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This page was generated on 2022-01-17 13:07:04 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 SparseSignatures on tokay2


To the developers/maintainers of the SparseSignatures package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SparseSignatures.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 1843/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SparseSignatures 2.4.0  (landing page)
Luca De Sano
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/SparseSignatures
git_branch: RELEASE_3_14
git_last_commit: 54424a2
git_last_commit_date: 2021-10-26 12:43:44 -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: SparseSignatures
Version: 2.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SparseSignatures_2.4.0.tar.gz
StartedAt: 2022-01-17 04:11:46 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 04:24:23 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 757.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SparseSignatures.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SparseSignatures_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SparseSignatures.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 'SparseSignatures/DESCRIPTION' ... OK
* this is package 'SparseSignatures' version '2.4.0'
* 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 '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.trinucleotides.counts: no visible global function definition for
  '.'
patients.plot: no visible binding for global variable 'Context'
patients.plot: no visible binding for global variable 'alt'
patients.plot: no visible binding for global variable 'patient'
patients.plot: no visible binding for global variable 'value'
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 alt patient 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 (user + system) or elapsed time > 5s
                              user system elapsed
lambdaRangeBetaEvaluation    83.16   0.19   83.35
lambdaRangeAlphaEvaluation   75.22   0.08   75.30
nmfLassoBootstrap            11.09   0.42   11.52
nmfLassoCV                   11.48   0.03   11.51
import.trinucleotides.counts  2.69   1.37   33.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
lambdaRangeBetaEvaluation  85.50   0.00   85.50
lambdaRangeAlphaEvaluation 76.38   0.06   76.47
nmfLassoBootstrap          12.83   0.07   12.89
nmfLassoCV                 12.39   0.01   12.41
nmfLasso                    5.88   0.00    5.87
* 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-3.14-bioc/meat/SparseSignatures.Rcheck/00check.log'
for details.



Installation output

SparseSignatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SparseSignatures_2.4.0.tar.gz && rm -rf SparseSignatures.buildbin-libdir && mkdir SparseSignatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SparseSignatures.buildbin-libdir SparseSignatures_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SparseSignatures_2.4.0.zip && rm SparseSignatures_2.4.0.tar.gz SparseSignatures_2.4.0.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
  1  790k    1 12027    0     0   187k      0  0:00:04 --:--:--  0:00:04  186k
100  790k  100  790k    0     0  3005k      0 --:--:-- --:--:-- --:--:-- 3003k

install for i386

* installing *source* package 'SparseSignatures' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SparseSignatures'
    finding HTML links ... done
    background                              html  
    background2                             html  
    cv_example                              html  
    import.trinucleotides.counts            html  
    imported_data                           html  
    lambdaRangeAlphaEvaluation              html  
    lambdaRangeBetaEvaluation               html  
    lambda_range_example                    html  
    mutation_categories                     html  
    nmfLasso                                html  
    nmfLassoBootstrap                       html  
    nmfLassoCV                              html  
    nmf_LassoK_example                      html  
    patients                                html  
    patients.plot                           html  
    sigAssignmentCV                         html  
    sigAssignmentEvaluation                 html  
    sigAssignmentLasso                      html  
    signatures.plot                         html  
    ssm560_reduced                          html  
    startingBetaEstimation                  html  
    starting_betas_example                  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 'SparseSignatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SparseSignatures' as SparseSignatures_2.4.0.zip
* DONE (SparseSignatures)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SparseSignatures' successfully unpacked and MD5 sums checked

Tests output

SparseSignatures.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 39/40

Attaching package: 'NMF'

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

    compare

> 
> test_check("SparseSignatures")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  10.26    0.92   11.17 

SparseSignatures.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 39/40

Attaching package: 'NMF'

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

    compare

> 
> test_check("SparseSignatures")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  11.04    0.32   11.35 

Example timings

SparseSignatures.Rcheck/examples_i386/SparseSignatures-Ex.timings

nameusersystemelapsed
import.trinucleotides.counts 2.69 1.3733.04
lambdaRangeAlphaEvaluation75.22 0.0875.30
lambdaRangeBetaEvaluation83.16 0.1983.35
nmfLasso4.830.004.82
nmfLassoBootstrap11.09 0.4211.52
nmfLassoCV11.48 0.0311.51
patients.plot0.860.020.88
sigAssignmentCV0.100.000.09
sigAssignmentEvaluation1.870.001.88
sigAssignmentLasso0.630.000.62
signatures.plot1.720.001.72
startingBetaEstimation3.460.113.58

SparseSignatures.Rcheck/examples_x64/SparseSignatures-Ex.timings

nameusersystemelapsed
import.trinucleotides.counts2.750.263.02
lambdaRangeAlphaEvaluation76.38 0.0676.47
lambdaRangeBetaEvaluation85.5 0.085.5
nmfLasso5.880.005.87
nmfLassoBootstrap12.83 0.0712.89
nmfLassoCV12.39 0.0112.41
patients.plot1.090.001.09
sigAssignmentCV0.060.020.08
sigAssignmentEvaluation2.050.002.05
sigAssignmentLasso0.810.030.84
signatures.plot2.020.022.03
startingBetaEstimation3.920.033.96