Roel Janssen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/MutationalPatterns |
| Branch: RELEASE_3_7 |
| Last Commit: 3254faa |
| Last Changed Date: 2018-10-11 04:00:18 -0400 (Thu, 11 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:43:04 -0400 (Wed, 17 Oct 2018).
| Package 970/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MutationalPatterns 1.6.1 Roel Janssen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MutationalPatterns |
| Version: 1.6.1 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MutationalPatterns_1.6.1.tar.gz |
| StartedAt: 2018-10-17 03:35:09 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:47:15 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 725.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MutationalPatterns.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MutationalPatterns_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/MutationalPatterns.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 'MutationalPatterns/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MutationalPatterns' version '1.6.1'
* 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 'MutationalPatterns' 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genomic_distribution 16.17 0.54 20.50
read_vcfs_as_granges 14.89 0.19 16.07
mut_matrix_stranded 11.42 0.51 12.49
plot_spectrum 6.28 0.23 6.52
mut_matrix 5.97 0.39 6.37
mut_type_occurrences 4.94 0.14 5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genomic_distribution 17.25 0.39 17.64
read_vcfs_as_granges 15.83 0.22 16.05
mut_matrix_stranded 13.60 0.48 14.08
plot_spectrum 7.92 0.16 8.10
mut_type_occurrences 5.81 0.17 5.98
mut_matrix 5.22 0.27 5.49
* 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: OK
MutationalPatterns.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/MutationalPatterns_1.6.1.tar.gz && rm -rf MutationalPatterns.buildbin-libdir && mkdir MutationalPatterns.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns_1.6.1.zip && rm MutationalPatterns_1.6.1.tar.gz MutationalPatterns_1.6.1.zip
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100 3135k 100 3135k 0 0 34.8M 0 --:--:-- --:--:-- --:--:-- 38.2M
install for i386
* installing *source* package 'MutationalPatterns' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MutationalPatterns'
finding HTML links ... done
MutationalPatterns-package html
binomial_test html
cluster_signatures html
cos_sim html
cos_sim_matrix html
enrichment_depletion_test html
explained_by_signatures html
extract_signatures html
fit_to_signatures html
genomic_distribution html
mut_context html
mut_matrix html
mut_matrix_stranded html
mut_strand html
mut_type html
mut_type_occurrences html
mutation_context html
mutation_types html
mutations_from_vcf html
plot_192_profile html
plot_96_profile html
plot_compare_profiles html
plot_contribution html
plot_contribution_heatmap html
plot_cosine_heatmap html
plot_enrichment_depletion html
plot_rainfall html
plot_signature_strand_bias html
plot_spectrum html
plot_strand html
plot_strand_bias html
read_vcfs_as_granges html
strand_bias_test html
strand_from_vcf html
strand_occurrences html
type_context html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'MutationalPatterns' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MutationalPatterns' as MutationalPatterns_1.6.1.zip
* DONE (MutationalPatterns)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'MutationalPatterns' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
MutationalPatterns.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.
> library(testthat)
> library(MutationalPatterns)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry
Attaching package: 'pkgmaker'
The following object is masked from 'package:S4Vectors':
new2
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:S4Vectors':
nrun
The following object is masked from 'package:testthat':
compare
>
> test_check("MutationalPatterns")
== testthat results ===========================================================
OK: 10 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
113.62 4.32 117.96
|
MutationalPatterns.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.
> library(testthat)
> library(MutationalPatterns)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry
Attaching package: 'pkgmaker'
The following object is masked from 'package:S4Vectors':
new2
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:S4Vectors':
nrun
The following object is masked from 'package:testthat':
compare
>
> test_check("MutationalPatterns")
== testthat results ===========================================================
OK: 10 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
118.43 2.93 121.40
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MutationalPatterns.Rcheck/examples_i386/MutationalPatterns-Ex.timings
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MutationalPatterns.Rcheck/examples_x64/MutationalPatterns-Ex.timings
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