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Type 'q()' to quit R. > #! /usr/bin/Rscript --vanilla > > ## make.r > ## 2016-06-03 [email protected] > ## my make file for developing R packages > > date () [1] "Sat Jan 27 22:12:04 2018" > rm (list = ls ()) > R.version.string ##"R version 3.2.1 (2015-06-18)" [1] "R version 3.4.3 (2017-11-30)" > library (devtools); packageDescription ("devtools", fields = "Version") #"1.11.1" [1] "1.13.4" > library (knitr); packageDescription ("knitr", fields = "Version") #"1.13" [1] "1.18" > #help (package = devtools) > > ################################################################################ > > > ## Clean up some directories. Usually not needed. > unlink ("local", recursive = TRUE) > unlink ("check", recursive = TRUE) > ##unlink ("pkg/man", recursive = TRUE) ## BE CAREFUL HERE !!! > ##unlink ("pkg/NAMESPACE") ## BE CAREFUL HERE !!! > > ### Create directories > dir.create ("local") ## to install the library locally > dir.create ("check") ## to keep the output of the check command > > ################################################################################ > > > ### Build documentation and NAMESPACE > document () Updating SNPediaR documentation Loading SNPediaR > > ################################################################################ > > > ### FULL CHECK > check (check_dir = "check") Updating SNPediaR documentation Loading SNPediaR Setting env vars -------------------------------------------------------------- CFLAGS : -Wall -pedantic CXXFLAGS: -Wall -pedantic Building SNPediaR ------------------------------------------------------------- '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD build \ '/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR' \ --no-resave-data --no-manual * checking for file '/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR/DESCRIPTION' ... OK * preparing 'SNPediaR': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK 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 * checking for empty or unneeded directories Removed empty directory 'SNPediaR/local' Removed empty directory 'SNPediaR/pkg' * building 'SNPediaR_1.5.1.tar.gz' Setting env vars -------------------------------------------------------------- _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE _R_CHECK_CRAN_INCOMING_ : FALSE _R_CHECK_FORCE_SUGGESTS_ : FALSE Checking SNPediaR ------------------------------------------------------------- '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD check '/tmp/RtmpdNHIIU/SNPediaR_1.5.1.tar.gz' --as-cran --timings \ --no-manual * using log directory '/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR/check/SNPediaR.Rcheck' * using R version 3.4.3 (2017-11-30) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using options '--no-manual --as-cran' * checking for file 'SNPediaR/DESCRIPTION' ... OK * this is package 'SNPediaR' version '1.5.1' * 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 * checking whether package 'SNPediaR' 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 * 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 * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... OK * DONE Status: OK R CMD check results 0 errors | 0 warnings | 0 notes > > ## ### 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") > > > ################################################################################ > > > ### Vignettes > build_vignettes () Building SNPediaR vignettes Moving SNPediaR.html, SNPediaR.R to inst/doc/ Copying SNPediaR.Rmd to inst/doc/ > > ## md format for Github > knit (input = "vignettes/SNPediaR.Rmd") processing file: vignettes/SNPediaR.Rmd | | | 0% | |... | 4% ordinary text without R code | |...... | 9% label: style (with options) List of 2 $ echo : logi FALSE $ results: chr "asis" | |........ | 13% ordinary text without R code | |........... | 17% label: unnamed-chunk-1 | |.............. | 22% ordinary text without R code | |................. | 26% label: unnamed-chunk-2 | |.................... | 30% ordinary text without R code | |....................... | 35% label: unnamed-chunk-3 | |......................... | 39% ordinary text without R code | |............................ | 43% label: unnamed-chunk-4 | |............................... | 48% ordinary text without R code | |.................................. | 52% label: unnamed-chunk-5 | |..................................... | 57% ordinary text without R code | |........................................ | 61% label: unnamed-chunk-6 | |.......................................... | 65% ordinary text without R code | |............................................. | 70% label: unnamed-chunk-7 | |................................................ | 74% ordinary text without R code | |................................................... | 78% label: unnamed-chunk-8 | |...................................................... | 83% ordinary text without R code | |......................................................... | 87% label: unnamed-chunk-9 | |........................................................... | 91% ordinary text without R code | |.............................................................. | 96% label: unnamed-chunk-10 | |.................................................................| 100% 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") > > ################################################################################ > > > ### Local Installation > install.packages (".", lib = "local", repos = NULL, INSTALL_opts = "--html") * installing *source* package 'SNPediaR' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'SNPediaR' finding HTML links ... done extractTags html getCategoryElements html getPages html ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (SNPediaR) > > ################################################################################ > > > ### Build the package > build (path = "dist", manual = TRUE, vignettes = TRUE) '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD build \ '/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR' \ --no-resave-data * checking for file '/var/host/media/removable/tgton/programas/mis_librerias/SNPediaR/DESCRIPTION' ... OK * preparing 'SNPediaR': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK 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 * checking for empty or unneeded directories Removed empty directory 'SNPediaR/pkg' * building 'SNPediaR_1.5.1.tar.gz' [1] "dist/SNPediaR_1.5.1.tar.gz" > > > ###EXIT > warnings () NULL > sessionInfo () R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) 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 locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocStyle_2.6.1 SNPediaR_1.5.1 knitr_1.18 devtools_1.13.4 loaded via a namespace (and not attached): [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 > q ("no") > proc.time() user system elapsed 79.930 6.925 135.037