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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:iASeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings iASeq_1.51.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/iASeq.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘iASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iASeq’ version ‘1.51.0’
* 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 ‘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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/iASeq.Rcheck/00check.log’
for details.