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This page was generated on 2021-12-03 13:04:45 -0500 (Fri, 03 Dec 2021).

CHECK results for clippda on nebbiolo2

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.
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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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:clippda.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings clippda_1.44.0.tar.gz
StartedAt: 2021-12-02 06:37:02 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 06:40:21 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 199.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: clippda.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:clippda.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings clippda_1.44.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/clippda.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
clippda-package          74.135  0.408  74.546
sampleSize               44.340  0.140  44.491
sampleSizeParameters     22.294  0.032  22.327
sample_technicalVariance  6.065  0.024   6.089
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/clippda.Rcheck/00check.log’
for details.



Installation output

clippda.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL clippda
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
ZvaluescasesVcontrolsPlots0.0090.0000.009
ZvaluesfrommultinomPlots1.1300.0481.177
aclinicalProteomicsData-class0.0530.0000.054
aclinicalProteomicsData-methods0.1670.1120.279
betweensampleVariance1.0270.0321.059
checkNo.replicates0.0660.0040.070
clippda-package74.135 0.40874.546
f0.0000.0000.001
fisherInformation0.060.000.06
liverRawData0.0040.0000.005
liver_pheno0.0010.0000.002
liverdata1.2670.0081.276
mostSimilarTwo0.0010.0000.002
negativeIntensitiesCorrection0.2310.0000.231
phenoDataFrame0.0510.0000.050
pheno_urine0.0010.0000.001
preProcRepeatedPeakData0.9690.0000.969
proteomicsExprsData0.1220.0000.121
proteomicspData0.0550.0030.058
replicateCorrelations3.8550.0003.855
sampleClusteredData0.4080.0000.408
sampleSize44.340 0.14044.491
sampleSize3DscatterPlots0.0170.0000.017
sampleSizeContourPlots0.0210.0040.025
sampleSizeParameters22.294 0.03222.327
sample_technicalVariance6.0650.0246.089
spectrumFilter0.8660.0000.867
ztwo000