Package: KCsmart

Version: 2.42.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KCsmart.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings KCsmart_2.42.0.tar.gz

StartedAt: 2019-10-16 04:44:13 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:47:02 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 169.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: KCsmart.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KCsmart.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings KCsmart_2.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/KCsmart.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KCsmart/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KCsmart' version '2.42.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
'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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
KCsmart-package     11.77   0.25   12.02
calcSpmCollection    5.20   0.17    5.38
getSigRegionsCompKC  4.96   0.17    5.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
KCsmart-package 11.66   0.11   11.77
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/KCsmart.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/KCsmart_2.42.0.tar.gz && rm -rf KCsmart.buildbin-libdir && mkdir KCsmart.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KCsmart.buildbin-libdir KCsmart_2.42.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL KCsmart_2.42.0.zip && rm KCsmart_2.42.0.tar.gz KCsmart_2.42.0.zip
###
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install for i386

* 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
  converting help for package 'KCsmart'
    finding HTML links ... done
    KCData-class                            html  
    KCsmart-package                         html  
    KcghData-class                          html  
    KcghDataMirror-class                    html  
    KcghDataSplit-class                     html  
    KcghDataSum-class                       html  
    calcSpm                                 html  
    calcSpmCollection                       html  
    compKc-class                            html  
    compKcSigRegions-class                  html  
    compareSpmCollection                    html  
    findSigLevelFdr                         html  
    findSigLevelTrad                        html  
    getSigRegionsCompKC                     html  
    getSigSegments                          html  
    hsMirrorLocs                            html  
    hsSampleData                            html  
    idPoints                                html  
    mmMirrorLocs                            html  
    plot                                    html  
    plotScaleSpace                          html  
    probeAnnotation-class                   html  
    samplePointMatrix-class                 html  
    sigSegments-class                       html  
    spmCollection-class                     html  
    write.table                             html  
** 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

install for x64

* installing *source* package 'KCsmart' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KCsmart' as KCsmart_2.42.0.zip
* DONE (KCsmart)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'KCsmart' successfully unpacked and MD5 sums checked