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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iASeq_1.50.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/iASeq.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iASeq’ version ‘1.50.0’
* 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 ‘iASeq’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ASErawfit: no visible global function definition for ‘var’
fdown.loglike: no visible global function definition for ‘pbeta’
fup.loglike: no visible global function definition for ‘pbeta’
iASeqmotiffit: no visible global function definition for ‘runif’
iASeqmotiffit: no visible global function definition for ‘var’
plotBIC: no visible global function definition for ‘lines’
plotMotif: no visible global function definition for ‘image’
singleEMfit: no visible global function definition for ‘var’
Undefined global functions or variables:
  image lines pbeta runif var
Consider adding
  importFrom("graphics", "image", "lines")
  importFrom("stats", "pbeta", "runif", "var")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) iASeqmotif.Rd:20: Lost braces; missing escapes or markup?
    20 | \details{For the i^{th} element of \eqn{K}, the function fits total number of \eqn{K[i]+1} motifs, \eqn{K[i]} non-null motifs and the null motif, to the data. Each SNP can belong to one of the \eqn{K[i]+1} possible motifs according to prior probability distribution, \eqn{motif.prior}. For SNPs in motif \eqn{j} \eqn{(j>=1)}, the probability that they are over expressed (or bound) for the reference allele in study \eqn{d} is \eqn{motif.qup(j,d)} and the probability that they are under expressed (or bound) is \eqn{motif.qdown(j,d)}. One should indicate the studyid, repid and refid for each column clearly.
       |                    ^
* 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/iASeq.Rcheck/00check.log’
for details.

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