Luca De Sano
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/SparseSignatures |
| Branch: RELEASE_3_12 |
| Last Commit: 39c8170 |
| Last Changed Date: 2020-10-27 11:34:26 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:33:43 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the SparseSignatures package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1757/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SparseSignatures 2.0.0 (landing page) Luca De Sano
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SparseSignatures |
| Version: 2.0.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SparseSignatures_2.0.0.tar.gz |
| StartedAt: 2021-05-06 07:10:03 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:25:18 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 914.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SparseSignatures.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SparseSignatures_2.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SparseSignatures.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.0.0'
* 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 126.67 0.11 127.08
lambdaRangeAlphaEvaluation 89.89 0.30 90.19
nmfLassoCV 17.53 0.01 17.55
nmfLassoBootstrap 15.92 0.42 16.34
nmfLasso 8.02 0.03 8.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
lambdaRangeBetaEvaluation 130.27 0.00 130.27
lambdaRangeAlphaEvaluation 112.61 0.14 112.77
nmfLassoCV 16.63 0.02 16.65
nmfLassoBootstrap 16.04 0.01 16.06
nmfLasso 5.41 0.00 5.40
* 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-3.12-bioc/meat/SparseSignatures.Rcheck/00check.log'
for details.
SparseSignatures.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SparseSignatures_2.0.0.tar.gz && rm -rf SparseSignatures.buildbin-libdir && mkdir SparseSignatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SparseSignatures.buildbin-libdir SparseSignatures_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SparseSignatures_2.0.0.zip && rm SparseSignatures_2.0.0.tar.gz SparseSignatures_2.0.0.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 787k 100 787k 0 0 32.1M 0 --:--:-- --:--:-- --:--:-- 33.4M
install for i386
* installing *source* package 'SparseSignatures' ...
** 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 'SparseSignatures'
finding HTML links ... done
background 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_2.0.0.zip
* DONE (SparseSignatures)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SparseSignatures' successfully unpacked and MD5 sums checked
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SparseSignatures.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
10.67 0.79 11.45
|
SparseSignatures.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
10.78 0.46 11.23
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SparseSignatures.Rcheck/examples_i386/SparseSignatures-Ex.timings
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SparseSignatures.Rcheck/examples_x64/SparseSignatures-Ex.timings
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