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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gatom.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gatom_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gatom.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gatom/DESCRIPTION’ ... OK
* this is package ‘gatom’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘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 ... 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 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 ... 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 ... OK
* checking Rd metadata ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
makeOrgGatomAnnotation 5.624  0.243   20.86
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::setdiff(component, V(m.connected)[nei(v)]$name)
    5. │ └─base::as.vector(y)
    6. ├─V(m.connected)[nei(v)]
    7. ├─igraph:::`[.igraph.vs`(V(m.connected), nei(v))
    8. │ └─base::lapply(args, rlang::eval_tidy, data = data_mask)
    9. │   └─rlang (local) FUN(X[[i]], ...)
   10. └─igraph (local) nei(v)
   11.   └─lifecycle::deprecate_stop("2.1.0", "nei()", ".nei()")
   12.     └─lifecycle:::deprecate_stop0(msg)
   13.       └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 83 ]
  Error: Test failures
  Execution halted
* 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 ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/gatom.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gatom
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* 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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gatom)
> 
> test_check("gatom")
[WARNING] Could not deduce format from file extension 
  Defaulting to html
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'file970c39b06d29' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 83 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_gatom.R:50:13'): overall pipeline works ────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `nei()` was deprecated in igraph 2.1.0 and is now defunct.
ℹ Please use `.nei()` instead.
Backtrace:
     ▆
  1. ├─testthat::expect_equivalent(...) at test_gatom.R:50:13
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─base::setdiff(component, V(m.connected)[nei(v)]$name)
  5. │ └─base::as.vector(y)
  6. ├─V(m.connected)[nei(v)]
  7. ├─igraph:::`[.igraph.vs`(V(m.connected), nei(v))
  8. │ └─base::lapply(args, rlang::eval_tidy, data = data_mask)
  9. │   └─rlang (local) FUN(X[[i]], ...)
 10. └─igraph (local) nei(v)
 11.   └─lifecycle::deprecate_stop("2.1.0", "nei()", ".nei()")
 12.     └─lifecycle:::deprecate_stop0(msg)
 13.       └─rlang::cnd_signal(...)

[ FAIL 1 | WARN 7 | SKIP 0 | PASS 83 ]
Error: Test failures
Execution halted