Hello all.
I am still struggling with this issue.
It appears that new installations are going to local drive.
# #Test 05/13/2020
# install.packages("abjutils")
# package ?abjutils? successfully unpacked and MD5 sums checked
#
# The downloaded binary packages are in
# C:\Users\A436798\AppData\Local\Temp\RtmpCuXNJn\downloaded_packages
However, when I run .libPaths() it indicates our UNC path
[1]
"\\\\winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-4.0.0patched/library"
Is there a way for me to change this myself in my instance of R?
Thank you.
WHP
Proprietary
-----Original Message-----
From: Ege Rubak <rubak at math.aau.dk>
Sent: Tuesday, May 12, 2020 7:43 AM
To: Poling, William <PolingW at aetna.com>; r-help at r-project.org
Subject: [EXTERNAL] Re: [R] Help with R-Markdown please
**** External Email - Use Caution ****
Looks like your files are on a Windows network drive (UNC path). I have
experienced many problems with this on a Windows laptop from work. If at all
possible you should avoid this. As an absolute minimum make sure your R library
(collection of installed packages) is on the local file system and not a UNC
path. If you are lucky this could be enough to make things work.
You can check your library location(s) with the command .libPaths() in an R
session.
Good luck.
Ege
On Tue, 2020-05-12 at 10:15 +0000, Poling, William via R-help
wrote:> #UPDATED 05/05/2020
> #RStudio Version Version 1.2.1335 need this one--> 1.2.5019
> sessionInfo()
> # R version 4.0.0 Patched (2020-05-03 r78349)
> #Platform: x86_64-w64-mingw32/x64 (64-bit) #Running under: Windows 10
> x64 (build 17763)
>
> Good morning.
>
> This is the first time I have tried RMarkdown on new laptop with new
> employer.
> I am not sure how to go about fixing this problem below?
>
> Would someone please advise course of action.
>
> Thank you.
>
> WHP
>
>
>
> processing file: Member-Geo-Location-Test-V1.Rmd
>
> |..........
> | 14%
> ordinary text without R code
>
>
> |....................
> | 29%
> label: unnamed-chunk-1 (with options) List of 1 $ echo: logi FALSE
>
>
> |..............................
> | 43%
> ordinary text without R code
>
>
> |........................................
> | 57%
> label: setup (with options)
> List of 2
> $ include: logi FALSE
> $ warning: logi FALSE
>
>
> |..................................................
> | 71%
> ordinary text without R code
>
>
> |............................................................
> | 86%
> label: Table1 (with options)
> List of 2
> $ echo : logi FALSE
> $ results: chr "asis"
>
>
> |....................................................................
> ..| 100%
> inline R code fragments
>
>
> output file: Member-Geo-Location-Test-V1.knit.md
>
> "C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS
Member-
> Geo-Location-Test-V1.utf8.md --to html4 --from
> markdown+autolink_bare_uris+tex_math_single_backslash+smart --output
> Member-Geo-Location-Test-V1.html --email-obfuscation none --self-
> contained --standalone --section-divs --template "\\winp-oaf-
> 113\FldrRedir_1$\A436798\Data\R\R-
> 4.0.0patched\library\rmarkdown\rmd\h\default.html" --no-highlight --
> variable highlightjs=1 --variable "theme:bootstrap" --include-in-
> header "C:\Users\A436798\AppData\Local\Temp\RtmpSajZla\rmarkdown-
> str2ae846253313.html" --mathjax --variable "mathjax-url:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mathjax.rstudio.c
>
om_latest_MathJax.js-3Fconfig-3DTeX-2DAMS-2DMML-5FHTMLorMML&d=DwIGaQ&c
> =wluqKIiwffOpZ6k5sqMWMBOn0vyYnlulRJmmvOXCFpM&r=j7MrcIQm2xjHa8v-2mTpmTC
>
tKvneM2ExlYvnUWbsByY&m=uBce0mQRO8wdLXO8BDTtjk4R92KVzpjtkQ-NqYiAHCo&s=S
> MNU_B--j9FvBKh-0u1NG5RHd7AtLkvyVsi9ybyUwYU&e> " --lua-filter
"\\winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-
> 4.0.0patched/library/rmarkdown/rmd/lua/pagebreak.lua" --lua-filter
> "\\winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-
> 4.0.0patched/library/rmarkdown/rmd/lua/latex-div.lua"
> Could not fetch http://?/UNC/winp-oaf-
> 113/FldrRedir_1$/A436798/Data/R/R-
> 4.0.0patched/library/rmarkdown/rmd/h/default.html
> HttpExceptionRequest Request {
> host = ""
> port = 80
> secure = False
> requestHeaders = []
> path = "/"
> queryString = "?/UNC/winp-oaf-
> 113/FldrRedir_1$/A436798/Data/R/R-
> 4.0.0patched/library/rmarkdown/rmd/h/default.html"
> method = "GET"
> proxy = Nothing
> rawBody = False
> redirectCount = 10
> responseTimeout = ResponseTimeoutDefault
> requestVersion = HTTP/1.1
> }
> (InvalidDestinationHost "")
> Error: pandoc document conversion failed with error 61 Execution
> halted
>
> WHP
>
>
> Proprietary
>
> NOTICE TO RECIPIENT OF INFORMATION:\ This e-mail may
> con...{{dropped:16}}
>
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--
Ege Rubak, Associate Professor,
Department of Mathematical Sciences, Aalborg University Skjernvej 4A, 9220
Aalborg East, Denmark
Phone: (+45)99408861
Mobile: (+45)30230252
Email: rubak at math.aau.dk
NOTICE TO RECIPIENT OF INFORMATION:
This e-mail may contain confidential or privileged information. If you think you
have received this e-mail in error, please advise the sender by reply e-mail and
then delete this e-mail immediately.
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any further disclosure without the express written consent of the person to whom
it pertains or as otherwise permitted by law. Any unauthorized further
disclosure may be considered a violation of federal and/or state law. A general
authorization for the release of medical or other information may NOT be
sufficient consent for release of this type of information.
Thank you. Aetna
On 2020-05-13 18:46 +0000, Poling, William via R-help wrote:> Hello all. > > I am still struggling with this issue. > > It appears that new installations are going > to local drive. > > # #Test 05/13/2020 > # install.packages("abjutils") > # package ?abjutils? successfully unpacked and MD5 sums checked > # > # The downloaded binary packages are in > # C:\Users\A436798\AppData\Local\Temp\RtmpCuXNJn\downloaded_packages > > However, when I run .libPaths() it > indicates our UNC path > > [1] "\\\\winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-4.0.0patched/library" > > Is there a way for me to change this myself > in my instance of R?Dear William, Perhaps you could try to set the variable R_LIBS_USER to some local folder. I do not know how to do this on Windows, but there seems to be some guys in this rstudio discussion thread that came to some sort of a conclusion: https://community.rstudio.com/t/help-regarding-package-installation-renviron-rprofile-r-libs-r-libs-site-and-r-libs-user-oh-my/13888/8 Since long ago, I have had this line in my ~/.zshrc.local :) [ -e /usr/bin/Rscript ] && R_LIBS_USER=`Rscript -e 'cat(Sys.getenv("R_LIBS_USER"))'` Best, Rasmus
Hi Rasmus, thank you I will see if this is something I can do without IT admin
access.
In the mean time I have reloaded rmarkdown. To local
package ?rmarkdown? successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\A436798\AppData\Local\Temp\RtmpYjSy7G\downloaded_packages
library(rmarkdown)
But R is still looking for it in : " Could not fetch
http://?/UNC/winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-4.0.0patched/library/rmarkdown/rmd/h/default.html"
More recently I have installed other pkgs for the first time use and they have
gone to local like above for rmarkdown and I have used functions from them so
they are being searched for correctly I guess?
Very confusing.
Thank you for your response Sir!
WHP
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS
Member-Geo-Location-Test-V1.utf8.md --to html4 --from
markdown+autolink_bare_uris+tex_math_single_backslash+smart --output
Member-Geo-Location-Test-V1.html --email-obfuscation none --self-contained
--standalone --section-divs --template
"\\winp-oaf-113\FldrRedir_1$\A436798\Data\R\R-4.0.0patched\library\rmarkdown\rmd\h\default.html"
--no-highlight --variable highlightjs=1 --variable "theme:bootstrap"
--include-in-header
"C:\Users\A436798\AppData\Local\Temp\RtmpglP9GJ\rmarkdown-str314c55414a00.html"
--mathjax --variable
"mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
--lua-filter
"\\winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-4.0.0patched/library/rmarkdown/rmd/lua/pagebreak.lua"
--lua-filter
"\\winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-4.0.0patched/library/rmarkdown/rmd/lua/latex-div.lua"
output file: Member-Geo-Location-Test-V1.knit.md
Could not fetch
http://?/UNC/winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-4.0.0patched/library/rmarkdown/rmd/h/default.html
HttpExceptionRequest Request {
host = ""
port = 80
secure = False
requestHeaders = []
path = "/"
queryString =
"?/UNC/winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-4.0.0patched/library/rmarkdown/rmd/h/default.html"
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
}
(InvalidDestinationHost "")
Error: pandoc document conversion failed with error 61
Execution halted
WHP
Proprietary
-----Original Message-----
From: Rasmus Liland <jral at posteo.no>
Sent: Wednesday, May 13, 2020 2:10 PM
To: Poling, William <PolingW at aetna.com>
Cc: r-help at r-project.org
Subject: [EXTERNAL] Re: [R] Help with R-Markdown please
**** External Email - Use Caution ****
On 2020-05-13 18:46 +0000, Poling, William via R-help
wrote:> Hello all.
>
> I am still struggling with this issue.
>
> It appears that new installations are going to local drive.
>
> # #Test 05/13/2020
> # install.packages("abjutils")
> # package ?abjutils? successfully unpacked and MD5 sums checked # #
> The downloaded binary packages are in #
> C:\Users\A436798\AppData\Local\Temp\RtmpCuXNJn\downloaded_packages
>
> However, when I run .libPaths() it
> indicates our UNC path
>
> [1]
"\\\\winp-oaf-113/FldrRedir_1$/A436798/Data/R/R-4.0.0patched/library"
>
> Is there a way for me to change this myself in my instance of R?
Dear William,
Perhaps you could try to set the variable R_LIBS_USER to some local folder. I
do not know how to do this on Windows, but there seems to be some guys in this
rstudio discussion thread that came to some sort of a
conclusion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__community.rstudio.com_t_help-2Dregarding-2Dpackage-2Dinstallation-2Drenviron-2Drprofile-2Dr-2Dlibs-2Dr-2Dlibs-2Dsite-2Dand-2Dr-2Dlibs-2Duser-2Doh-2Dmy_13888_8&d=DwIDaQ&c=wluqKIiwffOpZ6k5sqMWMBOn0vyYnlulRJmmvOXCFpM&r=j7MrcIQm2xjHa8v-2mTpmTCtKvneM2ExlYvnUWbsByY&m=q_5fam9luSaeNgs-KOUZS-w-YAVaPzQdZgIlejBCDFA&s=NWDnltFH8cjC-pj6K08lWXC1FjfFcyY1mueSZnor9Ng&e=
Since long ago, I have had this line in my ~/.zshrc.local :)
[ -e /usr/bin/Rscript ] && R_LIBS_USER=`Rscript -e
'cat(Sys.getenv("R_LIBS_USER"))'`
Best,
Rasmus
NOTICE TO RECIPIENT OF INFORMATION:
This e-mail may contain confidential or privileged information. If you think you
have received this e-mail in error, please advise the sender by reply e-mail and
then delete this e-mail immediately.
This e-mail may also contain protected health information (PHI) with information
about sensitive medical conditions, including, but not limited to, treatment for
substance use disorders, behavioral health, HIV/AIDS, or pregnancy. This type of
information may be protected by various federal and/or state laws which prohibit
any further disclosure without the express written consent of the person to whom
it pertains or as otherwise permitted by law. Any unauthorized further
disclosure may be considered a violation of federal and/or state law. A general
authorization for the release of medical or other information may NOT be
sufficient consent for release of this type of information.
Thank you. Aetna