BioC 3.2: CHECK report for KCsmart on linux1.bioconductor.org

Package: KCsmart

Version: 2.28.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings KCsmart_2.28.0.tar.gz

StartedAt: 2015-10-27 05:00:41 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:01:57 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 75.9 seconds

RetCode: 0

Status:  OK

CheckDir: KCsmart.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings KCsmart_2.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/KCsmart.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KCsmart/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KCsmart’ version ‘2.28.0’
* 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 ‘KCsmart’ can be installed ... [3s/3s] 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
* 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’
getSigRegionsCompKC: no visible global function definition for
  ‘findDelta’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/44s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
KCsmart-package      12.233  0.159  12.397
getSigRegionsCompKC   6.773  0.020   6.793
calcSpmCollection     6.113  0.036   6.157
compareSpmCollection  5.831  0.008   5.844
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/KCsmart.Rcheck/00check.log’
for details.

* installing *source* package ‘KCsmart’ ...
** R
** data
** inst
** preparing 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
* DONE (KCsmart)

name	user	system	elapsed
KCsmart-package	12.233	0.159	12.397
calcSpm	0.959	0.004	0.964
calcSpmCollection	6.113	0.036	6.157
compKc-class	0.002	0.000	0.001
compKcSigRegions-class	0.001	0.000	0.001
compareSpmCollection	5.831	0.008	5.844
findSigLevelFdr	1.759	0.004	1.763
findSigLevelTrad	1.471	0.000	1.473
getSigRegionsCompKC	6.773	0.020	6.793
getSigSegments	1.662	0.000	1.663
idPoints	0.011	0.000	0.012
plot	1.741	0.008	1.751
plotScaleSpace	2.680	0.004	2.684
samplePointMatrix-class	0.002	0.000	0.002
sigSegments-class	0.001	0.000	0.001
spmCollection-class	0.001	0.000	0.001
write.table	1.687	0.000	1.690