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CHECK report for SparseSignatures on tokay2

This page was generated on 2018-10-17 08:45:40 -0400 (Wed, 17 Oct 2018).

Package 1404/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SparseSignatures 1.0.3
Luca De Sano
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SparseSignatures
Branch: RELEASE_3_7
Last Commit: eb6a9a8
Last Changed Date: 2018-09-27 04:34:04 -0400 (Thu, 27 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SparseSignatures
Version: 1.0.3
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SparseSignatures_1.0.3.tar.gz
StartedAt: 2018-10-17 04:58:19 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:06:21 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 482.3 seconds
RetCode: 0
Status:  OK  
CheckDir: SparseSignatures.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SparseSignatures_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SparseSignatures.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SparseSignatures/DESCRIPTION' ... OK
* this is package 'SparseSignatures' version '1.0.3'
* 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 'SparseSignatures' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
import.counts.data: no visible global function definition for '.'
patient.plot: no visible binding for global variable 'Context'
patient.plot: no visible binding for global variable 'alt'
patient.plot: no visible binding for global variable 'N'
signatures.plot: no visible binding for global variable 'Context'
signatures.plot: no visible binding for global variable 'alt'
signatures.plot: no visible binding for global variable 'value'
Undefined global functions or variables:
  . Context N alt value
* 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
nmf.LassoK      40.31   0.41   40.72
signatures.plot  5.91   0.02    5.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
nmf.LassoK 39.26   0.08   39.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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-3.7-bioc/meat/SparseSignatures.Rcheck/00check.log'
for details.

Installation output

SparseSignatures.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SparseSignatures_1.0.3.tar.gz && rm -rf SparseSignatures.buildbin-libdir && mkdir SparseSignatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SparseSignatures.buildbin-libdir SparseSignatures_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SparseSignatures_1.0.3.zip && rm SparseSignatures_1.0.3.tar.gz SparseSignatures_1.0.3.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  650k  100  650k    0     0  10.3M      0 --:--:-- --:--:-- --:--:-- 11.7M

install for i386

* installing *source* package 'SparseSignatures' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SparseSignatures'
    finding HTML links ... done
    as.alpha                                html  
    as.alpha.in.range                       html  
    as.beta                                 html  
    as.beta.in.range                        html  
    as.loglik.progression                   html  
    as.loglik.progression.in.range          html  
    as.mean.squared.error                   html  
    as.starting.beta                        html  
    as.starting.beta.in.range               html  
    background                              html  
    cv_example                              html  
    evaluate.lambda.range                   html  
    import.counts.data                      html  
    lambda_range_example                    html  
    mutation_categories                     html  
    nmf.LassoCV                             html  
    nmf.LassoK                              html  
    nmf_LassoK_example                      html  
    patient.plot                            html  
    patients                                html  
    signatures.plot                         html  
    ssm560_reduced                          html  
    starting.betas.estimation               html  
    starting_betas_example                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SparseSignatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SparseSignatures' as SparseSignatures_1.0.3.zip
* DONE (SparseSignatures)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'SparseSignatures' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

SparseSignatures.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(SparseSignatures)
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 19/20

Attaching package: 'NMF'

The following object is masked from 'package:testthat':

    compare

> 
> test_check("SparseSignatures")
Performing the discovery of the signatures by NMF with Lasso... 
Performing a total of 5 iterations... 
Progress 20%... 
Progress 40%... 
Progress 60%... 
Progress 80%... 
Progress 100%... 
== testthat results  ===========================================================
OK: 10 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  40.92    0.79   41.70

SparseSignatures.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(SparseSignatures)
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 19/20

Attaching package: 'NMF'

The following object is masked from 'package:testthat':

    compare

> 
> test_check("SparseSignatures")
Performing the discovery of the signatures by NMF with Lasso... 
Performing a total of 5 iterations... 
Progress 20%... 
Progress 40%... 
Progress 60%... 
Progress 80%... 
Progress 100%... 
== testthat results  ===========================================================
OK: 10 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  47.82    0.51   48.32

Example timings

SparseSignatures.Rcheck/examples_i386/SparseSignatures-Ex.timings

nameusersystemelapsed
as.alpha0.000.010.01
as.alpha.in.range0.020.020.04
as.beta0.000.010.02
as.beta.in.range0.000.020.01
as.loglik.progression000
as.loglik.progression.in.range0.000.030.03
as.mean.squared.error0.020.000.02
as.starting.beta000
as.starting.beta.in.range000
import.counts.data2.880.433.31
nmf.LassoK40.31 0.4140.72
patient.plot1.250.001.25
signatures.plot5.910.025.92

SparseSignatures.Rcheck/examples_x64/SparseSignatures-Ex.timings

nameusersystemelapsed
as.alpha000
as.alpha.in.range0.020.000.02
as.beta000
as.beta.in.range0.000.010.02
as.loglik.progression0.010.000.01
as.loglik.progression.in.range0.000.020.02
as.mean.squared.error0.000.010.02
as.starting.beta0.000.020.01
as.starting.beta.in.range0.020.000.02
import.counts.data2.030.332.36
nmf.LassoK39.26 0.0839.34
patient.plot0.880.000.87
signatures.plot3.640.003.65