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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:attract.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings attract_1.58.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/attract.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 ‘attract/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘attract’ version ‘1.58.0’
* 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 ‘attract’ 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
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
  partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'adjust' to 'adjust.method'
* checking Rd files ... NOTE
checkRd: (-1) attract-package.Rd:34: Lost braces
    34 | M\"{u}ller F et al. 2008. Regulatory networks define phenotypic classes of human stem cell lines. Nature. 455(7211): 401. 
       |    ^
checkRd: (-1) exprs.dat.Rd:29: Lost braces
    29 | M\"{u}ller F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405.
       |    ^
checkRd: (-1) findOnepwaySynexprs.Rd:15: Lost braces
    15 |                 a single character string denoting the KEGG or reactome ID of the pathway module to be analyzed or a character code{vector} of gene names of a pathway. 
       |                                                                                                                                    ^
checkRd: (-1) findSynexprs.Rd:16: Lost braces
    16 |     It may also be a character code{vector} of gene names of a pathway if defining a custom pathway.
       |                                    ^
checkRd: (-1) loring.eset.Rd:23: Lost braces
    23 | M\"{u}ller, F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405.
       |    ^
checkRd: (-1) samp.info.Rd:28: Lost braces
    28 | M\"{u}ller F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405.
       |    ^
checkRd: (-1) subset.loring.eset.Rd:25: Lost braces
    25 | M\"{u}ller, F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405.
       |    ^
* 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
calcFuncSynexprs 25.090  2.752   29.78
findAttractors    7.917  0.398    8.75
* 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/attract.Rcheck/00check.log’
for details.