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CHECK report for CountClust on tokay2

This page was generated on 2019-10-16 12:35:22 -0400 (Wed, 16 Oct 2019).

Package 355/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CountClust 1.12.0
Kushal Dey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CountClust
Branch: RELEASE_3_9
Last Commit: 68a642a
Last Changed Date: 2019-05-02 11:54:01 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CountClust
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CountClust.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CountClust_1.12.0.tar.gz
StartedAt: 2019-10-16 02:57:49 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:00:22 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 153.1 seconds
RetCode: 0
Status:  OK  
CheckDir: CountClust.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CountClust.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CountClust_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CountClust.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CountClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CountClust' version '1.12.0'
* package encoding: UTF-8
* 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 'CountClust' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 or elapsed time > 5s
         user system elapsed
compGoM 13.64   0.89   14.61
FitGoM   5.00   0.10    5.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
compGoM 11.64   0.72   12.47
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/CountClust.Rcheck/00check.log'
for details.



Installation output

CountClust.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CountClust_1.12.0.tar.gz && rm -rf CountClust.buildbin-libdir && mkdir CountClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CountClust.buildbin-libdir CountClust_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CountClust_1.12.0.zip && rm CountClust_1.12.0.tar.gz CountClust_1.12.0.zip
###
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  % 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 6241k  100 6241k    0     0  47.3M      0 --:--:-- --:--:-- --:--:-- 49.9M

install for i386

* installing *source* package 'CountClust' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CountClust'
    finding HTML links ... done
    AbundanceGoM                            html  
    BatchCorrectedCounts                    html  
    ExtractHighCorFeatures                  html  
    ExtractTopFeatures                      html  
    FitGoM                                  html  
    GTExV6Brain.FitGoM                      html  
    MouseDeng2014.FitGoM                    html  
    MouseJaitinSpleen.FitGoM                html  
    RemoveSparseFeatures                    html  
    StructureGGplot                         html  
    compGoM                                 html  
    compare_omega                           html  
    ex.counts                               html  
    handleNA                                html  
    nullmodel_GoM                           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 'CountClust' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CountClust' as CountClust_1.12.0.zip
* DONE (CountClust)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CountClust' successfully unpacked and MD5 sums checked

Tests output


Example timings

CountClust.Rcheck/examples_i386/CountClust-Ex.timings

nameusersystemelapsed
BatchCorrectedCounts0.450.020.47
ExtractTopFeatures1.560.091.66
FitGoM5.00.15.1
RemoveSparseFeatures000
StructureGGplot0.830.000.83
compGoM13.64 0.8914.61
compare_omega0.030.000.03
handleNA000
nullmodel_GoM3.320.063.38

CountClust.Rcheck/examples_x64/CountClust-Ex.timings

nameusersystemelapsed
BatchCorrectedCounts0.850.000.85
ExtractTopFeatures1.750.051.79
FitGoM4.310.204.52
RemoveSparseFeatures0.020.000.01
StructureGGplot0.770.000.77
compGoM11.64 0.7212.47
compare_omega0.030.000.03
handleNA000
nullmodel_GoM3.440.243.67