Re: [R-pkg-devel] File name error

2017-12-29 Thread Uwe Ligges 



On 21.12.2017 18:22, Henrik Bengtsson wrote:
Uwe/Kurt, is this 


You mean the new check? This is R.


controlled by R itself or by the host system?  I
suspect one of my R.filesets tests(*) fails (since a few days) because
of this, but it might actually be a false positive.  I fail to
reproduce it on Ubuntu 16.04 with:

* using R Under development (unstable) (2017-12-20 r73933)
* using platform: x86_64-pc-linux-gnu (64-bit)

My test tries to verify that it can write to tempdir() using its
*relative* path (if such is possible) - a test that effectively does:


abs <- tempfile()
setwd(dirname(abs))
getwd()

[1] "/tmp/Rtmpa9riPQ"

rel <- file.path("..", "..", abs)
rel <- gsub("//", "/", rel, fixed = TRUE)
rel

[1] "../../tmp/Rtmpa9riPQ/file3251441e380d

cat("hello", file = res)


file = rel, I guess.




and fails in that last write on 'r-devel-linux-x86_64-debian-gcc'.  It
could, of course, be a bug in my code that is now being revealed, but
these tests been in place for many years, possibly more than a decade.

(*) https://cran.r-project.org/web/checks/check_results_R.filesets.html



Well, as this is also shown in R-release on Kurt's machines, I suspect 
this is either a problem where the directory you are working in is a 
link and the deriving the relative path fails or there is no space left 
in  tempdir() ...


In both cases, please ask Kurt who is on vacation, too.

Best,
Uwe







Thxs,

Henrik

On Thu, Dec 21, 2017 at 2:21 AM, Uwe Ligges
 wrote:

This is a new check:

You must not write into the user's filespace without explicit agreement by
the user (by specifying path/name).

Note that some users won't even have permissions to write into the package's
installation directory if that is set up site wide by an admin, for example.

So please use tempdir() in the examples.

Best,
Uwe Ligges





On 21.12.2017 09:21, Blume Christine wrote:


Hi Cathy,

I also had troubles with debian (Fedora only gave warnings) and no
problems with other systems. Mine was related to me writing a file (or
rather trying to write) in a working directory other than tempdir (can be
retrieved by tempdir()). I now write it to tempdir and then set the old
working directory again at the end of the example. Perhaps that is somehow
helpful for your case too?

I can highly recommend to test your tar.gz file with the check() function
of the rhub package. You can for example run check("pathtoyourpackage",
platform = "debian-gcc-devel") or
check_for_cran("pathtoyourpackage", platform = "debian-gcc-devel"), i.e.
test your package on debian without troubles.

Best,
Christine


-Ursprüngliche Nachricht-
Von: R-package-devel [mailto:r-package-devel-boun...@r-project.org] Im
Auftrag von Cathy Lee Gierke
Gesendet: Donnerstag, 21. Dezember 2017 07:15
An: R Package Development
Betreff: [R-pkg-devel] File name error

I am getting the following error from the auto-checks when trying to
submit a package to CRAN:
r-devel-linux-x86_64-debian-gcc


3.0.0.2 3.63 56.71 60.34 ERROR



Error in pdf(file = fileName4, width = 8, height = 10) :
cannot open file

'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CATkit/extdata/activity-stress-c57-2-part.txt--20Dec2017--03-51-46CAToutput.pdf'

Since this works for ALL other flavors, I am assuming it may be some file
name restrictions unique to debian-gcc???  I can't think what else would
cause it to fail only in the OS.

debian doesn't like "--"?

Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that. Hate cannot
drive out hate: only love can do that.” * *“The arc of the moral universe is
long, but it bends towards justice.”* *“Nothing in the world is more
dangerous than sincere ignorance and conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant attitude.” *
*“Injustice anywhere is a threat to justice everywhere.”  *

― Martin Luther King Jr.



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Re: [R-pkg-devel] File name error

2017-12-29 Thread Uwe Ligges 



On 27.12.2017 18:55, Cathy Lee Gierke wrote:

My program puts the output into the folder where it found the input.


Please let the user specify the output dir. Otherwise there is the risk 
to overwrite files that the user want to keep.





Must I move the input files to tmpdir() or are they already there?


Why shoudl files be in tmpdir()? Only those you created there...

Best,
Uwe Ligges





Cathy Lee Gierke

/“Darkness cannot drive out darkness: only light can do that. Hate 
cannot drive out hate: only love can do that.”

/
/“The arc of the moral universe is long, but it bends towards justice.”/
/“Nothing in the world is more dangerous than sincere ignorance and 
conscientious stupidity.” /

/“Never forget that everything Hitler did in Germany was legal.” /
/“Forgiveness is not an occasional act, it is a constant attitude.” /
/“Injustice anywhere is a threat to justice everywhere.” /

― Martin Luther King Jr.



On Thu, Dec 21, 2017 at 4:21 AM, Uwe Ligges 
> wrote:


This is a new check:

You must not write into the user's filespace without explicit
agreement by the user (by specifying path/name).

Note that some users won't even have permissions to write into the
package's installation directory if that is set up site wide by an
admin, for example.

So please use tempdir() in the examples.

Best,
Uwe Ligges





On 21.12.2017 09:21, Blume Christine wrote:

Hi Cathy,

I also had troubles with debian (Fedora only gave warnings) and
no problems with other systems. Mine was related to me writing a
file (or rather trying to write) in a working directory other
than tempdir (can be retrieved by tempdir()). I now write it to
tempdir and then set the old working directory again at the end
of the example. Perhaps that is somehow helpful for your case too?

I can highly recommend to test your tar.gz file with the check()
function of the rhub package. You can for example run
check("pathtoyourpackage", platform = "debian-gcc-devel") or
check_for_cran("pathtoyourpackage", platform =
"debian-gcc-devel"), i.e. test your package on debian without
troubles.

Best,
Christine


-Ursprüngliche Nachricht-
Von: R-package-devel
[mailto:r-package-devel-boun...@r-project.org
] Im Auftrag von
Cathy Lee Gierke
Gesendet: Donnerstag, 21. Dezember 2017 07:15
An: R Package Development
Betreff: [R-pkg-devel] File name error

I am getting the following error from the auto-checks when
trying to submit a package to CRAN:
r-devel-linux-x86_64-debian-gcc

>
3.0.0.2 3.63 56.71 60.34 ERROR

>

Error in pdf(file = fileName4, width = 8, height = 10) :
    cannot open file

'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CATkit/extdata/activity-stress-c57-2-part.txt--20Dec2017--03-51-46CAToutput.pdf'

Since this works for ALL other flavors, I am assuming it may be
some file name restrictions unique to debian-gcc???  I can't
think what else would cause it to fail only in the OS.

debian doesn't like "--"?

Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that.
Hate cannot drive out hate: only love can do that.” * *“The arc
of the moral universe is long, but it bends towards justice.”*
*“Nothing in the world is more dangerous than sincere ignorance
and conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant
attitude.” * *“Injustice anywhere is a threat to justice
everywhere.”  *

― Martin Luther King Jr.

>

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Re: [R-pkg-devel] File name error

2017-12-27 Thread Cathy Lee Gierke 
My program puts the output into the folder where it found the input.

Must I move the input files to tmpdir() or are they already there?

Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that. Hate cannot
drive out hate: only love can do that.” *
*“The arc of the moral universe is long, but it bends towards justice.”*
*“Nothing in the world is more dangerous than sincere ignorance and
conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant attitude.” *
*“Injustice anywhere is a threat to justice everywhere.”  *

― Martin Luther King Jr.



On Thu, Dec 21, 2017 at 4:21 AM, Uwe Ligges  wrote:

> This is a new check:
>
> You must not write into the user's filespace without explicit agreement by
> the user (by specifying path/name).
>
> Note that some users won't even have permissions to write into the
> package's installation directory if that is set up site wide by an admin,
> for example.
>
> So please use tempdir() in the examples.
>
> Best,
> Uwe Ligges
>
>
>
>
>
> On 21.12.2017 09:21, Blume Christine wrote:
>
>> Hi Cathy,
>>
>> I also had troubles with debian (Fedora only gave warnings) and no
>> problems with other systems. Mine was related to me writing a file (or
>> rather trying to write) in a working directory other than tempdir (can be
>> retrieved by tempdir()). I now write it to tempdir and then set the old
>> working directory again at the end of the example. Perhaps that is somehow
>> helpful for your case too?
>>
>> I can highly recommend to test your tar.gz file with the check() function
>> of the rhub package. You can for example run check("pathtoyourpackage",
>> platform = "debian-gcc-devel") or
>> check_for_cran("pathtoyourpackage", platform = "debian-gcc-devel"), i.e.
>> test your package on debian without troubles.
>>
>> Best,
>> Christine
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: R-package-devel [mailto:r-package-devel-boun...@r-project.org] Im
>> Auftrag von Cathy Lee Gierke
>> Gesendet: Donnerstag, 21. Dezember 2017 07:15
>> An: R Package Development
>> Betreff: [R-pkg-devel] File name error
>>
>> I am getting the following error from the auto-checks when trying to
>> submit a package to CRAN:
>> r-devel-linux-x86_64-debian-gcc
>> > devel-linux-x86_64-debian-gcc>
>> 3.0.0.2 3.63 56.71 60.34 ERROR
>> > 64-debian-gcc/CATkit-00check.html>
>>
>> Error in pdf(file = fileName4, width = 8, height = 10) :
>>cannot open file
>> '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CA
>> Tkit/extdata/activity-stress-c57-2-part.txt--20Dec2017--03-
>> 51-46CAToutput.pdf'
>>
>> Since this works for ALL other flavors, I am assuming it may be some file
>> name restrictions unique to debian-gcc???  I can't think what else would
>> cause it to fail only in the OS.
>>
>> debian doesn't like "--"?
>>
>> Cathy Lee Gierke
>>
>>
>> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
>> drive out hate: only love can do that.” * *“The arc of the moral universe
>> is long, but it bends towards justice.”* *“Nothing in the world is more
>> dangerous than sincere ignorance and conscientious stupidity.” *
>> *“Never forget that everything Hitler did in Germany was legal.”   *
>> *“Forgiveness is not an occasional act, it is a constant attitude.” *
>> *“Injustice anywhere is a threat to justice everywhere.”  *
>>
>> ― Martin Luther King Jr.
>>
>> 
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/l
>> istinfo/r-package-devel
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>>

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Re: [R-pkg-devel] File name error

2017-12-21 Thread Henrik Bengtsson 
Uwe/Kurt, is this controlled by R itself or by the host system?  I
suspect one of my R.filesets tests(*) fails (since a few days) because
of this, but it might actually be a false positive.  I fail to
reproduce it on Ubuntu 16.04 with:

* using R Under development (unstable) (2017-12-20 r73933)
* using platform: x86_64-pc-linux-gnu (64-bit)

My test tries to verify that it can write to tempdir() using its
*relative* path (if such is possible) - a test that effectively does:

> abs <- tempfile()
> setwd(dirname(abs))
> getwd()
[1] "/tmp/Rtmpa9riPQ"
> rel <- file.path("..", "..", abs)
> rel <- gsub("//", "/", rel, fixed = TRUE)
> rel
[1] "../../tmp/Rtmpa9riPQ/file3251441e380d
> cat("hello", file = res)

and fails in that last write on 'r-devel-linux-x86_64-debian-gcc'.  It
could, of course, be a bug in my code that is now being revealed, but
these tests been in place for many years, possibly more than a decade.

(*) https://cran.r-project.org/web/checks/check_results_R.filesets.html

Thxs,

Henrik

On Thu, Dec 21, 2017 at 2:21 AM, Uwe Ligges
 wrote:
> This is a new check:
>
> You must not write into the user's filespace without explicit agreement by
> the user (by specifying path/name).
>
> Note that some users won't even have permissions to write into the package's
> installation directory if that is set up site wide by an admin, for example.
>
> So please use tempdir() in the examples.
>
> Best,
> Uwe Ligges
>
>
>
>
>
> On 21.12.2017 09:21, Blume Christine wrote:
>>
>> Hi Cathy,
>>
>> I also had troubles with debian (Fedora only gave warnings) and no
>> problems with other systems. Mine was related to me writing a file (or
>> rather trying to write) in a working directory other than tempdir (can be
>> retrieved by tempdir()). I now write it to tempdir and then set the old
>> working directory again at the end of the example. Perhaps that is somehow
>> helpful for your case too?
>>
>> I can highly recommend to test your tar.gz file with the check() function
>> of the rhub package. You can for example run check("pathtoyourpackage",
>> platform = "debian-gcc-devel") or
>> check_for_cran("pathtoyourpackage", platform = "debian-gcc-devel"), i.e.
>> test your package on debian without troubles.
>>
>> Best,
>> Christine
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: R-package-devel [mailto:r-package-devel-boun...@r-project.org] Im
>> Auftrag von Cathy Lee Gierke
>> Gesendet: Donnerstag, 21. Dezember 2017 07:15
>> An: R Package Development
>> Betreff: [R-pkg-devel] File name error
>>
>> I am getting the following error from the auto-checks when trying to
>> submit a package to CRAN:
>> r-devel-linux-x86_64-debian-gcc
>>
>> 
>> 3.0.0.2 3.63 56.71 60.34 ERROR
>>
>> 
>>
>> Error in pdf(file = fileName4, width = 8, height = 10) :
>>cannot open file
>>
>> '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CATkit/extdata/activity-stress-c57-2-part.txt--20Dec2017--03-51-46CAToutput.pdf'
>>
>> Since this works for ALL other flavors, I am assuming it may be some file
>> name restrictions unique to debian-gcc???  I can't think what else would
>> cause it to fail only in the OS.
>>
>> debian doesn't like "--"?
>>
>> Cathy Lee Gierke
>>
>>
>> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
>> drive out hate: only love can do that.” * *“The arc of the moral universe is
>> long, but it bends towards justice.”* *“Nothing in the world is more
>> dangerous than sincere ignorance and conscientious stupidity.” *
>> *“Never forget that everything Hitler did in Germany was legal.”   *
>> *“Forgiveness is not an occasional act, it is a constant attitude.” *
>> *“Injustice anywhere is a threat to justice everywhere.”  *
>>
>> ― Martin Luther King Jr.
>>
>> 
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Re: [R-pkg-devel] File name error

2017-12-21 Thread Dirk Eddelbuettel 

Cristine,

On 21 December 2017 at 08:21, Blume Christine wrote:
| I also had troubles with debian (Fedora only gave warnings)

May I ask you to be a little more careful in your attribution?   Yes, it is
too that the instance labeleb 'r-devel-debian' gave you an error.  But that
was not because of Debian, but because _that r-devel instance_ carried a new
test.

So please don't leave sentences hanging (as you now have in several emails)
"failed on Debian" implying a particular flavour (as shipped by Debian)
failed.  It didn't. A [very recent] build of r-devel, instrumented with a new
test, failed for you. It happens to be running on a Debian platform. So
please refer to the failing test platform by its name. Preferably with the
compiler added because there are two each for Debian and Fedora. See eg
https://cloud.r-project.org/web/checks/check_results_digest.html

Thanks,  Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] File name error

2017-12-21 Thread Uwe Ligges 

This is a new check:

You must not write into the user's filespace without explicit agreement 
by the user (by specifying path/name).


Note that some users won't even have permissions to write into the 
package's installation directory if that is set up site wide by an 
admin, for example.


So please use tempdir() in the examples.

Best,
Uwe Ligges




On 21.12.2017 09:21, Blume Christine wrote:

Hi Cathy,

I also had troubles with debian (Fedora only gave warnings) and no problems 
with other systems. Mine was related to me writing a file (or rather trying to 
write) in a working directory other than tempdir (can be retrieved by 
tempdir()). I now write it to tempdir and then set the old working directory 
again at the end of the example. Perhaps that is somehow helpful for your case 
too?

I can highly recommend to test your tar.gz file with the check() function of the rhub package. You 
can for example run check("pathtoyourpackage", platform = "debian-gcc-devel") or
check_for_cran("pathtoyourpackage", platform = "debian-gcc-devel"), i.e. test 
your package on debian without troubles.

Best,
Christine


-Ursprüngliche Nachricht-
Von: R-package-devel [mailto:r-package-devel-boun...@r-project.org] Im Auftrag 
von Cathy Lee Gierke
Gesendet: Donnerstag, 21. Dezember 2017 07:15
An: R Package Development
Betreff: [R-pkg-devel] File name error

I am getting the following error from the auto-checks when trying to submit a 
package to CRAN:
r-devel-linux-x86_64-debian-gcc

3.0.0.2 3.63 56.71 60.34 ERROR


Error in pdf(file = fileName4, width = 8, height = 10) :
   cannot open file
'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CATkit/extdata/activity-stress-c57-2-part.txt--20Dec2017--03-51-46CAToutput.pdf'

Since this works for ALL other flavors, I am assuming it may be some file name 
restrictions unique to debian-gcc???  I can't think what else would cause it to 
fail only in the OS.

debian doesn't like "--"?

Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that. Hate cannot drive 
out hate: only love can do that.” * *“The arc of the moral universe is long, 
but it bends towards justice.”* *“Nothing in the world is more dangerous than 
sincere ignorance and conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant attitude.” * 
*“Injustice anywhere is a threat to justice everywhere.”  *

― Martin Luther King Jr.



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Re: [R-pkg-devel] File name error

2017-12-21 Thread Blume Christine 
Hi Cathy,

I also had troubles with debian (Fedora only gave warnings) and no problems 
with other systems. Mine was related to me writing a file (or rather trying to 
write) in a working directory other than tempdir (can be retrieved by 
tempdir()). I now write it to tempdir and then set the old working directory 
again at the end of the example. Perhaps that is somehow helpful for your case 
too?

I can highly recommend to test your tar.gz file with the check() function of 
the rhub package. You can for example run check("pathtoyourpackage", platform = 
"debian-gcc-devel") or 
check_for_cran("pathtoyourpackage", platform = "debian-gcc-devel"), i.e. test 
your package on debian without troubles.

Best,
Christine


-Ursprüngliche Nachricht-
Von: R-package-devel [mailto:r-package-devel-boun...@r-project.org] Im Auftrag 
von Cathy Lee Gierke
Gesendet: Donnerstag, 21. Dezember 2017 07:15
An: R Package Development
Betreff: [R-pkg-devel] File name error

I am getting the following error from the auto-checks when trying to submit a 
package to CRAN:
r-devel-linux-x86_64-debian-gcc

3.0.0.2 3.63 56.71 60.34 ERROR


Error in pdf(file = fileName4, width = 8, height = 10) :
  cannot open file
'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CATkit/extdata/activity-stress-c57-2-part.txt--20Dec2017--03-51-46CAToutput.pdf'

Since this works for ALL other flavors, I am assuming it may be some file name 
restrictions unique to debian-gcc???  I can't think what else would cause it to 
fail only in the OS.

debian doesn't like "--"?

Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that. Hate cannot drive 
out hate: only love can do that.” * *“The arc of the moral universe is long, 
but it bends towards justice.”* *“Nothing in the world is more dangerous than 
sincere ignorance and conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant attitude.” * 
*“Injustice anywhere is a threat to justice everywhere.”  *

― Martin Luther King Jr.



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