Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:02 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 clippda on lconway


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? 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 339/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.48.0  (landing page)
Stephen Nyangoma
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/clippda
git_branch: RELEASE_3_16
git_last_commit: 45a4976
git_last_commit_date: 2022-11-01 11:04:36 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: clippda
Version: 1.48.0
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_1.48.0.tar.gz
StartedAt: 2023-04-10 19:24:55 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:28:10 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 194.7 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_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/clippda.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.48.0’
* 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          66.812  3.116  70.367
sampleSize               38.142  2.021  40.341
sampleSizeParameters     18.942  1.039  20.126
sample_technicalVariance  5.420  0.251   5.721
* 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-3.16-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/4.2/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
ZvaluescasesVcontrolsPlots0.0080.0020.010
ZvaluesfrommultinomPlots0.8670.0740.943
aclinicalProteomicsData-class0.0360.0050.041
aclinicalProteomicsData-methods0.2040.3610.573
betweensampleVariance0.9900.1011.096
checkNo.replicates0.0670.0120.079
clippda-package66.812 3.11670.367
f0.0010.0000.001
fisherInformation0.0430.0050.048
liverRawData0.0030.0010.004
liver_pheno0.0010.0020.003
liverdata0.9680.1481.125
mostSimilarTwo0.0010.0010.001
negativeIntensitiesCorrection0.2280.0740.305
phenoDataFrame0.0320.0040.036
pheno_urine0.0010.0010.003
preProcRepeatedPeakData0.8980.1131.016
proteomicsExprsData0.0810.0040.085
proteomicspData0.0340.0040.038
replicateCorrelations3.3510.1903.553
sampleClusteredData0.2200.0380.260
sampleSize38.142 2.02140.341
sampleSize3DscatterPlots0.0130.0020.014
sampleSizeContourPlots0.0220.0030.025
sampleSizeParameters18.942 1.03920.126
sample_technicalVariance5.4200.2515.721
spectrumFilter0.8770.1281.014
ztwo0.0000.0000.001