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This page was generated on 2022-01-17 13:07:51 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for KCsmart on machv2


To the developers/maintainers of the KCsmart package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/KCsmart.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 977/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KCsmart 2.52.0  (landing page)
Jorma de Ronde
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/KCsmart
git_branch: RELEASE_3_14
git_last_commit: e6b33a9
git_last_commit_date: 2021-10-26 11:53:01 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: KCsmart
Version: 2.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:KCsmart.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings KCsmart_2.52.0.tar.gz
StartedAt: 2022-01-16 14:26:28 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 14:28:46 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 137.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: KCsmart.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:KCsmart.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings KCsmart_2.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/KCsmart.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.52.0’
* 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 ... 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
KCsmart-package      12.059  0.804  12.946
calcSpmCollection     5.825  0.497   6.325
compareSpmCollection  5.360  0.509   5.874
getSigRegionsCompKC   5.194  0.442   5.669
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/KCsmart.Rcheck/00check.log’
for details.



Installation output

KCsmart.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL KCsmart
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output


Example timings

KCsmart.Rcheck/KCsmart-Ex.timings

nameusersystemelapsed
KCsmart-package12.059 0.80412.946
calcSpm1.0690.0901.161
calcSpmCollection5.8250.4976.325
compKc-class0.0010.0010.001
compKcSigRegions-class0.0010.0010.001
compareSpmCollection5.3600.5095.874
findSigLevelFdr2.2810.1162.403
findSigLevelTrad1.9350.0962.035
getSigRegionsCompKC5.1940.4425.669
getSigSegments1.8320.0771.910
idPoints0.0160.0050.020
plot2.7830.1172.977
plotScaleSpace3.4930.2143.716
samplePointMatrix-class0.0010.0010.002
sigSegments-class0.0010.0010.001
spmCollection-class0.0010.0010.001
write.table1.6380.0741.714