Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:07:12 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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 325/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.45.0  (landing page)
Stephen Nyangoma
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/clippda
git_branch: master
git_last_commit: 2acb6b4
git_last_commit_date: 2021-10-26 11:54:30 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: clippda
Version: 1.45.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clippda.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings clippda_1.45.0.tar.gz
StartedAt: 2022-03-17 18:44:01 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 18:47:00 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 178.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: clippda.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clippda.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings clippda_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/clippda.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clippda/DESCRIPTION' ... OK
* this is package 'clippda' version '1.45.0'
* 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 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      56.29   1.50   57.80
sampleSize           42.50   0.50   43.00
sampleSizeParameters 15.97   0.22   16.19
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/clippda.Rcheck/00check.log'
for details.



Installation output

clippda.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL clippda
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'clippda'
    finding HTML links ... done
    ZvaluescasesVcontrolsPlots              html  
    ZvaluesfrommultinomPlots                html  
    aclinicalProteomicsData-class           html  
    aclinicalProteomicsData-methods         html  
    betweensampleVariance-methods           html  
    betweensampleVariance                   html  
    checkNo.replicates                      html  
    clippda-package                         html  
    f                                       html  
    fisherInformation-methods               html  
    fisherInformation                       html  
    liverRawData                            html  
    liver_pheno                             html  
    liverdata                               html  
    mostSimilarTwo                          html  
    negativeIntensitiesCorrection           html  
    phenoDataFrame                          html  
    pheno_urine                             html  
    preProcRepeatedPeakData                 html  
    proteomicsExprsData-methods             html  
    proteomicsExprsData                     html  
    proteomicspData-methods                 html  
    proteomicspData                         html  
    replicateCorrelations-methods           html  
    replicateCorrelations                   html  
    sampleClusteredData                     html  
    sampleSize-methods                      html  
    sampleSize                              html  
    sampleSize3DscatterPlots                html  
    sampleSizeContourPlots                  html  
    sampleSizeParameters-methods            html  
    sampleSizeParameters                    html  
    sample_technicalVariance-methods        html  
    sample_technicalVariance                html  
    show-methods                            html  
    spectrumFilter                          html  
    ztwo                                    html  
** 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)
Making 'packages.html' ... done

Tests output


Example timings

clippda.Rcheck/clippda-Ex.timings

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.040.000.04
ZvaluesfrommultinomPlots1.050.071.13
aclinicalProteomicsData-class0.050.000.06
aclinicalProteomicsData-methods0.170.190.36
betweensampleVariance0.940.081.02
checkNo.replicates0.030.050.07
clippda-package56.29 1.5057.80
f000
fisherInformation0.050.000.04
liverRawData0.010.000.02
liver_pheno000
liverdata0.910.070.98
mostSimilarTwo000
negativeIntensitiesCorrection0.140.070.21
phenoDataFrame0.050.000.04
pheno_urine000
preProcRepeatedPeakData0.570.040.63
proteomicsExprsData0.110.000.11
proteomicspData0.040.020.05
replicateCorrelations2.950.053.00
sampleClusteredData0.170.000.17
sampleSize42.5 0.543.0
sampleSize3DscatterPlots0.020.000.01
sampleSizeContourPlots0.010.000.02
sampleSizeParameters15.97 0.2216.19
sample_technicalVariance4.390.014.40
spectrumFilter0.750.050.80
ztwo000