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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:KCsmart.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings KCsmart_2.64.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/KCsmart.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘KCsmart/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KCsmart’ version ‘2.64.0’
* 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 ‘KCsmart’ 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.
* 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 ... NOTE
'library' or 'require' call to ‘siggenes’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘siggenes’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.add2spmc’ ‘.checkMirrorLocs’ ‘.comparativeKcPerms’
  ‘.comparativeKcSiggenes’ ‘.convertCGHbase’ ‘.findCutoffByFdr’
  ‘.findPeaks’ ‘.findfdrcutoff’ ‘.getRegions’ ‘.getSigRegions’
  ‘.makePermutations’ ‘.mirrorData’ ‘.permutedSpm’ ‘.samplePointMatrix’
  ‘.samplePointMatrixOld’ ‘.snr’ ‘.spm2spmc’ ‘.varr’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.comparativeKcSiggenes: no visible binding for global variable ‘sam’
.samplePointMatrix: no visible global function definition for ‘locpoly’
.samplePointMatrix: no visible global function definition for ‘bkde’
.samplePointMatrixOld: no visible global function definition for
  ‘aggregate’
.samplePointMatrixOld: no visible global function definition for
  ‘dnorm’
.snr: no visible global function definition for ‘quantile’
getSigRegionsCompKC: no visible global function definition for
  ‘findDelta’
idPoints: no visible global function definition for ‘dev.set’
idPoints: no visible global function definition for ‘identify’
plot,compKc-missing: no visible global function definition for ‘layout’
plot,compKc-missing: no visible global function definition for ‘abline’
plot,compKc-missing: no visible global function definition for ‘rect’
plot,compKc-missing: no visible global function definition for ‘lines’
plot,compKc-missing: no visible global function definition for ‘text’
plot,compKc-missing: no visible global function definition for ‘axis’
plot,samplePointMatrix-missing: no visible global function definition
  for ‘layout’
plot,samplePointMatrix-missing: no visible global function definition
  for ‘abline’
plot,samplePointMatrix-missing: no visible global function definition
  for ‘tail’
plot,samplePointMatrix-missing: no visible global function definition
  for ‘polygon’
plot,samplePointMatrix-missing: no visible global function definition
  for ‘lines’
plot,samplePointMatrix-missing: no visible global function definition
  for ‘segments’
plot,samplePointMatrix-missing: no visible global function definition
  for ‘text’
plot,samplePointMatrix-missing: no visible global function definition
  for ‘axis’
plot,scaleSpace-missing: no visible global function definition for
  ‘dev.cur’
plot,scaleSpace-missing: no visible global function definition for
  ‘x11’
plot,scaleSpace-missing: no visible global function definition for
  ‘heat.colors’
plot,scaleSpace-missing: no visible global function definition for
  ‘dev.set’
plot,scaleSpace-missing: no visible global function definition for
  ‘segments’
plot,scaleSpace-missing: no visible global function definition for
  ‘abline’
plot,scaleSpace-missing: no visible global function definition for
  ‘text’
plot,scaleSpace-missing: no visible global function definition for
  ‘axis’
Undefined global functions or variables:
  abline aggregate axis bkde dev.cur dev.set dnorm findDelta
  heat.colors identify layout lines locpoly polygon quantile rect sam
  segments tail text x11
Consider adding
  importFrom("grDevices", "dev.cur", "dev.set", "heat.colors", "x11")
  importFrom("graphics", "abline", "axis", "identify", "layout", "lines",
             "polygon", "rect", "segments", "text")
  importFrom("stats", "aggregate", "dnorm", "quantile")
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) write.table.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.table.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.table.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.table.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.table.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.table.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.table.Rd:76: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'probeAnnotation,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
KCsmart-package 6.636  0.144    6.78
* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/KCsmart.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL KCsmart
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘KCsmart’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘write.table’ from package ‘utils’ in package ‘KCsmart’
** 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 (KCsmart)