* using log directory 'd:/Rcompile/CRANpkg/local/3.3/BioInstaller.Rcheck' * using R version 3.3.3 (2017-03-06) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'BioInstaller/DESCRIPTION' ... OK * this is package 'BioInstaller' version '0.3.3' * 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 'BioInstaller' 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 use of S3 registration ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'BioInstaller-Ex.R' failed The error most likely occurred in: > ### Name: install.bioinfo > ### Title: Download and install biology software or database > ### Aliases: install.bioinfo > > ### ** Examples > > db <- sprintf('%s/.BioInstaller', tempdir()) > set.biosoftwares.db(db) > install.bioinfo('bwa', show.all.versions = TRUE) INFO [2018-04-24 15:55:02] Fetching bwa versions.... Error in function (type, msg, asError = TRUE) : error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version Calls: install.bioinfo ... getURL -> curlPerform -> .Call -> -> fun Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [44s] ERROR Running 'testthat.R' [43s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(BioInstaller) > > > test_check("BioInstaller") -- 1. Error: install.github (@test_install.R#10) ------------------------------ error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version 1: install.github(name = "github_demo", destdir = destdir, download.dir = destdir, verbose = F) at testthat/test_install.R:10 2: show.avaliable.versions(config.parsed, name) 3: get.github.version(config) 4: github2versions(config$github_url) 5: getURL(url, headerfunction = h$update, httpheader = myheader) 6: curlPerform(curl = curl, .opts = opts, .encoding = .encoding) 7: function (type, msg, asError = TRUE) { if (!is.character(type)) { i = match(type, CURLcodeValues) typeName = if (is.na(i)) character() else names(CURLcodeValues)[i] } typeName = gsub("^CURLE_", "", typeName) fun = (if (asError) stop else warning) fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError", "error", "condition"))) }(35L, "error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version", TRUE) trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt' Content type 'text/plain; charset=utf-8' length 3131 bytes ================================================== downloaded 3131 bytes trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt' Content type 'text/plain; charset=utf-8' length 3131 bytes ================================================== downloaded 3131 bytes trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt' Content type 'text/plain; charset=utf-8' length 3131 bytes ================================================== downloaded 3131 bytes -- 2. Error: install.bioinfo (@test_install.R#57) ----------------------------- error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version 1: install.bioinfo(name = "github_demo", destdir = destdir, download.dir = destdir, verbose = F) at testthat/test_install.R:57 2: install.github(name = i, destdir = destdir[count], download.dir = download.dir[count], github.cfg = github.cfg, name.saved = name.saved[count], version = version[count], local.source = local.source[count], show.all.versions = show.all.versions, db = db, download.only = download.only, verbose = verbose, showWarnings = showWarnings, dependence.need = dependence.need, extra.list = extra.list, rmcd.parse = rcmd.parse, bash.parse = bash.parse, glue.parse = glue.parse, glue.flag = glue.flag, save.to.db = save.to.db, ...) 3: show.avaliable.versions(config.parsed, name) 4: get.github.version(config) 5: github2versions(config$github_url) 6: getURL(url, headerfunction = h$update, httpheader = myheader) 7: curlPerform(curl = curl, .opts = opts, .encoding = .encoding) 8: function (type, msg, asError = TRUE) { if (!is.character(type)) { i = match(type, CURLcodeValues) typeName = if (is.na(i)) character() else names(CURLcodeValues)[i] } typeName = gsub("^CURLE_", "", typeName) fun = (if (asError) stop else warning) fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError", "error", "condition"))) }(35L, "error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version", TRUE) -- 3. Error: initial (@test_install_uilts.R#39) ------------------------------- error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version 1: show.avaliable.versions(config) at testthat/test_install_uilts.R:39 2: get.github.version(config) 3: github2versions(config$github_url) 4: getURL(url, headerfunction = h$update, httpheader = myheader) 5: curlPerform(curl = curl, .opts = opts, .encoding = .encoding) 6: function (type, msg, asError = TRUE) { if (!is.character(type)) { i = match(type, CURLcodeValues) typeName = if (is.na(i)) character() else names(CURLcodeValues)[i] } typeName = gsub("^CURLE_", "", typeName) fun = (if (asError) stop else warning) fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError", "error", "condition"))) }(35L, "error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version", TRUE) -- 4. Error: dependence (@test_install_uilts.R#88) ---------------------------- error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version 1: install.dependence("github_demo", "master", destdir, destdir, F) at testthat/test_install_uilts.R:88 2: install.bioinfo(name = need.install, download.dir = download.dir, destdir = rep(destdir, length(download.dir)), version = need.install.version, verbose = verbose, github.cfg = github.cfg, nongithub.cfg = nongithub.cfg) 3: install.github(name = i, destdir = destdir[count], download.dir = download.dir[count], github.cfg = github.cfg, name.saved = name.saved[count], version = version[count], local.source = local.source[count], show.all.versions = show.all.versions, db = db, download.only = download.only, verbose = verbose, showWarnings = showWarnings, dependence.need = dependence.need, extra.list = extra.list, rmcd.parse = rcmd.parse, bash.parse = bash.parse, glue.parse = glue.parse, glue.flag = glue.flag, save.to.db = save.to.db, ...) 4: show.avaliable.versions(config.parsed, name) 5: get.github.version(config) 6: github2versions(config$github_url) 7: getURL(url, headerfunction = h$update, httpheader = myheader) 8: curlPerform(curl = curl, .opts = opts, .encoding = .encoding) 9: function (type, msg, asError = TRUE) { if (!is.character(type)) { i = match(type, CURLcodeValues) typeName = if (is.na(i)) character() else names(CURLcodeValues)[i] } typeName = gsub("^CURLE_", "", typeName) fun = (if (asError) stop else warning) fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError", "error", "condition"))) }(35L, "error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version", TRUE) cloning into 'D:/temp/RtmpUXreal/denpendence1'... -- 5. Error: git.download (@test_install_uilts.R#102) ------------------------- unknown certificate check failure 1: git.download("github_demo", destdir, "master", url, TRUE, FALSE, FALSE) at testthat/test_install_uilts.R:102 2: git2r::clone(github_url, destdir) 3: git2r::clone(github_url, destdir) 123 > D:/temp/RtmpUXreal/123 123 > D:/temp/RtmpUXreal/123 123 > D:/temp/RtmpUXreal/123 123 > D:/temp/RtmpUXreal/123 D:\temp\RtmpUXreal/destdir.initial not empty, overwrite?[y] Please input y/n/Y/N! D:\temp\RtmpUXreal/destdir.initial not empty, overwrite?[y] Please input y/n/Y/N! D:\temp\RtmpUXreal/destdir.initial not empty, overwrite?[y] More than 3 counts input, default is not to overwrite. D:\temp\RtmpUXreal/destdir.initial existed, overwrite?[y] Please input y/n/Y/N! D:\temp\RtmpUXreal/destdir.initial existed, overwrite?[y] Please input y/n/Y/N! D:\temp\RtmpUXreal/destdir.initial existed, overwrite?[y] More than 3 counts input, default is not to overwrite. trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//README' downloaded 107 bytes trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html' ... downloaded 3574 bytes == testthat results =========================================================== OK: 59 SKIPPED: 0 FAILED: 5 1. Error: install.github (@test_install.R#10) 2. Error: install.bioinfo (@test_install.R#57) 3. Error: initial (@test_install_uilts.R#39) 4. Error: dependence (@test_install_uilts.R#88) 5. Error: git.download (@test_install_uilts.R#102) Error: testthat unit tests failed Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [7s] WARNING Error in re-building vignettes: ... * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING