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This page was generated on 2021-12-03 13:05:42 -0500 (Fri, 03 Dec 2021).

CHECK results for clippda on machv2

To the developers/maintainers of the clippda package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clippda.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 327/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.44.0  (landing page)
Stephen Nyangoma
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/clippda
git_branch: RELEASE_3_14
git_last_commit: 2d11172
git_last_commit_date: 2021-10-26 11:54:30 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: clippda
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clippda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clippda_1.44.0.tar.gz
StartedAt: 2021-12-02 12:52:10 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 12:57:00 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 289.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: clippda.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clippda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clippda_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/clippda.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 ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.44.0’
* checking package namespace information ... NOTE
  Namespaces with empty importFrom:
  ‘Biobase’ ‘tools’
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma', 'statmod', 'rgl', 'lattice', 'scatterplot3d', 'Biobase',
  'tools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘clippda’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): argument "textVersion" is missing, with no default
* 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' calls to packages already attached by Depends:
  ‘lattice’ ‘limma’ ‘rgl’ ‘scatterplot3d’ ‘statmod’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ZvaluescasesVcontrolsPlots: no visible global function definition for
  ‘lines’
ZvaluescasesVcontrolsPlots: no visible global function definition for
  ‘legend’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘rmultinom’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘density’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘lines’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘legend’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘cloud’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘var’
Undefined global functions or variables:
  cloud density legend lines rmultinom var
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "density", "rmultinom", "var")
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 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
clippda-package          101.037  2.857 103.970
sampleSize                60.307  1.784  62.136
sampleSizeParameters      29.960  0.940  30.920
sample_technicalVariance   7.747  0.209   7.960
replicateCorrelations      5.838  0.166   6.008
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/clippda.Rcheck/00check.log’
for details.



Installation output

clippda.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘clippda’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (clippda)

Tests output


Example timings

clippda.Rcheck/clippda-Ex.timings

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.0190.0040.023
ZvaluesfrommultinomPlots1.2110.1041.320
aclinicalProteomicsData-class0.0680.0070.075
aclinicalProteomicsData-methods0.4550.7601.253
betweensampleVariance1.5890.1191.709
checkNo.replicates0.1300.0190.149
clippda-package101.037 2.857103.970
f0.0010.0000.002
fisherInformation0.090.010.10
liverRawData0.0050.0010.007
liver_pheno0.0010.0020.004
liverdata1.8420.1932.036
mostSimilarTwo0.0030.0010.004
negativeIntensitiesCorrection0.3950.0520.448
phenoDataFrame0.0650.0050.069
pheno_urine0.0020.0020.003
preProcRepeatedPeakData1.5980.2421.841
proteomicsExprsData0.1720.0150.186
proteomicspData0.0570.0060.063
replicateCorrelations5.8380.1666.008
sampleClusteredData0.5480.0490.597
sampleSize60.307 1.78462.136
sampleSize3DscatterPlots0.0220.0030.026
sampleSizeContourPlots0.0420.0040.046
sampleSizeParameters29.96 0.9430.92
sample_technicalVariance7.7470.2097.960
spectrumFilter1.4150.0901.506
ztwo000