding for global variable ‘parent.len’
writeDoTerms: no visible binding for global variable ‘child.len’
writeResult: no visible binding for global variable ‘cg.arr’
writeResult: no visible binding for global variable ‘cg.len’
writeResult: no visible binding for global variable ‘ig.len’
writeResult: no visible binding for global variable ‘gene.len’
writeResult: no visible binding for global variable ‘dotermgenes’
writeResult: no visible binding for global variable ‘DOID’
writeResult: no visible binding for global variable ‘DOTerm’
writeResult: no visible binding for global variable ‘p’
writeResult: no visible binding for global variable ‘geneRatio’
writeResult: no visible binding for global variable ‘bgRatio’
writeResult: no visible binding for global variable ‘cg’
Undefined global functions or variables:
  DO DOID DOID_C DOTerm bgRatio cg cg.arr cg.len child.arr child.len
  children dotermgenes doterms enrich gene.arr gene.len geneRatio genes
  ig.len level log10p na.omit p parent.arr parent.len parents reorder
  str text weight.arr weight_matrix
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "na.omit", "reorder")
  importFrom("utils", "str")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘EnrichDO/R/EnrichDO_algorithm.R’:
  assign("doterms", doterms, pos = 1)
  assign("enrich", enrich, pos = 1)
  assign("enrich", NULL, pos = 1)
  assign("DOID_C", NULL, pos = 1)
  assign("doterms", doterms, pos = 1)
File ‘EnrichDO/R/EnrichDO_visualization.R’:
  assign("weight_matrix", NULL, pos = 1)
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [114s/114s] OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
doEnrich       42.372  1.096  43.468
writeDoTerms   10.525  0.416  10.843
drawPointGraph 10.400  0.488  10.889
writeResult    10.312  0.472  10.706
drawBarGraph    9.775  0.559  10.333
drawGraphViz    9.788  0.501  10.289
drawHeatmap     9.838  0.239  10.078
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO.Rcheck/00check.log’
for details.





===============================

 BiocCheck('EnrichDO_0.99.3.tar.gz')

===============================

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: EnrichDO
─ PackageVersion: 0.99.3
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZcM7EN/file31a820521b1a/EnrichDO
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZcM7EN/file31a8536bc304
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 3.5.0 to 4.4.0.
* 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 of less
      than 3 sentences. Provide a more detailed description of the
      package.
* 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 recommended DESCRIPTION fields...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of EnrichDO...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 21 times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 3 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...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 103 lines (11%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 28 lines (3%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 268 lines
      (28%) 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...
    * ERROR: Subscribe to the Bioc-devel mailing list by going to
      https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 16 NOTES

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

lconway BUILD BIN output

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===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir EnrichDO_0.99.3.tar.gz'
>>>>>>> 

* installing *source* package ‘EnrichDO’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (EnrichDO)



nebbiolo2 Summary

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Package: EnrichDO
Version: 0.99.3
RVersion: 4.4
BiocVersion: 3.20
BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EnrichDO
BuildTime: 0 minutes 52.72 seconds
CheckCommand: BiocCheckGitClone('EnrichDO') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3468/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO.install-out.txt EnrichDO_0.99.3.tar.gz && BiocCheck('EnrichDO_0.99.3.tar.gz', `new-package`=TRUE)
CheckTime: 5 minutes 11.40 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 3854.56 KiB
BuildID:: EnrichDO_20240706091115
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: EnrichDO. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1.

nebbiolo2 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘EnrichDO/DESCRIPTION’ ... OK
* preparing ‘EnrichDO’:
* 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 ‘EnrichDO_0.99.3.tar.gz’


nebbiolo2 CHECK output

[top]

===============================

 BiocCheckGitClone('EnrichDO')

===============================

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: EnrichDO
─ PackageVersion: 0.99.3
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO
─ 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...
    * NOTE: (Optional) CITATION file not found. Only include a CITATION
      file if there is a preprint or publication for this Bioconductor
      package. Note that Bioconductor packages are not required to have
      a CITATION file but it is useful both for users and for tracking
      Bioconductor project-wide metrics. When including a CITATION
      file, add the publication using the 'doi' argument of
      'bibentry()'.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES

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




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichDO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnrichDO’ version ‘0.99.3’
* 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 ‘EnrichDO’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    extdata   5.2Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [21s/21s] NOTE
TermStruct: no visible binding for global variable ‘doterms’
TermStruct: no visible binding for global variable ‘DOID’
TermStruct: no visible binding for global variable ‘parent.arr’
TermStruct: no visible binding for global variable ‘gene.len’
TermStruct: no visible binding for global variable ‘geneRatio’
TermStruct: no visible binding for global variable ‘p’
binomTest: no visible binding for global variable ‘dotermgenes’
chisqTest: no visible binding for global variable ‘dotermgenes’
computeTermSig: no visible binding for '<<-' assignment to ‘enrich’
computeTermSig: no visible binding for global variable ‘enrich’
computeTermSig : <anonymous>: no visible binding for global variable
  ‘enrich’
computeTermSig : <anonymous>: no visible binding for '<<-' assignment
  to ‘enrich’
computeTermSig : <anonymous>: no visible binding for global variable
  ‘DOID_C’
computeTermSig : <anonymous> : <anonymous>: no visible binding for
  global variable ‘enrich’
computeTermSig : <anonymous> : <anonymous>: no visible binding for
  '<<-' assignment to ‘enrich’
doEnrich: no visible binding for global variable ‘dotermgenes’
doEnrich: no visible binding for '<<-' assignment to ‘enrich’
doEnrich: no visible binding for global variable ‘enrich’
doEnrich: no visible binding for global variable ‘gene.arr’
doEnrich: no visible binding for global variable ‘cg.arr’
doEnrich: no visible binding for global variable ‘cg.len’
doEnrich: no visible binding for global variable ‘gene.len’
doEnrich: no visible binding for '<<-' assignment to ‘DOID_C’
doEnrich : <anonymous>: no visible binding for '<<-' assignment to
  ‘enrich’
doEnrich : <anonymous>: no visible binding for global variable ‘enrich’
doEnrich : <anonymous>: no visible binding for global variable ‘DOID_C’
doEnrich: no visible binding for global variable ‘level’
doEnrich: no visible binding for global variable ‘DOID’
doEnrich: no visible binding for global variable ‘DOID_C’
doEnrich: no visible binding for global variable ‘p’
drawBarGraph: no visible binding for global variable ‘p’
drawBarGraph: no visible binding for global variable ‘DOID’
drawBarGraph: no visible binding for global variable ‘DOTerm’
drawBarGraph: no visible binding for global variable ‘cg.len’
drawBarGraph: no visible binding for global variable ‘ig.len’
drawBarGraph: no visible global function definition for ‘na.omit’
drawBarGraph: no visible global function definition for ‘reorder’
drawBarGraph: no visible binding for global variable ‘DO’
drawBarGraph: no visible binding for global variable ‘log10p’
drawBarGraph: no visible binding for global variable ‘geneRatio’
drawGraphViz: no visible binding for global variable ‘enrich’
drawGraphViz: no visible binding for global variable ‘p’
drawGraphViz: no visible binding for global variable ‘DOID’
drawGraphViz: no visible binding for global variable ‘DOTerm’
drawGraphViz: no visible binding for global variable ‘parent.arr’
drawGraphViz: no visible binding for global variable ‘cg.len’
drawGraphViz: no visible binding for global variable ‘log10p’
drawGraphViz: no visible global function definition for ‘text’
drawHeatmap: no visible binding for '<<-' assignment to ‘weight_matrix’
drawHeatmap : <anonymous>: no visible binding for '<<-' assignment to
  ‘weight_matrix’
drawHeatmap : <anonymous>: no visible binding for global variable
  ‘weight_matrix’
drawHeatmap: no visible binding for global variable ‘weight_matrix’
drawPointGraph: no visible binding for global variable ‘p’
drawPointGraph: no visible binding for global variable ‘DOID’
drawPointGraph: no visible binding for global variable ‘DOTerm’
drawPointGraph: no visible binding for global variable ‘cg.len’
drawPointGraph: no visible binding for global variable ‘gene.len’
drawPointGraph: no visible binding for global variable ‘ig.len’
drawPointGraph: no visible global function definition for ‘na.omit’
drawPointGraph: no visible binding for global variable ‘geneRatio’
drawPointGraph: no visible global function definition for ‘reorder’
drawPointGraph: no visible binding for global variable ‘DO’
drawPointGraph: no visible binding for global variable ‘log10p’
fisherTest: no visible binding for global variable ‘dotermgenes’
getAncestors: no visible binding for global variable ‘enrich’
getAncestors: no visible global function definition for ‘str’
hypergeomTest: no visible binding for global variable ‘dotermgenes’
init: no visible binding for global variable ‘doterms’
init: no visible binding for '<<-' assignment to ‘enrich’
init: no visible binding for global variable ‘gene.len’
init: no visible binding for global variable ‘gene.arr’
init: no visible binding for global variable ‘weight.arr’
logoddTest: no visible binding for global variable ‘dotermgenes’
writeDoTerms: no visible binding for global variable ‘gene.arr’
writeDoTerms: no visible binding for global variable ‘parent.arr’
writeDoTerms: no visible binding for global variable ‘child.arr’
writeDoTerms: no visible binding for global variable ‘DOID’
writeDoTerms: no visible binding for global variable ‘DOTerm’
writeDoTerms: no visible binding for global variable ‘level’
writeDoTerms: no visible binding for global variable ‘genes’
writeDoTerms: no visible binding for global variable ‘parents’
writeDoTerms: no visible binding for global variable ‘children’
writeDoTerms: no visible binding for global variable ‘gene.len’
writeDoTerms: no visible binding for global variable ‘parent.len’
writeDoTerms: no visible binding for global variable ‘child.len’
writeResult: no visible binding for global variable ‘cg.arr’
writeResult: no visible binding for global variable ‘cg.len’
writeResult: no visible binding for global variable ‘ig.len’
writeResult: no visible binding for global variable ‘gene.len’
writeResult: no visible binding for global variable ‘dotermgenes’
writeResult: no visible binding for global variable ‘DOID’
writeResult: no visible binding for global variable ‘DOTerm’
writeResult: no visible binding for global variable ‘p’
writeResult: no visible binding for global variable ‘geneRatio’
writeResult: no visible binding for global variable ‘bgRatio’
writeResult: no visible binding for global variable ‘cg’
Undefined global functions or variables:
  DO DOID DOID_C DOTerm bgRatio cg cg.arr cg.len child.arr child.len
  children dotermgenes doterms enrich gene.arr gene.len geneRatio genes
  ig.len level log10p na.omit p parent.arr parent.len parents reorder
  str text weight.arr weight_matrix
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "na.omit", "reorder")
  importFrom("utils", "str")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘EnrichDO/R/EnrichDO_algorithm.R’:
  assign("doterms", doterms, pos = 1)
  assign("enrich", enrich, pos = 1)
  assign("enrich", NULL, pos = 1)
  assign("DOID_C", NULL, pos = 1)
  assign("doterms", doterms, pos = 1)
File ‘EnrichDO/R/EnrichDO_visualization.R’:
  assign("weight_matrix", NULL, pos = 1)
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [168s/168s] OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
doEnrich       65.188  0.656  65.845
writeDoTerms   15.865  0.258  16.014
writeResult    15.516  0.236  15.663
drawPointGraph 15.683  0.032  15.716
drawHeatmap    14.954  0.023  14.980
drawGraphViz   14.854  0.119  14.974
drawBarGraph   14.775  0.108  14.884
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE

Status: 2 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO.Rcheck/00check.log’
for details.





===============================

 BiocCheck('EnrichDO_0.99.3.tar.gz')

===============================

─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: EnrichDO
─ PackageVersion: 0.99.3
─ sourceDir: /tmp/RtmpTfYTEY/file3b1e374c6d46bb/EnrichDO
─ installDir: /tmp/RtmpTfYTEY/file3b1e371ddadcb1
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3468/aef8420194e39f971e88a5541d44fe77141a49a5/EnrichDO.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 3.5.0 to 4.4.0.
* 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 of less
      than 3 sentences. Provide a more detailed description of the
      package.
* 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 recommended DESCRIPTION fields...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of EnrichDO...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 21 times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 3 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...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 103 lines (11%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 28 lines (3%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 268 lines
      (28%) 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...
    * ERROR: Subscribe to the Bioc-devel mailing list by going to
      https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 16 NOTES

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

nebbiolo2 BUILD BIN output

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