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R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu (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.
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> #! /usr/bin/Rscript --vanilla
>
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> ## make.r
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> ## 2016-06-03 [email protected]
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> ## my make file for developing R packages
>
> date ()
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[1] "Sat Jan 27 22:12:04 2018"
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> rm (list = ls ())
> R.version.string ##"R version 3.2.1 (2015-06-18)"
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[1] "R version 3.4.3 (2017-11-30)"
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> library (devtools); packageDescription ("devtools", fields = "Version") #"1.11.1"
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[1] "1.13.4"
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> library (knitr); packageDescription ("knitr", fields = "Version") #"1.13"
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[1] "1.18"
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> #help (package = devtools)
>
> ################################################################################
>
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>
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> ## Clean up some directories. Usually not needed.
> unlink ("local", recursive = TRUE)
> unlink ("check", recursive = TRUE)
> ##unlink ("pkg/man", recursive = TRUE) ## BE CAREFUL HERE !!!
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> ##unlink ("pkg/NAMESPACE") ## BE CAREFUL HERE !!!
>
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> ### Create directories
> dir.create ("local") ## to install the library locally
> dir.create ("check") ## to keep the output of the check command
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>
> ################################################################################
>
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>
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> ### Build documentation and NAMESPACE
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> document ()
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Updating SNPediaR documentation
Loading SNPediaR
>
> ################################################################################
>
>
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> ### FULL CHECK
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> check (check_dir = "check")
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Updating SNPediaR documentation
Loading SNPediaR
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Setting env vars --------------------------------------------------------------
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CFLAGS : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
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Building SNPediaR -------------------------------------------------------------
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'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
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CMD build \
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'/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR' \
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--no-resave-data --no-manual
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* checking for file '/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR/DESCRIPTION' ... OK
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* preparing 'SNPediaR':
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* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
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Warning: 'inst/doc' files
'SNPediaR.Rmd', 'SNPediaR.html', 'SNPediaR.R'
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* checking for LF line-endings in source and make files and shell scripts
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* checking for empty or unneeded directories
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Removed empty directory 'SNPediaR/local'
Removed empty directory 'SNPediaR/pkg'
* building 'SNPediaR_1.5.1.tar.gz'
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Setting env vars --------------------------------------------------------------
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_R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_ : FALSE
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Checking SNPediaR -------------------------------------------------------------
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'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
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CMD check '/tmp/RtmpdNHIIU/SNPediaR_1.5.1.tar.gz' --as-cran --timings \
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--no-manual
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* using log directory '/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR/check/SNPediaR.Rcheck'
* using R version 3.4.3 (2017-11-30)
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* using platform: x86_64-pc-linux-gnu (64-bit)
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* using session charset: ASCII
* using options '--no-manual --as-cran'
* checking for file 'SNPediaR/DESCRIPTION' ... OK
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* this is package 'SNPediaR' version '1.5.1'
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* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
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* checking whether package 'SNPediaR' can be installed ... OK
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* checking installed package size ... OK
* checking package directory ... OK
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* checking 'build' directory ... OK
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* 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
* 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 loading without being on the library search path ... 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 line widths ... 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
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* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
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* checking examples ... OK
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* checking for unstated dependencies in 'tests' ... OK
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* checking tests ...
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Running 'testthat.R'
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OK
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* checking for unstated dependencies in vignettes ... OK
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* checking package vignettes in 'inst/doc' ... OK
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* checking re-building of vignette outputs ... OK
* DONE
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Status: OK
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R CMD check results
0 errors | 0 warnings | 0 notes
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>
> ## ### First (quick) CHECK of the library
> ## see how to avoid testing here ???
> ## check (pkg = "pkg",
> ## document = FALSE, ## document: if ‘TRUE’ (the default), will update and check documentation before running formal check.
> ## check_dir = "check", ## check_dir: the directory in which the package is checked
> ## vignettes = FALSE, ## do not run vignette code ............ when BUILDING
> ## args = c ("--no-examples", "--no-vignettes") ## do not run vignette code and examples when CHECKING -> args: Additional arguments passed to ‘R CMD check’
> ## )
>
> ## ## Examples: run separately from check
> ## run_examples (pkg = "pkg")
>
> ## ### Test
> ## test (pkg = "pkg")
>
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>
> ################################################################################
>
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>
> ### Vignettes
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> build_vignettes ()
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Building SNPediaR vignettes
Moving SNPediaR.html, SNPediaR.R to inst/doc/
Copying SNPediaR.Rmd to inst/doc/
>
> ## md format for Github
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> knit (input = "vignettes/SNPediaR.Rmd")
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processing file: vignettes/SNPediaR.Rmd
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| | 0%
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|... | 4%
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ordinary text without R code
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|...... | 9%
label: style (with options)
List of 2
$ echo : logi FALSE
$ results: chr "asis"
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|........ | 13%
ordinary text without R code
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|........... | 17%
label: unnamed-chunk-1
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|.............. | 22%
ordinary text without R code
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|................. | 26%
label: unnamed-chunk-2
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|.................... | 30%
ordinary text without R code
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label: unnamed-chunk-3
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|......................... | 39%
ordinary text without R code
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|............................ | 43%
label: unnamed-chunk-4
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|............................... | 48%
ordinary text without R code
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|.................................. | 52%
label: unnamed-chunk-5
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|..................................... | 57%
ordinary text without R code
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|........................................ | 61%
label: unnamed-chunk-6
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|.......................................... | 65%
ordinary text without R code
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|............................................. | 70%
label: unnamed-chunk-7
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|................................................ | 74%
ordinary text without R code
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label: unnamed-chunk-8
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ordinary text without R code
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label: unnamed-chunk-9
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ordinary text without R code
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label: unnamed-chunk-10
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inline R code fragments
output file: SNPediaR.md
[1] "SNPediaR.md"
> li <- readLines ("SNPediaR.md")
> li <- li[-(1:which (li == "</style>"))]
> writeLines (li, "SNPediaR.md")
> ##system ("pandoc -f markdown -t html -o SNPediaR.html SNPediaR.md")
>
> ################################################################################
>
>
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> ### Local Installation
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> install.packages (".", lib = "local", repos = NULL, INSTALL_opts = "--html")
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* installing *source* package 'SNPediaR' ...
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** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
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converting help for package 'SNPediaR'
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finding HTML links ... done
extractTags html
getCategoryElements html
getPages html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPediaR)
>
> ################################################################################
>
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>
> ### Build the package
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> build (path = "dist", manual = TRUE, vignettes = TRUE)
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'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
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CMD build \
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'/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR' \
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--no-resave-data
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* checking for file '/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR/DESCRIPTION' ... OK
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* preparing 'SNPediaR':
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* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
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Warning: 'inst/doc' files
'SNPediaR.Rmd', 'SNPediaR.html', 'SNPediaR.R'
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* checking for LF line-endings in source and make files and shell scripts
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* checking for empty or unneeded directories
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Removed empty directory 'SNPediaR/pkg'
* building 'SNPediaR_1.5.1.tar.gz'
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[1] "dist/SNPediaR_1.5.1.tar.gz"
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>
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>
> ###EXIT
> warnings ()
NULL
> sessionInfo ()
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R version 3.4.3 (2017-11-30)
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Platform: x86_64-pc-linux-gnu (64-bit)
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Running under: Ubuntu 16.04.3 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
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locale:
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[1] C
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attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
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[1] BiocStyle_2.6.1 SNPediaR_1.5.1 knitr_1.18 devtools_1.13.4
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loaded via a namespace (and not attached):
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[1] Rcpp_0.12.15 xml2_1.1.1 magrittr_1.5
[4] roxygen2_6.0.1 R6_2.2.2 rlang_0.1.6
[7] stringr_1.2.0 tools_3.4.3 withr_2.1.1
[10] htmltools_0.3.6 commonmark_1.4 yaml_2.1.16
[13] digest_0.6.14 assertthat_0.2.0 rprojroot_1.3-2
[16] bookdown_0.5 crayon_1.3.4 bitops_1.0-6
[19] RCurl_1.95-4.10 testthat_2.0.0 evaluate_0.10.1
[22] memoise_1.1.0 rmarkdown_1.8 stringi_1.1.6
[25] compiler_3.4.3 BiocInstaller_1.28.0 desc_1.1.1
[28] backports_1.1.2 jsonlite_1.5
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> q ("no")
> proc.time()
user system elapsed
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79.930 6.925 135.037
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