Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘gatom/DESCRIPTION’ ... OK
* preparing ‘gatom’:
* 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 ‘gatom_0.99.2.tar.gz’

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 BiocCheckGitClone('gatom')

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─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: gatom
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3170/b59259c944421bce38b097712d716abda71f15f9/gatom
─ 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...
* Checking that provided CITATION file is correctly formatted...

─ 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/3170/b59259c944421bce38b097712d716abda71f15f9/gatom.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 ‘gatom/DESCRIPTION’ ... OK
* this is package ‘gatom’ version ‘0.99.2’
* 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 ‘gatom’ 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘htmlwidgets:::createWidgetId’
  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 ... [12s/12s] NOTE
.makeEdgeTable: no visible binding for global variable ‘gene’
.makeEdgeTable: no visible binding for global variable ‘ID’
.makeEdgeTable: no visible binding for global variable ‘pval’
.makeEdgeTable: no visible binding for global variable ‘enzyme’
.makeEdgeTable: no visible binding for global variable ‘reaction’
.makeEdgeTable: no visible binding for global variable ‘origin’
.makeEdgeTable: no visible binding for global variable ‘atom.x’
.makeEdgeTable: no visible binding for global variable ‘atom.y’
.makeVertexTable: no visible binding for global variable ‘ID’
.makeVertexTable: no visible binding for global variable ‘pval’
.makeVertexTable: no visible binding for global variable ‘metabolite’
.makeVertexTable: no visible binding for global variable
  ‘base_metabolite’
.makeVertexTable: no visible binding for global variable ‘atom’
.makeVertexTable: no visible binding for global variable ‘origin’
addHighlyExpressedEdges: no visible binding for global variable ‘from’
addHighlyExpressedEdges: no visible binding for global variable ‘to’
addHighlyExpressedEdges: no visible binding for global variable
  ‘signalRank’
collapseAtomsIntoMetabolites: no visible global function definition for
  ‘setNames’
collapseAtomsIntoMetabolites: no visible binding for global variable
  ‘metabolite’
collapseAtomsIntoMetabolites: no visible binding for global variable
  ‘name’
collapseAtomsIntoMetabolites: no visible binding for global variable
  ‘from’
collapseAtomsIntoMetabolites: no visible binding for global variable
  ‘to’
convertPvalDT: no visible binding for global variable ‘pval’
findColumn: no visible global function definition for ‘na.omit’
force_alg: no visible global function definition for ‘aggregate’
getDotColor: no visible global function definition for ‘rgb’
getEdgeDotStrings : <anonymous>: no visible global function definition
  for ‘na.omit’
getEdgeXmlStrings : <anonymous>: no visible global function definition
  for ‘na.omit’
getMetabolicPathways: no visible global function definition for
  ‘na.omit’
getMetabolicPathways: no visible binding for global variable ‘PATHNAME’
getMetabolicPathways: no visible global function definition for
  ‘read.table’
getModulePdfLayout: no visible global function definition for ‘pdf’
getModulePdfLayout: no visible global function definition for ‘dev.off’
getNodeDotStrings : <anonymous>: no visible global function definition
  for ‘na.omit’
getNodeXmlStrings : <anonymous>: no visible global function definition
  for ‘na.omit’
makeMetabolicGraph: no visible binding for global variable ‘signalRank’
makeMetabolicGraph: no visible binding for global variable ‘atom.x’
makeMetabolicGraph: no visible binding for global variable ‘atom.y’
makeMetabolicGraph: no visible binding for global variable
  ‘metabolite.x’
makeMetabolicGraph: no visible binding for global variable
  ‘metabolite.y’
makeMetabolicGraph: no visible binding for global variable ‘metabolite’
makeOrgGatomAnnotation: no visible binding for global variable
  ‘species’
makeOrgGatomAnnotation: no visible binding for global variable
  ‘organism’
makeOrgGatomAnnotation: no visible global function definition for
  ‘keys’
makeOrgGatomAnnotation: no visible binding for global variable ‘gene’
makeOrgGatomAnnotation: no visible binding for global variable ‘symbol’
makeOrgGatomAnnotation: no visible binding for global variable ‘enzyme’
makeOrgGatomAnnotation: no visible global function definition for
  ‘tail’
makeOrgGatomAnnotation: no visible global function definition for
  ‘na.omit’
prepareDEColumn: no visible binding for global variable ‘ID’
prepareDEColumn: no visible binding for global variable ‘pval’
saveModuleToPdf: no visible global function definition for ‘pdf’
saveModuleToPdf: no visible global function definition for ‘dev.off’
scoreGraph: no visible binding for global variable ‘pval’
scoreGraph: no visible binding for global variable ‘signal’
scoreGraph: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  ID PATHNAME aggregate atom atom.x atom.y base_metabolite dev.off
  enzyme from gene keys metabolite metabolite.x metabolite.y na.omit
  name organism origin pdf pval reaction read.table rgb setNames signal
  signalRank species symbol tail to
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rgb")
  importFrom("stats", "aggregate", "na.omit", "setNames")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
* 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/42s] OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
makeOrgGatomAnnotation 9.001  0.507  32.295
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [23s/41s]
 [23s/41s] OK
* 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 ... [4s/4s] OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3170/b59259c944421bce38b097712d716abda71f15f9/gatom.Rcheck/00check.log’
for details.






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 BiocCheck('gatom_0.99.2.tar.gz')

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─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: gatom
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQSLU0I/filef11a45f9c690/gatom
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQSLU0I/filef11a7cb4e432
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3170/b59259c944421bce38b097712d716abda71f15f9/gatom.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...
* Checking package size...
* Checking individual file sizes...
    * WARNING: Package files exceed the 5MB size limit.
* 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
* 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 gatom...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid system() ; use system2()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 10 functions greater than 50 lines.
* Checking man page documentation...
    * 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; 271 lines (7%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 361 lines
      (10%) 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 | 10 NOTES

See the gatom.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 gatom_0.99.2.tar.gz'
>>>>>>> 

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