Re: [Bioc-devel] EXTERNAL: Re: Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0
Sorry about that Martin. Here's my thank you reply to Hervé from August 2nd.
Thanks Hervé and no problem about the Windows binary.
Richard did get DelayedArray installed today (I think using biocLite)! ^^
Best,
Leo
On Fri, Aug 3, 2018 at 8:27 AM Martin Morgan
wrote:
>
>
> The large number of people cc'd on this thread causes the mailman
> software to block posts. I'm removing individuals, please respond to
> this message.
>
> On 08/02/2018 01:57 PM, Hervé Pagès wrote:
> > Hi Leonardo,
> >
> > Hope you were able to solve your connection problems.
> > Just to let you that I fixed the DelayedArray timeout on
> > Windows and the zip files are now available for this
> > platform:
> >
> >https://bioconductor.org/packages/DelayedArray
> >
> > Sorry for the inconvenience.
> >
> > Cheers,
> > H.
> >
> >
> > On 08/01/2018 02:23 PM, Leonardo Collado Torres wrote:
> >> Hi,
> >>
> >> Just as a quick update. Everything worked yesterday when Richard used
> >> another PC computer from his home (another network). So it's
> >> definitely not a Bioc problem.
> >>
> >> Yet I have no idea how to troubleshoot it beyond burning it all and
> >> starting from scratch: re-installing R and everything and checking if
> >> that works. Well, or testing using a hotspot wifi connection with one
> >> of our phones and seeing if that works to bypass the wifi network from
> >> work.
> >>
> >> Best,
> >> Leo
> >>
> >> On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr.
> >> wrote:
> >>>
> >>> are you sure his tmp directory isn't full
> >>>
> >>> --t
> >>>
> >>>
> >>> On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres
> >>> wrote:
>
> From Richard:
>
> > BiocManager::install("DelayedArray")
>
> Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
>
> Installing package(s) 'BiocVersion', 'DelayedArray'
>
> trying URL
> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_bin_windows_contrib_3.5_BiocVersion-5F3.7.4.zip=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=RdZdVvOSqc562aHV7-SuXUDX1UWmqQS3vui_2xYItgQ='
>
>
> Content type 'application/zip' length 8649 bytes
>
> downloaded 8649 bytes
>
>
>
> package ‘BiocVersion’ successfully unpacked and MD5 sums checked
>
>
>
> The downloaded binary packages are in
>
> C:\Users\Richard
> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages
>
> installing the source package ‘DelayedArray’
>
>
>
> trying URL
> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_src_contrib_DelayedArray-5F0.6.2.tar.gz=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=vz1NGwOvFQqQbsZ2yqnCyV188YNc_k7oDMiD78DpRqY='
>
>
> Content type 'application/x-gzip' length 486139 bytes (474 KB)
>
> downloaded 474 KB
>
>
>
> Error in untar2(tarfile, files, list, exdir, restore_times) :
>
> incomplete block on file
>
> In R CMD INSTALL
>
>
>
> The downloaded source packages are in
>
> ‘C:\Users\Richard
> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages’
>
> installation path not writeable, unable to update packages: foreign,
> MASS, mgcv, survival
>
> Update old packages: 'openssl', 'stringi'
>
> Update all/some/none? [a/s/n]:
>
> n
>
> Warning message:
>
> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
>
> installation of package ‘DelayedArray’ had non-zero exit status
>
> >
>
>
>
> Also, at
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_release_bioc_html_DelayedArray.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=sIiQvz3aJN2aHqxD1FLQLygGYRequcJnj2ywQlGrkds=
>
> I don't see the tar for the Windows binary.
>
>
>
>
> On Mon, Jul 30, 2018 at 2:57 PM Tim Triche, Jr.
> wrote:
> >
> > BiocManager::install(whatever) doesn't work?
> >
> > biocLite is supposed to die, you see...
> >
> >
> > --t
> >
> >
> > On Mon, Jul 30, 2018 at 2:45 PM Leonardo Collado Torres
> > wrote:
> >>
> >> Hi bioc-devel,
> >>
> >> A co-worker of mine (Richard) tried several times to install the
> >> DelayedArray package. We got a couple of errors but it ultimately
> >> looks like it's an internet connection problem. The truth is that
> >> might be something affecting us on our side since I can't access
> >>
Re: [Bioc-devel] EXTERNAL: Re: Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0
The large number of people cc'd on this thread causes the mailman
software to block posts. I'm removing individuals, please respond to
this message.
On 08/02/2018 01:57 PM, Hervé Pagès wrote:
Hi Leonardo,
Hope you were able to solve your connection problems.
Just to let you that I fixed the DelayedArray timeout on
Windows and the zip files are now available for this
platform:
https://bioconductor.org/packages/DelayedArray
Sorry for the inconvenience.
Cheers,
H.
On 08/01/2018 02:23 PM, Leonardo Collado Torres wrote:
Hi,
Just as a quick update. Everything worked yesterday when Richard used
another PC computer from his home (another network). So it's
definitely not a Bioc problem.
Yet I have no idea how to troubleshoot it beyond burning it all and
starting from scratch: re-installing R and everything and checking if
that works. Well, or testing using a hotspot wifi connection with one
of our phones and seeing if that works to bypass the wifi network from
work.
Best,
Leo
On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr.
wrote:
are you sure his tmp directory isn't full
--t
On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres
wrote:
From Richard:
BiocManager::install("DelayedArray")
Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
Installing package(s) 'BiocVersion', 'DelayedArray'
trying URL
'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_bin_windows_contrib_3.5_BiocVersion-5F3.7.4.zip=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=RdZdVvOSqc562aHV7-SuXUDX1UWmqQS3vui_2xYItgQ='
Content type 'application/zip' length 8649 bytes
downloaded 8649 bytes
package ‘BiocVersion’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Richard
Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages
installing the source package ‘DelayedArray’
trying URL
'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_src_contrib_DelayedArray-5F0.6.2.tar.gz=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=vz1NGwOvFQqQbsZ2yqnCyV188YNc_k7oDMiD78DpRqY='
Content type 'application/x-gzip' length 486139 bytes (474 KB)
downloaded 474 KB
Error in untar2(tarfile, files, list, exdir, restore_times) :
incomplete block on file
In R CMD INSTALL
The downloaded source packages are in
‘C:\Users\Richard
Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages’
installation path not writeable, unable to update packages: foreign,
MASS, mgcv, survival
Update old packages: 'openssl', 'stringi'
Update all/some/none? [a/s/n]:
n
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘DelayedArray’ had non-zero exit status
Also, at
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_release_bioc_html_DelayedArray.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=sIiQvz3aJN2aHqxD1FLQLygGYRequcJnj2ywQlGrkds=
I don't see the tar for the Windows binary.
On Mon, Jul 30, 2018 at 2:57 PM Tim Triche, Jr.
wrote:
BiocManager::install(whatever) doesn't work?
biocLite is supposed to die, you see...
--t
On Mon, Jul 30, 2018 at 2:45 PM Leonardo Collado Torres
wrote:
Hi bioc-devel,
A co-worker of mine (Richard) tried several times to install the
DelayedArray package. We got a couple of errors but it ultimately
looks like it's an internet connection problem. The truth is that
might be something affecting us on our side since I can't access
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.comunidadbioinfo.org_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=mqn4K670CsFEqikTzeMFSYQasmpt-lJcGZNmmpMUFFA=
either but collaborators in Mexico
(cc'ed) can right now. Me (on a Mac) and Emily (on a PC) on the same
network can't access that website.
One of the errors we saw with Richard (on a PC) was about a missing
tar block. We failed to save that error message (for what's it's
worth, that was using RStudio). We then tried again and ran into this
error:
## try http:// if https:// URLs are not supported
source("https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_biocLite.R=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=iQdulMCYkOcfK1OVbMaabLmodIoXbm_0o-E_wljDJq8=;)
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
InternetOpenUrl failed: 'A connection with the server could not be
established'
