Luca De Sano
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SparseSignatures |
| Branch: RELEASE_3_9 |
| Last Commit: f3de1de |
| Last Changed Date: 2019-05-02 11:54:11 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:41:09 -0400 (Wed, 16 Oct 2019).
| Package 1559/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SparseSignatures 1.4.0 Luca De Sano
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SparseSignatures |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SparseSignatures_1.4.0.tar.gz |
| StartedAt: 2019-10-16 07:16:34 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:27:24 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 650.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SparseSignatures.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SparseSignatures_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SparseSignatures.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.4.0'
* 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.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 36.82 0.81 37.62
import.counts.data 2.38 1.85 170.51
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
nmf.LassoK 42.33 0.07 42.4
* 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-3.9-bioc/meat/SparseSignatures.Rcheck/00check.log'
for details.
SparseSignatures.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SparseSignatures_1.4.0.tar.gz && rm -rf SparseSignatures.buildbin-libdir && mkdir SparseSignatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SparseSignatures.buildbin-libdir SparseSignatures_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SparseSignatures_1.4.0.zip && rm SparseSignatures_1.4.0.tar.gz SparseSignatures_1.4.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 650k 100 650k 0 0 9650k 0 --:--:-- --:--:-- --:--:-- 10.5M
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
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 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_1.4.0.zip
* DONE (SparseSignatures)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SparseSignatures' successfully unpacked and MD5 sums checked
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SparseSignatures.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 39/40
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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
41.71 1.25 42.95
|
SparseSignatures.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 39/40
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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
50.20 0.68 50.87
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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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