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This page was generated on 2021-10-23 14:06:44 -0400 (Sat, 23 Oct 2021).

CHECK results for scDD on riesling1

To the developers/maintainers of the scDD package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDD.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 1719/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDD 1.17.0  (landing page)
Keegan Korthauer
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/scDD
git_branch: master
git_last_commit: 33ea732
git_last_commit_date: 2021-05-19 12:25:01 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: scDD
Version: 1.17.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDD.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scDD_1.17.0.tar.gz
StartedAt: 2021-10-23 08:21:02 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 08:32:31 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 688.7 seconds
RetCode: 0
Status:   OK  
CheckDir: scDD.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDD.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scDD_1.17.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/scDD.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scDD/DESCRIPTION' ... OK
* this is package 'scDD' version '1.17.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'scDD' 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 ... OK
* 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
Namespaces in Imports field not imported from:
  'grDevices' 'graphics' 'stats'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcMV: no visible global function definition for 'var'
classifyDD: no visible global function definition for 'quantile'
classifyDD: no visible global function definition for 'rt'
classifyDD: no visible global function definition for 'lm'
classifyDD: no visible global function definition for 't.test'
feDP: no visible global function definition for 'runif'
feDP: no visible global function definition for 'lm'
feDP: no visible global function definition for 't.test'
feDP: no visible global function definition for 'fisher.test'
feDP: no visible global function definition for 'p.adjust'
findFC : createFindFC: no visible global function definition for
  'quantile'
findFC : createFindFC : f: no visible global function definition for
  'runif'
findFC: no visible global function definition for 'par'
findFC: no visible global function definition for 'points'
mclustRestricted: no visible global function definition for 'runif'
permMclustCov: no visible global function definition for 'model.matrix'
permMclustCov: no visible global function definition for 'lm'
permMclustCov : getPerm: no visible global function definition for
  'residuals'
permMclustGene: no visible global function definition for
  'model.matrix'
permMclustGene: no visible global function definition for 'lm'
permMclustGene: no visible global function definition for 'residuals'
scDD: no visible global function definition for 'p.adjust'
scDD : fishersCombinedPval: no visible global function definition for
  'pchisq'
sideHist : ggplotColours: no visible global function definition for
  'hcl'
sideHist: no visible global function definition for 'hist'
sideHist: no visible global function definition for 'axis'
sideHist: no visible global function definition for 'rect'
sideHist: no visible global function definition for 'lines'
sideHist: no visible global function definition for 'density'
simuDB: no visible global function definition for 'rnbinom'
simuDE: no visible global function definition for 'rnbinom'
simuDE: no visible global function definition for 'var'
simuDM: no visible global function definition for 'rnbinom'
simuDP: no visible global function definition for 'rbinom'
simuDP: no visible global function definition for 'rnbinom'
simulateSet: no visible global function definition for 'pdf'
simulateSet: no visible global function definition for 'dev.off'
simulateSet: no visible global function definition for 'runif'
singleCellSimu: no visible global function definition for 'var'
singleCellSimu: no visible global function definition for 'lm'
testKS : onegene: no visible global function definition for 'ks.test'
testKS: no visible global function definition for 'p.adjust'
testZeroes : onegene: no visible global function definition for
  'binomial'
validation : <anonymous>: no visible global function definition for
  'var'
validation: no visible binding for global variable 'var'
validation: no visible global function definition for 'par'
validation: no visible global function definition for 'abline'
validation: no visible global function definition for 'points'
Undefined global functions or variables:
  abline axis binomial density dev.off fisher.test hcl hist ks.test
  lines lm model.matrix p.adjust par pchisq pdf points quantile rbinom
  rect residuals rnbinom rt runif t.test var
Consider adding
  importFrom("grDevices", "dev.off", "hcl", "pdf")
  importFrom("graphics", "abline", "axis", "hist", "lines", "par",
             "points", "rect")
  importFrom("stats", "binomial", "density", "fisher.test", "ks.test",
             "lm", "model.matrix", "p.adjust", "pchisq", "quantile",
             "rbinom", "residuals", "rnbinom", "rt", "runif", "t.test",
             "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
scDD        22.48   0.26   74.85
results     20.49   0.21   40.40
simulateSet  3.35   0.06   68.14
testKS       1.04   0.05    9.71
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
scDD        23.94   0.22   75.68
results     22.33   0.23   46.33
simulateSet  3.76   0.06   86.23
testKS       1.80   0.00   25.16
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/scDD.Rcheck/00check.log'
for details.



Installation output

scDD.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/scDD_1.17.0.tar.gz && rm -rf scDD.buildbin-libdir && mkdir scDD.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scDD.buildbin-libdir scDD_1.17.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scDD_1.17.0.zip && rm scDD_1.17.0.tar.gz scDD_1.17.0.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
  0  522k    0  1139    0     0  13559      0  0:00:39 --:--:--  0:00:39 13400
100  522k  100  522k    0     0  1964k      0 --:--:-- --:--:-- --:--:-- 1956k

install for i386

* installing *source* package 'scDD' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scDD'
    finding HTML links ... done
    calcMV                                  html  
    calcRP                                  html  
    classifyDD                              html  
    feDP                                    html  
    findFC                                  html  
    findIndex                               html  
    findOutliers                            html  
    getPosteriorParams                      html  
    jointPosterior                          html  
    lu                                      html  
    luOutlier                               html  
    mclustRestricted                        html  
    permMclust                              html  
    permMclustCov                           html  
    permMclustGene                          html  
    permZero                                html  
    preprocess                              html  
    results                                 html  
    scDD                                    html  
    scDatEx                                 html  
    scDatExList                             html  
    scDatExSim                              html  
    sideHist                                html  
    sideViolin                              html  
    simuDB                                  html  
    simuDE                                  html  
    simuDM                                  html  
    simuDP                                  html  
    simulateSet                             html  
    singleCellSimu                          html  
    testKS                                  html  
    testZeroes                              html  
    validation                              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 'scDD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scDD' as scDD_1.17.0.zip
* DONE (scDD)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'scDD' successfully unpacked and MD5 sums checked

Tests output


Example timings

scDD.Rcheck/examples_i386/scDD-Ex.timings

nameusersystemelapsed
preprocess1.560.011.58
results20.49 0.2140.40
scDD22.48 0.2674.85
scDatEx0.050.020.06
scDatExList0.010.000.01
scDatExSim0.020.010.03
sideViolin1.170.051.22
simulateSet 3.35 0.0668.14
testKS1.040.059.71

scDD.Rcheck/examples_x64/scDD-Ex.timings

nameusersystemelapsed
preprocess0.900.050.96
results22.33 0.2346.33
scDD23.94 0.2275.68
scDatEx0.030.020.05
scDatExList000
scDatExSim0.020.000.02
sideViolin1.140.031.17
simulateSet 3.76 0.0686.23
testKS 1.80 0.0025.16