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 |
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