Multiple platform build/check report for BioC 3.14 - CHECK results for SparseSignatures on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	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*

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: 2022-04-13 03:18:45 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:32:31 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 826.3 seconds

RetCode: 0

Status: OK

CheckDir: SparseSignatures.Rcheck

Warnings: 0

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### 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
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SparseSignatures.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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    84.00   0.09   84.09
lambdaRangeAlphaEvaluation   77.07   0.20   77.34
nmfLassoBootstrap            12.27   0.39   12.65
nmfLassoCV                   11.84   0.01   11.86
nmfLasso                      5.25   0.07    5.32
import.trinucleotides.counts  2.77   1.58   83.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
lambdaRangeBetaEvaluation  89.10   0.03   89.13
lambdaRangeAlphaEvaluation 83.34   0.02   83.36
nmfLassoBootstrap          11.59   0.02   11.61
nmfLassoCV                 11.19   0.01   11.20
nmfLasso                    5.34   0.00    5.34
* 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-3.14-bioc/meat/SparseSignatures.Rcheck/00check.log'
for details.

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###
### 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
###
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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  790k  100  790k    0     0  1011k      0 --:--:-- --:--:-- --:--:-- 1012k

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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  13.57    1.10   14.67


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  14.85    0.45   15.29

name	user	system	elapsed
import.trinucleotides.counts	2.77	1.58	83.92
lambdaRangeAlphaEvaluation	77.07	0.20	77.34
lambdaRangeBetaEvaluation	84.00	0.09	84.09
nmfLasso	5.25	0.07	5.32
nmfLassoBootstrap	12.27	0.39	12.65
nmfLassoCV	11.84	0.01	11.86
patients.plot	0.87	0.02	0.89
sigAssignmentCV	0.08	0.01	0.10
sigAssignmentEvaluation	1.92	0.02	1.93
sigAssignmentLasso	0.61	0.00	0.61
signatures.plot	1.68	0.01	1.69
startingBetaEstimation	3.48	0.11	3.59

name	user	system	elapsed
import.trinucleotides.counts	1.79	0.21	2.02
lambdaRangeAlphaEvaluation	83.34	0.02	83.36
lambdaRangeBetaEvaluation	89.10	0.03	89.13
nmfLasso	5.34	0.00	5.34
nmfLassoBootstrap	11.59	0.02	11.61
nmfLassoCV	11.19	0.01	11.20
patients.plot	0.88	0.00	0.88
sigAssignmentCV	0.08	0.00	0.08
sigAssignmentEvaluation	1.82	0.00	1.83
sigAssignmentLasso	0.58	0.00	0.58
signatures.plot	1.54	0.00	1.55
startingBetaEstimation	3.57	0.00	3.56

CHECK results for SparseSignatures on tokay2

Summary

Command output

Installation output

Tests output

Example timings