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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metaSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metaSeq_1.45.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/metaSeq.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 ‘metaSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaSeq’ version ‘1.45.0’
* 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 ‘metaSeq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 objects imported by ':::' calls:
  ‘NOISeq:::busca’ ‘NOISeq:::n.menor’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘oneside.noiseq’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘metaSeq/R/Accelerate.NOISeq.R’:
  assignInNamespace("busca", busca, ns = "NOISeq", envir = env)
  assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env)
  assignInNamespace("busca", busca, ns = "NOISeq", envir = env)
  assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env)
File ‘metaSeq/R/Reset.Accelerate.NOISeq.R’:
  assignInNamespace("busca", original.busca, ns = "NOISeq", envir = env)
  assignInNamespace("n.menor", original.n.menor, ns = "NOISeq", 
    envir = env)
File ‘metaSeq/R/oneside.noiseq.R’:
  assignInNamespace("probdeg", custom.probdeg, ns = "NOISeq", envir = env)
  assignInNamespace("MD", custom.MD, ns = "NOISeq", envir = env)
  assignInNamespace("probdeg", original.probdeg, ns = "NOISeq", 
    envir = env)
  assignInNamespace("MD", original.MD, ns = "NOISeq", envir = env)

Accelerate.NOISeq: no visible global function definition for ‘data’
Accelerate.NOISeq: no visible binding for global variable
  ‘text.n.menor_unix’
Accelerate.NOISeq: no visible binding for global variable
  ‘text.busca_unix’
Accelerate.NOISeq: no visible global function definition for
  ‘assignInNamespace’
Accelerate.NOISeq: no visible binding for global variable ‘busca’
Accelerate.NOISeq: no visible binding for global variable ‘nmenor’
Accelerate.NOISeq: no visible binding for global variable
  ‘text.n.menor_win’
Accelerate.NOISeq: no visible binding for global variable
  ‘text.busca_win’
Reset.Accelerate.NOISeq: no visible global function definition for
  ‘assignInNamespace’
custom.MD: no visible global function definition for ‘combn’
custom.probdeg: no visible global function definition for ‘na.omit’
each.Fisher.ignore.test: no visible global function definition for
  ‘pchisq’
each.Fisher.test: no visible global function definition for ‘pchisq’
each.Stouffer.ignore.test: no visible global function definition for
  ‘qnorm’
each.Stouffer.ignore.test: no visible global function definition for
  ‘pnorm’
each.Stouffer.test: no visible global function definition for ‘qnorm’
each.Stouffer.test: no visible global function definition for ‘pnorm’
oneside.noiseq: no visible global function definition for
  ‘assignInNamespace’
original.MD: no visible global function definition for ‘combn’
original.probdeg: no visible global function definition for ‘na.omit’
original.probdeg: no visible binding for global variable ‘n.menor’
original.probdeg: no visible binding for global variable ‘busca’
Undefined global functions or variables:
  assignInNamespace busca combn data n.menor na.omit nmenor pchisq
  pnorm qnorm text.busca_unix text.busca_win text.n.menor_unix
  text.n.menor_win
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm", "qnorm")
  importFrom("utils", "assignInNamespace", "combn", "data")
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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘Fig1.jpeg’, ‘Fig2.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/metaSeq.Rcheck/00check.log’
for details.

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