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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAGeCKFlute.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MAGeCKFlute_2.9.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MAGeCKFlute.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MAGeCKFlute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAGeCKFlute' version '2.9.0'
* 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 whether package 'MAGeCKFlute' can be installed ... WARNING
Found the following significant warnings:
  Warning: Not internet connectivity. Unable to create Hub accessors.
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MAGeCKFlute.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 20.7Mb
  sub-directories of 1Mb or more:
    extdata  20.3Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
EnrichedFilter: no visible global function definition for 'is'
EnrichedGeneView: no visible global function definition for 'is'
EnrichedView: no visible global function definition for 'is'
EnrichedView: no visible global function definition for 'slot'
enrich.HGT: no visible global function definition for 'new'
Undefined global functions or variables:
  is new slot
Consider adding
  importFrom("methods", "is", "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) FluteMLE.Rd:87: Lost braces; missing escapes or markup?
    87 |   \item {QC}: {Quality control}
       |               ^
checkRd: (-1) FluteMLE.Rd:88: Lost braces; missing escapes or markup?
    88 |   \item {Selection}: {Positive selection and negative selection.}
       |                      ^
checkRd: (-1) FluteMLE.Rd:89: Lost braces; missing escapes or markup?
    89 |   \item {Enrichment}: {Enrichment analysis for positive and negative selection genes.}
       |                       ^
checkRd: (-1) FluteMLE.Rd:90: Lost braces; missing escapes or markup?
    90 |   \item {PathwayView}: {Pathway view for top enriched pathways.}
       |                        ^
checkRd: (-1) getOrg.Rd:18: Lost braces
    18 | \code{pkg}{annotation package name}
       |           ^
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
MAView 19.97   0.21   20.18
* 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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/MAGeCKFlute.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MAGeCKFlute
###
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'MAGeCKFlute' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: Not internet connectivity. Unable to create Hub accessors.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Not internet connectivity. Unable to create Hub accessors.
** testing if installed package can be loaded from final location
Warning: Not internet connectivity. Unable to create Hub accessors.
** testing if installed package keeps a record of temporary installation path
* DONE (MAGeCKFlute)