* Re: pandoc document conversion to html fails with error 67 on PC network
[not found] ` <539b3ef0-60e3-4e72-bf26-bba286ceafcc-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2019-04-08 19:03 ` John MacFarlane
[not found] ` <m2imvocoa5.fsf-pgq/RBwaQ+zq8tPRBa0AtqxOck334EZe@public.gmane.org>
2019-10-03 9:54 ` Andy Field
` (2 subsequent siblings)
3 siblings, 1 reply; 6+ messages in thread
From: John MacFarlane @ 2019-04-08 19:03 UTC (permalink / raw)
To: Andy Field, pandoc-discuss
I'd be good to know the version of pandoc that is
being used. Some issues affecting use of shared
drives have been fixed in recent versions, so if you
can try the most recent version, that would be helpful.
Andy Field <profandyfield-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
> I work at a UK university where I teach R Studio and R Markdown. We have a
> problem with knitting Markdown documents to HTML when students are working
> on networked university PCs.
> The problem in brief
>
> - R Markdown documents knitted to html fail with with error 67
> - Changing the YAML to self_contained: no results in a successfully
> knitted document, but this doesn’t help us because (obviously) the html is
> no longer self-contained and instead images and other references are stored
> in a separate folder. Students can’t submit non-self-contained html for
> assessment. We need the resulting html files to be self-contained.
> - Knitting to Word works
> - I recently asked ITS to do a test install of latex and try knitting to
> PDF. That worked (on a test file) too.
>
> Contextual information
>
> - Students work on networked PCs.
> - The R library is set up for each user within their Documents folder on
> the network mapped to a drive: N:/Documents/R/win-library/3.5
> - We have had an issue with *some* (but not all) packages needing us to
> specify the library path (e.g., install.packages('package_name'), lib =
> N:/Documents/R/win-library/3.5). Reading around, this seems to be to do
> with UNC paths, but I don’t know enough about UNC paths to understand what
> the issue is and ITS don’t understand enough about R Studio to know why UNC
> paths are a problem:-)
>
> More detail on the error
>
> This is the error from pandoc when knitting the default R markdown template
> document:
>
> pandoc.exe: Could not fetch \xx.xx.xx.ac.uk-library.5-1.11.3.min.js
> FailedConnectionException2 “xx.xx.xx.ac.uk” 80 False connect: failed
> (Connection timed out (WSAETIMEDOUT)) Error: pandoc document conversion
> failed with error 67 Execution halted`
>
> xx.xx.xx.ac.uk is the home drive of the university network (with xs to
> replace the actual path) and ‘username’ would be the users username. The
> error looks as though it is looking for ‘jquery.min.js’ but timing out
> before finding it. The file jquery.min.js exists at the specified location
> (\xx.xx.xx.ac.uk-library.5-1.11.3)
> Questions
>
> I’m hitting a brick wall with this issue. My ITS support are *really* helpful
> but they don’t know anything about pandoc or R Studio. Conversely, I know
> nothing about networking, so they say ‘it’s a pandoc issue you’ll have to
> ask the developers’, but everything I have read on error 67 suggests
> firewalls/UNC paths as the issue, which I have no control over (unless I
> can give ITS some specific info on *why* UNC paths/firewalls messes up
> knitting to html and a way to resolve it). Despite many hours on the
> internet, I haven’t found a way to resolve the issue other than setting
> self_contained: no in the YAML, which doesn’t help me.
>
> We’re changing all of our UG teaching in my school to R next year, and it’d
> really make life a lot easier if we can have students not to self-contained
> html. So, my questions:
>
> 1. If it is a UNC path/firewall issue does anyone have a workaround
> other than putting self_contained: no in the YAML? If you do have a
> solution that involves knowing about networking or UNC paths can you
> possibly give me info that will make sense to to my ITS staff (or point me
> somewhere for more info).
> 2. If it’s not a UNC path/firewall issue, what is the problem and is
> there a solution?
>
> --
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^ permalink raw reply [flat|nested] 6+ messages in thread* Re: pandoc document conversion to html fails with error 67 on PC network
[not found] ` <539b3ef0-60e3-4e72-bf26-bba286ceafcc-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2019-04-08 19:03 ` John MacFarlane
@ 2019-10-03 9:54 ` Andy Field
2019-10-03 9:55 ` Andy Field
2019-10-03 9:58 ` Andy Field
3 siblings, 0 replies; 6+ messages in thread
From: Andy Field @ 2019-10-03 9:54 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 5244 bytes --]
We tried updating pandoc as suggested but the error persisted. However, we
found a solution. In case others have the same issue I'm going to post this
solution.
We get users to create a .Renviron file (tutorial here
<https://csgillespie.github.io/efficientR/3-3-r-startup.html#renviron>).
This file sets the library path to the mapped drive rather than the UNC
path. In our case (see original question for why) the file contains this
text:
---
R_LIBS_USER = "N:/Documents/R/win-library/3.6"
R_USER = "N:/Documents"
---
ITS managed to use an app management system that creates this file
automatically for users when the boot up RStudio, however, if users need to
create this file themselves, you can get them to run the following script
(edited to fit your drive location):
---
user_renviron = path.expand(file.path("~", ".Renviron"))
if(!file.exists(user_renviron)) # check to see if the file already exists
file.create(user_renviron)
conn = file(user_renviron)
writeLines('R_LIBS_USER="N:/Documents/R/win-library/3.6"\nR_USER="N:/Documents"',
con = conn)
close(conn)
---
Knitting works like a charm now.
andy
On Monday, 8 April 2019 15:57:31 UTC+1, Andy Field wrote:
>
> I work at a UK university where I teach R Studio and R Markdown. We have a
> problem with knitting Markdown documents to HTML when students are working
> on networked university PCs.
> The problem in brief
>
> - R Markdown documents knitted to html fail with with error 67
> - Changing the YAML to self_contained: no results in a successfully
> knitted document, but this doesn’t help us because (obviously) the html is
> no longer self-contained and instead images and other references are stored
> in a separate folder. Students can’t submit non-self-contained html for
> assessment. We need the resulting html files to be self-contained.
> - Knitting to Word works
> - I recently asked ITS to do a test install of latex and try knitting
> to PDF. That worked (on a test file) too.
>
> Contextual information
>
> - Students work on networked PCs.
> - The R library is set up for each user within their Documents folder
> on the network mapped to a drive: N:/Documents/R/win-library/3.5
> - We have had an issue with *some* (but not all) packages needing us
> to specify the library path (e.g., install.packages('package_name'),
> lib = N:/Documents/R/win-library/3.5). Reading around, this seems to
> be to do with UNC paths, but I don’t know enough about UNC paths to
> understand what the issue is and ITS don’t understand enough about R Studio
> to know why UNC paths are a problem:-)
>
> More detail on the error
>
> This is the error from pandoc when knitting the default R markdown
> template document:
>
> pandoc.exe: Could not fetch \xx.xx.xx.ac.uk-library.5-1.11.3.min.js
> FailedConnectionException2 “xx.xx.xx.ac.uk” 80 False connect: failed
> (Connection timed out (WSAETIMEDOUT)) Error: pandoc document conversion
> failed with error 67 Execution halted`
>
> xx.xx.xx.ac.uk is the home drive of the university network (with xs to
> replace the actual path) and ‘username’ would be the users username. The
> error looks as though it is looking for ‘jquery.min.js’ but timing out
> before finding it. The file jquery.min.js exists at the specified location
> (\xx.xx.xx.ac.uk-library.5-1.11.3)
> Questions
>
> I’m hitting a brick wall with this issue. My ITS support are *really* helpful
> but they don’t know anything about pandoc or R Studio. Conversely, I know
> nothing about networking, so they say ‘it’s a pandoc issue you’ll have to
> ask the developers’, but everything I have read on error 67 suggests
> firewalls/UNC paths as the issue, which I have no control over (unless I
> can give ITS some specific info on *why* UNC paths/firewalls messes up
> knitting to html and a way to resolve it). Despite many hours on the
> internet, I haven’t found a way to resolve the issue other than setting
> self_contained: no in the YAML, which doesn’t help me.
>
> We’re changing all of our UG teaching in my school to R next year, and
> it’d really make life a lot easier if we can have students not to
> self-contained html. So, my questions:
>
> 1. If it is a UNC path/firewall issue does anyone have a workaround
> other than putting self_contained: no in the YAML? If you do have a
> solution that involves knowing about networking or UNC paths can you
> possibly give me info that will make sense to to my ITS staff (or point me
> somewhere for more info).
> 2. If it’s not a UNC path/firewall issue, what is the problem and is
> there a solution?
>
>
--
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[-- Attachment #1.2: Type: text/html, Size: 10599 bytes --]
^ permalink raw reply [flat|nested] 6+ messages in thread* Re: pandoc document conversion to html fails with error 67 on PC network
[not found] ` <539b3ef0-60e3-4e72-bf26-bba286ceafcc-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2019-04-08 19:03 ` John MacFarlane
2019-10-03 9:54 ` Andy Field
@ 2019-10-03 9:55 ` Andy Field
2019-10-03 9:58 ` Andy Field
3 siblings, 0 replies; 6+ messages in thread
From: Andy Field @ 2019-10-03 9:55 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 5240 bytes --]
We tried updating pandoc as suggested but the error persisted. However, we
found a solution. In case others have the same issue I'm going to post this
solution.
We get users to create a .Renviron file (tutorial here
<https://csgillespie.github.io/efficientR/3-3-r-startup.html#renviron>).
This file sets the library path to the mapped drive rather than the UNC
path. In our case (see original question for why) the file contains this
text:
```
R_LIBS_USER = "N:/Documents/R/win-library/3.6"
R_USER = "N:/Documents"
```
ITS managed to use an app management system that creates this file
automatically for users when the boot up RStudio, however, if users need to
create this file themselves, you can get them to run the following script
(edited to fit your drive location):
```
user_renviron = path.expand(file.path("~", ".Renviron"))
if(!file.exists(user_renviron)) # check to see if the file already exists
file.create(user_renviron)
conn = file(user_renviron)
writeLines('R_LIBS_USER="N:/Documents/R/win-library/3.6"\nR_USER="N:/Documents"',
con = conn)
close(conn)
```
Knitting works like a charm now.
andy
On Monday, 8 April 2019 15:57:31 UTC+1, Andy Field wrote:
>
> I work at a UK university where I teach R Studio and R Markdown. We have a
> problem with knitting Markdown documents to HTML when students are working
> on networked university PCs.
> The problem in brief
>
> - R Markdown documents knitted to html fail with with error 67
> - Changing the YAML to self_contained: no results in a successfully
> knitted document, but this doesn’t help us because (obviously) the html is
> no longer self-contained and instead images and other references are stored
> in a separate folder. Students can’t submit non-self-contained html for
> assessment. We need the resulting html files to be self-contained.
> - Knitting to Word works
> - I recently asked ITS to do a test install of latex and try knitting
> to PDF. That worked (on a test file) too.
>
> Contextual information
>
> - Students work on networked PCs.
> - The R library is set up for each user within their Documents folder
> on the network mapped to a drive: N:/Documents/R/win-library/3.5
> - We have had an issue with *some* (but not all) packages needing us
> to specify the library path (e.g., install.packages('package_name'),
> lib = N:/Documents/R/win-library/3.5). Reading around, this seems to
> be to do with UNC paths, but I don’t know enough about UNC paths to
> understand what the issue is and ITS don’t understand enough about R Studio
> to know why UNC paths are a problem:-)
>
> More detail on the error
>
> This is the error from pandoc when knitting the default R markdown
> template document:
>
> pandoc.exe: Could not fetch \xx.xx.xx.ac.uk-library.5-1.11.3.min.js
> FailedConnectionException2 “xx.xx.xx.ac.uk” 80 False connect: failed
> (Connection timed out (WSAETIMEDOUT)) Error: pandoc document conversion
> failed with error 67 Execution halted`
>
> xx.xx.xx.ac.uk is the home drive of the university network (with xs to
> replace the actual path) and ‘username’ would be the users username. The
> error looks as though it is looking for ‘jquery.min.js’ but timing out
> before finding it. The file jquery.min.js exists at the specified location
> (\xx.xx.xx.ac.uk-library.5-1.11.3)
> Questions
>
> I’m hitting a brick wall with this issue. My ITS support are *really* helpful
> but they don’t know anything about pandoc or R Studio. Conversely, I know
> nothing about networking, so they say ‘it’s a pandoc issue you’ll have to
> ask the developers’, but everything I have read on error 67 suggests
> firewalls/UNC paths as the issue, which I have no control over (unless I
> can give ITS some specific info on *why* UNC paths/firewalls messes up
> knitting to html and a way to resolve it). Despite many hours on the
> internet, I haven’t found a way to resolve the issue other than setting
> self_contained: no in the YAML, which doesn’t help me.
>
> We’re changing all of our UG teaching in my school to R next year, and
> it’d really make life a lot easier if we can have students not to
> self-contained html. So, my questions:
>
> 1. If it is a UNC path/firewall issue does anyone have a workaround
> other than putting self_contained: no in the YAML? If you do have a
> solution that involves knowing about networking or UNC paths can you
> possibly give me info that will make sense to to my ITS staff (or point me
> somewhere for more info).
> 2. If it’s not a UNC path/firewall issue, what is the problem and is
> there a solution?
>
>
--
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[-- Attachment #1.2: Type: text/html, Size: 10627 bytes --]
^ permalink raw reply [flat|nested] 6+ messages in thread* Re: pandoc document conversion to html fails with error 67 on PC network
[not found] ` <539b3ef0-60e3-4e72-bf26-bba286ceafcc-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
` (2 preceding siblings ...)
2019-10-03 9:55 ` Andy Field
@ 2019-10-03 9:58 ` Andy Field
3 siblings, 0 replies; 6+ messages in thread
From: Andy Field @ 2019-10-03 9:58 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 5234 bytes --]
We tried updating pandoc as suggested but the error persisted. However, we
found a solution. In case others have the same issue I'm going to post this
solution.
We get users to create a .Renviron file (tutorial here
<https://csgillespie.github.io/efficientR/3-3-r-startup.html#renviron>).
This file sets the library path to the mapped drive rather than the UNC
path. In our case (see original question for why) the file contains this
text:
R_LIBS_USER = "N:/Documents/R/win-library/3.6"
R_USER = "N:/Documents"
ITS managed to use an app management system that creates this file
automatically for users when the boot up RStudio, however, if users need to
create this file themselves, you can get them to run the following script
(edited to fit your drive location):
user_renviron = path.expand(file.path("~", ".Renviron"))
if(!file.exists(user_renviron)) # check to see if the file already exists
file.create(user_renviron)
conn = file(user_renviron)
writeLines(
'R_LIBS_USER="N:/Documents/R/win-library/3.6"\nR_USER="N:/Documents"', con =
conn)
close(conn)
Knitting works like a charm now.
andy
On Monday, 8 April 2019 15:57:31 UTC+1, Andy Field wrote:
>
> I work at a UK university where I teach R Studio and R Markdown. We have a
> problem with knitting Markdown documents to HTML when students are working
> on networked university PCs.
> The problem in brief
>
> - R Markdown documents knitted to html fail with with error 67
> - Changing the YAML to self_contained: no results in a successfully
> knitted document, but this doesn’t help us because (obviously) the html is
> no longer self-contained and instead images and other references are stored
> in a separate folder. Students can’t submit non-self-contained html for
> assessment. We need the resulting html files to be self-contained.
> - Knitting to Word works
> - I recently asked ITS to do a test install of latex and try knitting
> to PDF. That worked (on a test file) too.
>
> Contextual information
>
> - Students work on networked PCs.
> - The R library is set up for each user within their Documents folder
> on the network mapped to a drive: N:/Documents/R/win-library/3.5
> - We have had an issue with *some* (but not all) packages needing us
> to specify the library path (e.g., install.packages('package_name'),
> lib = N:/Documents/R/win-library/3.5). Reading around, this seems to
> be to do with UNC paths, but I don’t know enough about UNC paths to
> understand what the issue is and ITS don’t understand enough about R Studio
> to know why UNC paths are a problem:-)
>
> More detail on the error
>
> This is the error from pandoc when knitting the default R markdown
> template document:
>
> pandoc.exe: Could not fetch \xx.xx.xx.ac.uk-library.5-1.11.3.min.js
> FailedConnectionException2 “xx.xx.xx.ac.uk” 80 False connect: failed
> (Connection timed out (WSAETIMEDOUT)) Error: pandoc document conversion
> failed with error 67 Execution halted`
>
> xx.xx.xx.ac.uk is the home drive of the university network (with xs to
> replace the actual path) and ‘username’ would be the users username. The
> error looks as though it is looking for ‘jquery.min.js’ but timing out
> before finding it. The file jquery.min.js exists at the specified location
> (\xx.xx.xx.ac.uk-library.5-1.11.3)
> Questions
>
> I’m hitting a brick wall with this issue. My ITS support are *really* helpful
> but they don’t know anything about pandoc or R Studio. Conversely, I know
> nothing about networking, so they say ‘it’s a pandoc issue you’ll have to
> ask the developers’, but everything I have read on error 67 suggests
> firewalls/UNC paths as the issue, which I have no control over (unless I
> can give ITS some specific info on *why* UNC paths/firewalls messes up
> knitting to html and a way to resolve it). Despite many hours on the
> internet, I haven’t found a way to resolve the issue other than setting
> self_contained: no in the YAML, which doesn’t help me.
>
> We’re changing all of our UG teaching in my school to R next year, and
> it’d really make life a lot easier if we can have students not to
> self-contained html. So, my questions:
>
> 1. If it is a UNC path/firewall issue does anyone have a workaround
> other than putting self_contained: no in the YAML? If you do have a
> solution that involves knowing about networking or UNC paths can you
> possibly give me info that will make sense to to my ITS staff (or point me
> somewhere for more info).
> 2. If it’s not a UNC path/firewall issue, what is the problem and is
> there a solution?
>
>
--
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^ permalink raw reply [flat|nested] 6+ messages in thread