Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:07 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 tokay2


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: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
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 20.04.4 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: clippda
Version: 1.44.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clippda.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings clippda_1.44.0.tar.gz
StartedAt: 2022-01-20 17:35:41 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 17:41:59 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 378.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: clippda.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clippda.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings clippda_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/clippda.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.44.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
clippda-package          67.82   0.30   68.14
sampleSize               42.48   0.18   42.66
sampleSizeParameters     22.61   0.04   22.65
sample_technicalVariance  5.44   0.02    5.46
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
clippda-package          71.53   0.45   72.00
sampleSize               43.45   0.12   43.58
sampleSizeParameters     21.29   0.08   21.37
sample_technicalVariance  6.22   0.01    6.24
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/clippda.Rcheck/00check.log'
for details.



Installation output

clippda.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/clippda_1.44.0.tar.gz && rm -rf clippda.buildbin-libdir && mkdir clippda.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clippda.buildbin-libdir clippda_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL clippda_1.44.0.zip && rm clippda_1.44.0.tar.gz clippda_1.44.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  420k  100  420k    0     0  1405k      0 --:--:-- --:--:-- --:--:-- 1409k

install for i386

* 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

install for x64

* installing *source* package 'clippda' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clippda' as clippda_1.44.0.zip
* DONE (clippda)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'clippda' successfully unpacked and MD5 sums checked

Tests output


Example timings

clippda.Rcheck/examples_i386/clippda-Ex.timings

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.070.000.08
ZvaluesfrommultinomPlots1.550.051.59
aclinicalProteomicsData-class0.060.000.06
aclinicalProteomicsData-methods0.250.120.38
betweensampleVariance1.170.031.20
checkNo.replicates0.060.000.07
clippda-package67.82 0.3068.14
f000
fisherInformation0.090.000.09
liverRawData000
liver_pheno0.000.010.02
liverdata0.830.000.82
mostSimilarTwo000
negativeIntensitiesCorrection0.200.020.22
phenoDataFrame0.050.020.06
pheno_urine000
preProcRepeatedPeakData0.780.010.80
proteomicsExprsData0.150.020.17
proteomicspData0.050.010.06
replicateCorrelations3.480.023.50
sampleClusteredData0.190.010.20
sampleSize42.48 0.1842.66
sampleSize3DscatterPlots0.050.000.04
sampleSizeContourPlots0.060.000.07
sampleSizeParameters22.61 0.0422.65
sample_technicalVariance5.440.025.46
spectrumFilter0.790.000.79
ztwo000

clippda.Rcheck/examples_x64/clippda-Ex.timings

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.060.000.07
ZvaluesfrommultinomPlots1.400.021.42
aclinicalProteomicsData-class0.060.020.08
aclinicalProteomicsData-methods0.220.090.31
betweensampleVariance1.180.001.19
checkNo.replicates0.080.000.08
clippda-package71.53 0.4572.00
f000
fisherInformation0.070.020.07
liverRawData000
liver_pheno000
liverdata1.230.011.25
mostSimilarTwo000
negativeIntensitiesCorrection0.240.000.24
phenoDataFrame0.040.020.06
pheno_urine0.020.000.02
preProcRepeatedPeakData0.890.000.89
proteomicsExprsData0.140.000.14
proteomicspData0.050.020.07
replicateCorrelations3.670.023.69
sampleClusteredData0.240.000.23
sampleSize43.45 0.1243.58
sampleSize3DscatterPlots0.030.000.03
sampleSizeContourPlots0.020.000.02
sampleSizeParameters21.29 0.0821.37
sample_technicalVariance6.220.016.24
spectrumFilter1.030.001.03
ztwo000