[Bioc-devel] Check error on malbec2

[Shepherd, Lori]

>From the looks of your code, when a user runs the examples/vignette they have the option of a tempdir() which is what you show and run as default for the examples, or specifying their own unique directory for the output. The output directory is passed as an argument to your functions which is good.  While they are in the same R session, the tempdir() will remain and should be accessible by following the path  dir.name  [because in your example you do: dir.name <- tempdir()] . We try to encourage not to write to a user's system permanently by default in examples/vignettes as they are not always cognizant that this is occurring and because in some cases a user may not have write privileges if they are using a shared computer or do not have admin writes.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Aimin Yan <aimin.at.work at gmail.com>
Sent: Wednesday, April 5, 2017 9:39:59 AM
To: Shepherd, Lori
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Check error on malbec2

Yes, it is.

Aimin

On Wed, Apr 5, 2017 at 7:20 AM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

Are these permanent system files or files that are created during examples/vignettes?


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Aimin Yan <aimin.at.work at gmail.com<mailto:aimin.at.work at gmail.com>>
Sent: Tuesday, April 4, 2017 3:41:02 PM
To: Shepherd, Lori
Cc: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Check error on malbec2

Thank you, I changed to use tempdir(), and it works now.
One more question is how to locate those outputs in temporary directory since I want users to use those outputs.

Aimin

On Tue, Apr 4, 2017 at 2:00 PM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

Write and access your output to a temporary directory instead using tempdir().



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Aimin Yan <aimin.at.work at gmail.com<mailto:aimin.at.work at gmail.com>>
Sent: Tuesday, April 4, 2017 1:45:28 PM
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Subject: [Bioc-devel] Check error on malbec2

In the package I am trying ti submit to bioconductor, I got the following
error for check.

Warning in dir.create(output.file.dir) :
  cannot create dir '/home/pkgbuild/OutputEnmap', reason 'Permission denied'
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/pkgbuild/OutputEnmap/enrichmap_GO.xls': No such
file or directory
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: enrichmentmap -> write.table -> file

It seems I do not have permission to create a directory.
Does anyone know how to fix this check error?


Thanks,
Aimin

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.


This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]