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This page was generated on 2022-01-14 13:06:10 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 Clonality on tokay2


To the developers/maintainers of the Clonality package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Clonality.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 332/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clonality 1.42.0  (landing page)
Irina Ostrovnaya
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/Clonality
git_branch: RELEASE_3_14
git_last_commit: 3792eeb
git_last_commit_date: 2021-10-26 11:57:48 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Clonality
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Clonality.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Clonality_1.42.0.tar.gz
StartedAt: 2022-01-13 17:13:16 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 17:17:19 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 243.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Clonality.Rcheck
Warnings: 0

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:Clonality.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Clonality_1.42.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Clonality.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 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.42.0'
* 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 'Clonality' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Foreign function call to a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
get.mutation.frequencies: no visible binding for global variable
  'freqdata'
Undefined global functions or variables:
  freqdata
* 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 installed files from 'inst/doc' ... 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
clonality.analysis  43.47   0.25   44.02
LRtesting3or4tumors 20.47   0.00   20.47
LOHclonality         7.83   0.00    7.83
ECMtesting           7.14   0.00    7.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
clonality.analysis  49.05   0.27   49.31
LRtesting3or4tumors 20.70   0.00   20.70
LOHclonality         9.34   0.00    9.34
ECMtesting           8.83   0.00    8.83
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/Clonality.Rcheck/00check.log'
for details.



Installation output

Clonality.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/Clonality_1.42.0.tar.gz && rm -rf Clonality.buildbin-libdir && mkdir Clonality.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Clonality.buildbin-libdir Clonality_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Clonality_1.42.0.zip && rm Clonality_1.42.0.tar.gz Clonality_1.42.0.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 2436k  100 2436k    0     0  5195k      0 --:--:-- --:--:-- --:--:-- 5205k

install for i386

* installing *source* package 'Clonality' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Clonality'
    finding HTML links ... done
    Clonality-internal                      html  
    Clonality-package                       html  
    ECMtesting                              html  
    LOHclonality                            html  
    LRtesting3or4tumors                     html  
    SNVtest                                 html  
    SNVtest2                                html  
    ave.adj.probes                          html  
    chromosomePlots                         html  
    clonEM                                  html  
    clonality.analysis                      html  
    create.mutation.matrix                  html  
    freqdata                                html  
    genomewidePlots                         html  
    get.mutation.frequencies                html  
    grid.lik                                html  
    histogramPlot                           html  
    lcis                                    html  
    model.lik                               html  
    mutation.proba                          html  
    mutation.rem                            html  
    print.mutation.proba                    html  
    print.mutation.rem                      html  
    splitChromosomes                        html  
    xidens                                  html  
** building package indices
** installing vignettes
   'Clonality.Rnw' 
** 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 'Clonality' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Clonality' as Clonality_1.42.0.zip
* DONE (Clonality)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Clonality' successfully unpacked and MD5 sums checked

Tests output


Example timings

Clonality.Rcheck/examples_i386/Clonality-Ex.timings

nameusersystemelapsed
ECMtesting7.140.007.14
LOHclonality7.830.007.83
LRtesting3or4tumors20.47 0.0020.47
SNVtest2.630.162.78
SNVtest20.420.000.42
ave.adj.probes1.340.011.36
chromosomePlots000
clonality.analysis43.47 0.2544.02
create.mutation.matrix1.310.041.34
genomewidePlots000
get.mutation.frequencies1.190.031.22
histogramPlot000
mutation.proba1.530.011.54
mutation.rem2.100.022.11
splitChromosomes000

Clonality.Rcheck/examples_x64/Clonality-Ex.timings

nameusersystemelapsed
ECMtesting8.830.008.83
LOHclonality9.340.009.34
LRtesting3or4tumors20.7 0.020.7
SNVtest2.850.082.92
SNVtest20.540.010.56
ave.adj.probes1.560.001.57
chromosomePlots000
clonality.analysis49.05 0.2749.31
create.mutation.matrix2.080.012.09
genomewidePlots000
get.mutation.frequencies1.450.031.49
histogramPlot000
mutation.proba2.190.002.18
mutation.rem2.610.022.63
splitChromosomes0.020.000.01