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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ConsensusClusterPlus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ConsensusClusterPlus_1.64.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ConsensusClusterPlus.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ConsensusClusterPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ConsensusClusterPlus’ version ‘1.64.0’
* 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 ‘ConsensusClusterPlus’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
GPL version 2
Standardizable: TRUE
Standardized license specification:
GPL-2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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
Namespace in Imports field not imported from: ‘ALL’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ConsensusClusterPlus: warning in heatmap(pc, Colv = NA, Rowv = NA, symm
= FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F,
labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk,
sep = ""), ColSideCol = oc): partial argument match of 'mar' to
'margins'
ConsensusClusterPlus: warning in heatmap(pc, Colv = NA, Rowv = NA, symm
= FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F,
labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk,
sep = ""), ColSideCol = oc): partial argument match of 'ColSideCol'
to 'ColSideColors'
ConsensusClusterPlus: warning in heatmap(pc, Colv = as.dendrogram(hc),
Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE,
labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix
k=", tk, sep = ""), ColSideCol = colorList[[1]]): partial argument
match of 'mar' to 'margins'
ConsensusClusterPlus: warning in heatmap(pc, Colv = as.dendrogram(hc),
Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE,
labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix
k=", tk, sep = ""), ColSideCol = colorList[[1]]): partial argument
match of 'ColSideCol' to 'ColSideColors'
ConsensusClusterPlus: no visible global function definition for
‘bitmap’
ConsensusClusterPlus: no visible global function definition for
‘postscript’
calcICL: no visible global function definition for ‘postscript’
calcICL: no visible global function definition for ‘bitmap’
Undefined global functions or variables:
bitmap postscript
Consider adding
importFrom("grDevices", "bitmap", "postscript")
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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ConsensusClusterPlus.Rcheck/00check.log’
for details.
