[R-pkg-devel] File name error

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


-----Urspr?ngliche Nachricht-----
Von: R-package-devel [mailto:r-package-devel-bounces at 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
<https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-gcc>
3.0.0.2 3.63 56.71 60.34 ERROR
<https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_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/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.

<http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>

	[[alternative HTML version deleted]]

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

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

cat("hello", file = res)

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


-----Urspr?ngliche Nachricht-----
Von: R-package-devel [mailto:r-package-devel-bounces at 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

<https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-gcc>
3.0.0.2 3.63 56.71 60.34 ERROR

<https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_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/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.

<http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>

        [[alternative HTML version deleted]]

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


-----Urspr?ngliche Nachricht-----
Von: R-package-devel [mailto:r-package-devel-bounces at 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
<https://cran.r-project.org/web/checks/check_flavors.html#r-
devel-linux-x86_64-debian-gcc>
3.0.0.2 3.63 56.71 60.34 ERROR
<https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_
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.

<http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>

        [[alternative HTML version deleted]]

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.

<http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>

On Thu, Dec 21, 2017 at 4:21 AM, Uwe Ligges 
<ligges at statistik.tu-dortmund.de 
<mailto:ligges at statistik.tu-dortmund.de>> 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


        -----Urspr?ngliche Nachricht-----
        Von: R-package-devel
        [mailto:r-package-devel-bounces at r-project.org
        <mailto:r-package-devel-bounces at 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
        <https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-gcc
        <https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-gcc>>
        3.0.0.2 3.63 56.71 60.34 ERROR
        <https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/CATkit-00check.html
        <https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_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/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.

        <http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_
        <http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>>

         ? ? ? ? [[alternative HTML version deleted]]

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
<ligges at statistik.tu-dortmund.de> 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


-----Urspr?ngliche Nachricht-----
Von: R-package-devel [mailto:r-package-devel-bounces at 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

<https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-gcc>
3.0.0.2 3.63 56.71 60.34 ERROR

<https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_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/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.

<http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>

         [[alternative HTML version deleted]]