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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BLMA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BLMA_1.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BLMA.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 ‘BLMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BLMA’ version ‘1.31.0’
* 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'
 INFO
Depends: includes the non-default packages:
  'ROntoTools', 'GSA', 'PADOG', 'limma', 'graph', 'parallel',
  'Biobase', 'metafor'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘BLMA’ 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
addCLT: warning in pnorm(mean(x), 1/2, sqrt(1/(12 * n)), lower = TRUE):
  partial argument match of 'lower' to 'lower.tail'
additiveMethod: warning in pnorm(sum(x), n/2, sqrt(n/12), lower =
  TRUE): partial argument match of 'lower' to 'lower.tail'
bilevelAnalysisGeneset : <anonymous>: warning in topTable(fit2, adjust
  = "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
  pCutoff): partial argument match of 'adjust' to 'adjust.method'
bilevelAnalysisPathway : <anonymous>: warning in topTable(fit2, adjust
  = "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
  pCutoff): partial argument match of 'adjust' to 'adjust.method'
fisherMethod: warning in pchisq(-2 * sum(log(x)), df = 2 * length(x),
  lower = FALSE): partial argument match of 'lower' to 'lower.tail'
getStatistics: warning in topTable(fit2, adjust = "fdr", sort.by = "B",
  number = Inf): partial argument match of 'adjust' to 'adjust.method'
intraAnalysisGene : <anonymous>: warning in topTable(fit2, adjust =
  "none", sort.by = "none", number = Inf): partial argument match of
  'adjust' to 'adjust.method'
intraAnalysisGene: warning in topTable(fit2, adjust = "none", sort.by =
  "none", number = Inf): partial argument match of 'adjust' to
  'adjust.method'
calculateFC: no visible binding for global variable ‘m1i’
calculateFC: no visible binding for global variable ‘sd1i’
calculateFC: no visible binding for global variable ‘n1i’
calculateFC: no visible binding for global variable ‘m2i’
calculateFC: no visible binding for global variable ‘sd2i’
calculateFC: no visible binding for global variable ‘n2i’
calculateFC: no visible binding for global variable ‘yi’
getStatistics: no visible binding for global variable ‘d’
hierClustering: no visible binding for global variable ‘km’
hierClustering: no visible global function definition for ‘clusGap’
hierClustering: no visible global function definition for ‘maxSE’
intraAnalysisGene: no visible binding for global variable ‘d’
Undefined global functions or variables:
  clusGap d km m1i m2i maxSE n1i n2i sd1i sd2i yi
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bilevelAnalysisGeneset.Rd: GSA, padog
  bilevelAnalysisPathway.Rd: graphNEL, pe
  loadKEGGPathways.Rd: graphNEL, keggPathwayGraphs, keggPathwayNames
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
getStatistics          74.109  0.475  74.595
bilevelAnalysisGeneset 70.138  0.346  70.493
bilevelAnalysisPathway 59.521  0.197  59.718
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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/BLMA.Rcheck/00check.log’
for details.