CRAN Package Check Results for Package BioInstaller

Last updated on 2018-08-21 08:48:44 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.3 4.95 86.72 91.67 ERROR
r-devel-linux-x86_64-debian-gcc 0.3.3 3.88 68.50 72.38 ERROR
r-devel-linux-x86_64-fedora-clang 0.3.3 106.32 ERROR
r-devel-linux-x86_64-fedora-gcc 0.3.3 105.25 ERROR
r-devel-windows-ix86+x86_64 0.3.3 12.00 136.00 148.00 ERROR
r-patched-linux-x86_64 0.3.3 4.67 80.86 85.53 ERROR
r-patched-solaris-x86 0.3.3 115.00 ERROR
r-release-linux-x86_64 0.3.3 4.89 81.00 85.89 ERROR
r-release-windows-ix86+x86_64 0.3.3 12.00 137.00 149.00 ERROR
r-release-osx-x86_64 0.3.3 ERROR
r-oldrel-windows-ix86+x86_64 0.3.3 7.00 103.00 110.00 ERROR
r-oldrel-osx-x86_64 0.3.3 OK

Check Details

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [11s/39s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BioInstaller)
     >
     >
     > test_check("BioInstaller")
     cloning into '/tmp/Rtmp0PpMOB/github_demo0'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmp0PpMOB/github_demo2'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     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
    
     cloning into '/tmp/Rtmp0PpMOB/github_demo3'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmp0PpMOB/github_demo'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmp0PpMOB/denpendence1'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     /tmp/Rtmp0PpMOB/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmp0PpMOB/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmp0PpMOB/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     /tmp/Rtmp0PpMOB/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmp0PpMOB/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmp0PpMOB/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'
     Content type 'unknown' length 107 bytes
     ==================================================
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
     Content type 'unknown' length 3574 bytes
     ==================================================
     ── 1. Failure: nongithub.versions (@test_versions.R#6) ────────────────────────
     `x` not equal to `expected`.
     1 element mismatch
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 69 SKIPPED: 0 FAILED: 1
     1. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     In addition: Warning message:
     In getPackageName(topenv(parent.frame())) :
     closing unused connection 4 (http://research-pub.gene.com/gmap/src/)
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [8s/42s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BioInstaller)
     >
     >
     > test_check("BioInstaller")
     cloning into '/home/hornik/tmp/scratch/RtmpPrVFK9/github_demo0'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/home/hornik/tmp/scratch/RtmpPrVFK9/github_demo2'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     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
    
     cloning into '/home/hornik/tmp/scratch/RtmpPrVFK9/github_demo3'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/home/hornik/tmp/scratch/RtmpPrVFK9/github_demo'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/home/hornik/tmp/scratch/RtmpPrVFK9/denpendence1'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     /home/hornik/tmp/scratch/RtmpPrVFK9/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /home/hornik/tmp/scratch/RtmpPrVFK9/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /home/hornik/tmp/scratch/RtmpPrVFK9/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     /home/hornik/tmp/scratch/RtmpPrVFK9/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /home/hornik/tmp/scratch/RtmpPrVFK9/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /home/hornik/tmp/scratch/RtmpPrVFK9/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'
     Content type 'unknown' length 107 bytes
     ==================================================
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
     Content type 'unknown' length 3574 bytes
     ==================================================
     ── 1. Failure: nongithub.versions (@test_versions.R#6) ────────────────────────
     `x` not equal to `expected`.
     1 element mismatch
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 69 SKIPPED: 0 FAILED: 1
     1. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     In addition: Warning message:
     In .getClassesFromCache(Class) :
     closing unused connection 4 (http://research-pub.gene.com/gmap/src/)
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [12s/35s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BioInstaller)
     >
     >
     > test_check("BioInstaller")
     cloning into '/tmp/Rtmpne6556/github_demo0'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmpne6556/github_demo2'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     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
    
     cloning into '/tmp/Rtmpne6556/github_demo3'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmpne6556/github_demo'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmpne6556/denpendence1'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     /tmp/Rtmpne6556/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmpne6556/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmpne6556/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     /tmp/Rtmpne6556/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmpne6556/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmpne6556/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'
     Content type 'unknown' length 107 bytes
     ==================================================
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
     Content type 'unknown' length 3574 bytes
     ==================================================
     ── 1. Failure: nongithub.versions (@test_versions.R#6) ────────────────────────
     `x` not equal to `expected`.
     1 element mismatch
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 69 SKIPPED: 0 FAILED: 1
     1. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     In addition: Warning message:
     In getPackageName(topenv(parent.frame())) :
     closing unused connection 4 (http://research-pub.gene.com/gmap/src/)
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [12s/32s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BioInstaller)
     >
     >
     > test_check("BioInstaller")
     cloning into '/tmp/Rtmp74jCLy/github_demo0'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmp74jCLy/github_demo2'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     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
    
     cloning into '/tmp/Rtmp74jCLy/github_demo3'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmp74jCLy/github_demo'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/Rtmp74jCLy/denpendence1'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     /tmp/Rtmp74jCLy/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmp74jCLy/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmp74jCLy/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     /tmp/Rtmp74jCLy/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmp74jCLy/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/Rtmp74jCLy/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'
     Content type 'unknown' length 107 bytes
     ==================================================
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
     Content type 'unknown' length 3574 bytes
     ==================================================
     ── 1. Failure: nongithub.versions (@test_versions.R#6) ────────────────────────
     `x` not equal to `expected`.
     1 element mismatch
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 69 SKIPPED: 0 FAILED: 1
     1. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     In addition: Warning message:
     In if (is.list(value)) value <- .resolveClassList(value, where, :
     closing unused connection 4 (http://research-pub.gene.com/gmap/src/)
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.3.3
Check: examples
Result: 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 [2018-08-19 13:56:57] 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 ... github2versions -> getURL -> curlPerform -> <Anonymous> -> fun
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.3.3
Check: tests
Result: ERROR
     Running 'testthat.R' [32s]
    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/RtmpiQsi8z/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)
    
     123 > D:/temp/RtmpiQsi8z/123
     123 > D:/temp/RtmpiQsi8z/123
     123 > D:/temp/RtmpiQsi8z/123
     123 > D:/temp/RtmpiQsi8z/123
     D:\temp\RtmpiQsi8z/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\RtmpiQsi8z/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\RtmpiQsi8z/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     D:\temp\RtmpiQsi8z/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\RtmpiQsi8z/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\RtmpiQsi8z/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
    
     -- 6. Failure: nongithub.versions (@test_versions.R#6) ------------------------
     `x` not equal to `expected`.
     1 element mismatch
    
     == testthat results ===========================================================
     OK: 58 SKIPPED: 0 FAILED: 6
     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)
     6. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.3.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 46-70 (BioInstaller.Rmd)
    Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
    error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [10s/38s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BioInstaller)
     >
     >
     > test_check("BioInstaller")
     cloning into '/tmp/RtmpvjEzFS/github_demo0'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpvjEzFS/github_demo2'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     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
    
     cloning into '/tmp/RtmpvjEzFS/github_demo3'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpvjEzFS/github_demo'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpvjEzFS/denpendence1'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     /tmp/RtmpvjEzFS/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpvjEzFS/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpvjEzFS/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     /tmp/RtmpvjEzFS/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpvjEzFS/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpvjEzFS/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'
     Content type 'unknown' length 107 bytes
     ==================================================
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
     Content type 'unknown' length 3574 bytes
     ==================================================
     ── 1. Failure: nongithub.versions (@test_versions.R#6) ────────────────────────
     `x` not equal to `expected`.
     1 element mismatch
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 69 SKIPPED: 0 FAILED: 1
     1. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     In addition: Warning message:
     In .Internal(get0(x, envir, mode, inherits, ifnotfound)) :
     closing unused connection 4 (http://research-pub.gene.com/gmap/src/)
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [12s/200s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BioInstaller)
     >
     >
     > test_check("BioInstaller")
     cloning into '/tmp/RtmpoRaWYz/github_demo0'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpoRaWYz/github_demo2'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     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
    
     cloning into '/tmp/RtmpoRaWYz/github_demo3'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpoRaWYz/github_demo'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpoRaWYz/denpendence1'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     /tmp/RtmpoRaWYz/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpoRaWYz/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpoRaWYz/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     /tmp/RtmpoRaWYz/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpoRaWYz/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpoRaWYz/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'
     Content type 'unknown' length 107 bytes
     ==================================================
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
     Content type 'unknown' length 3574 bytes
     ==================================================
     ── 1. Failure: nongithub.versions (@test_versions.R#6) ────────────────────────
     `x` not equal to `expected`.
     1 element mismatch
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 69 SKIPPED: 0 FAILED: 1
     1. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [10s/40s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BioInstaller)
     >
     >
     > test_check("BioInstaller")
     cloning into '/tmp/RtmpPoUxB1/github_demo0'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpPoUxB1/github_demo2'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     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
    
     cloning into '/tmp/RtmpPoUxB1/github_demo3'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpPoUxB1/github_demo'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     cloning into '/tmp/RtmpPoUxB1/denpendence1'...
     Receiving objects: 16% (1/6), 0 kb
     Receiving objects: 33% (2/6), 0 kb
     Receiving objects: 50% (3/6), 0 kb
     Receiving objects: 66% (4/6), 0 kb
     Receiving objects: 83% (5/6), 0 kb
     Receiving objects: 100% (6/6), 0 kb, done.
     /tmp/RtmpPoUxB1/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpPoUxB1/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpPoUxB1/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     /tmp/RtmpPoUxB1/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpPoUxB1/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     /tmp/RtmpPoUxB1/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'
     Content type 'unknown' length 107 bytes
     ==================================================
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
     Content type 'unknown' length 3574 bytes
     ==================================================
     ── 1. Failure: nongithub.versions (@test_versions.R#6) ────────────────────────
     `x` not equal to `expected`.
     1 element mismatch
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 69 SKIPPED: 0 FAILED: 1
     1. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     In addition: Warning message:
     closing unused connection 4 (http://research-pub.gene.com/gmap/src/)
     Execution halted
Flavor: r-release-linux-x86_64

Version: 0.3.3
Check: examples
Result: 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 [2018-08-20 08:49:14] 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 ... github2versions -> getURL -> curlPerform -> <Anonymous> -> fun
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.3.3
Check: tests
Result: ERROR
     Running 'testthat.R' [32s]
    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/RtmpQLpA8G/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)
    
     123 > D:/temp/RtmpQLpA8G/123
     123 > D:/temp/RtmpQLpA8G/123
     123 > D:/temp/RtmpQLpA8G/123
     123 > D:/temp/RtmpQLpA8G/123
     D:\temp\RtmpQLpA8G/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\RtmpQLpA8G/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\RtmpQLpA8G/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     D:\temp\RtmpQLpA8G/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\RtmpQLpA8G/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\RtmpQLpA8G/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
    
     -- 6. Failure: nongithub.versions (@test_versions.R#6) ------------------------
     `x` not equal to `expected`.
     1 element mismatch
    
     == testthat results ===========================================================
     OK: 58 SKIPPED: 0 FAILED: 6
     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)
     6. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [8s/29s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//README'
     Content type 'unknown' length 107 bytes
     ==================================================
     trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
     Content type 'unknown' length 3574 bytes
     ==================================================
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 61 SKIPPED: 0 FAILED: 4
     1. Error: install.github (@test_install.R#10)
     2. Error: install.bioinfo (@test_install.R#57)
     3. Error: dependence (@test_install_uilts.R#88)
     4. Error: git.download (@test_install_uilts.R#102)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-osx-x86_64

Version: 0.3.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    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
    
    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
    
    Quitting from lines 102-109 (BioInstaller.Rmd)
    Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
    Error in 'git2r_clone': SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.3.3
Check: examples
Result: 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 [2018-08-19 02:00:54] 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 -> <Anonymous> -> fun
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.3.3
Check: tests
Result: ERROR
     Running 'testthat.R' [31s]
    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/Rtmp0qQkwE/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)
    
     123 > D:/temp/Rtmp0qQkwE/123
     123 > D:/temp/Rtmp0qQkwE/123
     123 > D:/temp/Rtmp0qQkwE/123
     123 > D:/temp/Rtmp0qQkwE/123
     D:\temp\Rtmp0qQkwE/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\Rtmp0qQkwE/destdir.initial not empty, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\Rtmp0qQkwE/destdir.initial not empty, overwrite?[y]
     More than 3 counts input, default is not to overwrite.
     D:\temp\Rtmp0qQkwE/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\Rtmp0qQkwE/destdir.initial existed, overwrite?[y]
     Please input y/n/Y/N!
     D:\temp\Rtmp0qQkwE/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
    
     -- 6. Failure: nongithub.versions (@test_versions.R#6) ------------------------
     `x` not equal to `expected`.
     1 element mismatch
    
     == testthat results ===========================================================
     OK: 58 SKIPPED: 0 FAILED: 6
     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)
     6. Failure: nongithub.versions (@test_versions.R#6)
    
     Error: testthat unit tests failed
     Execution halted
     Warning message:
     closing unused connection 4 (http://research-pub.gene.com/gmap/src/)
Flavor: r-oldrel-windows-ix86+x86_64