Hi, I've just noticed that the function getHPa package has recently changed in the devel branch of the package, as follows: # Old function (in the current release branch) getHpa(id, hpadata = "NormalTissue") #New function (in the current devel branch) getHpa(id, hpadata = "hpaNormalTissue") A function of my package (MetaboSignal) uses this function from the hpar package, so today I had to update my code according to this modification of the getHpa function. I just wanted to confirm that the next release version of hpar is going to keep this new version of the getHpa function. Otherwise, I guess this might cause trouble with the upcoming release version of MetaboSignal. Would it be worthy to write my own getHpa function to avoid this kind of problems ? Thanks very much in advance, Andrea
[Bioc-devel] Change in the function getHPa( ) of the hpar package
5 messages · Rodriguez Martinez, Andrea, Shepherd, Lori, Laurent Gatto
Hi, Please do not write your own function. We encourage utilizing existing functionality. As long as you are using the development version of hpar, that will be the version that is used in the upcoming release. Over the next few weeks I would recommend checking that you are using/testing with the most recent development version of that package. 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> on behalf of Rodriguez Martinez, Andrea <andrea.rodriguez-martinez13 at imperial.ac.uk>
Sent: Thursday, September 29, 2016 10:24:31 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Change in the function getHPa( ) of the hpar package
Sent: Thursday, September 29, 2016 10:24:31 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Change in the function getHPa( ) of the hpar package
Hi,
I've just noticed that the function getHPa package has recently changed in the devel branch of the package, as follows:
# Old function (in the current release branch)
getHpa(id, hpadata = "NormalTissue")
#New function (in the current devel branch)
getHpa(id, hpadata = "hpaNormalTissue")
A function of my package (MetaboSignal) uses this function from the hpar package, so today I had to update my code according to this modification of the getHpa function. I just wanted to confirm that the next release version of hpar is going to keep this new version of the getHpa function. Otherwise, I guess this might cause trouble with the upcoming release version of MetaboSignal. Would it be worthy to write my own getHpa function to avoid this kind of problems ?
Thanks very much in advance,
Andrea
[[alternative HTML version deleted]]
_______________________________________________
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.
Ok! Thanks very much! Andrea
From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: 29 September 2016 15:53:15
To: Rodriguez Martinez, Andrea; bioc-devel at r-project.org
Subject: Re: Change in the function getHPa( ) of the hpar package
Sent: 29 September 2016 15:53:15
To: Rodriguez Martinez, Andrea; bioc-devel at r-project.org
Subject: Re: Change in the function getHPa( ) of the hpar package
Hi,
Please do not write your own function. We encourage utilizing existing functionality.
As long as you are using the development version of hpar, that will be the version that is used in the upcoming release. Over the next few weeks I would recommend checking that you are using/testing with the most recent development version of that package.
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> on behalf of Rodriguez Martinez, Andrea <andrea.rodriguez-martinez13 at imperial.ac.uk>
Sent: Thursday, September 29, 2016 10:24:31 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Change in the function getHPa( ) of the hpar package
Hi,
I've just noticed that the function getHPa package has recently changed in the devel branch of the package, as follows:
# Old function (in the current release branch)
getHpa(id, hpadata = "NormalTissue")
#New function (in the current devel branch)
getHpa(id, hpadata = "hpaNormalTissue")
A function of my package (MetaboSignal) uses this function from the hpar package, so today I had to update my code according to this modification of the getHpa function. I just wanted to confirm that the next release version of hpar is going to keep this new version of the getHpa function. Otherwise, I guess this might cause trouble with the upcoming release version of MetaboSignal. Would it be worthy to write my own getHpa function to avoid this kind of problems ?
Thanks very much in advance,
Andrea
[[alternative HTML version deleted]]
_______________________________________________
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.
Dear Andrea, There won't be any additional changes to the hpar package before the upcoming release. A new version of the HPA data is expected by the end of the year, but that should not lead to any changes to the interface. Best wishes, Laurent
On 29 September 2016 15:24, Rodriguez Martinez, Andrea wrote:
Hi, I've just noticed that the function getHPa package has recently changed in the devel branch of the package, as follows: # Old function (in the current release branch) getHpa(id, hpadata = "NormalTissue") #New function (in the current devel branch) getHpa(id, hpadata = "hpaNormalTissue") A function of my package (MetaboSignal) uses this function from the hpar package, so today I had to update my code according to this modification of the getHpa function. I just wanted to confirm that the next release version of hpar is going to keep this new version of the getHpa function. Otherwise, I guess this might cause trouble with the upcoming release version of MetaboSignal. Would it be worthy to write my own getHpa function to avoid this kind of problems ? Thanks very much in advance, Andrea [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/
Thanks very much! It's nice to see that you've added gene symbols to the new hpaNormalTissue dataset. Best wishes, Andrea
From: Laurent Gatto <lg390 at cam.ac.uk>
Sent: 29 September 2016 16:01:57
To: Rodriguez Martinez, Andrea
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Change in the function getHPa( ) of the hpar package
Sent: 29 September 2016 16:01:57
To: Rodriguez Martinez, Andrea
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Change in the function getHPa( ) of the hpar package
Dear Andrea, There won't be any additional changes to the hpar package before the upcoming release. A new version of the HPA data is expected by the end of the year, but that should not lead to any changes to the interface. Best wishes, Laurent On 29 September 2016 15:24, Rodriguez Martinez, Andrea wrote: > Hi, > > > I've just noticed that the function getHPa package has recently > changed in the devel branch of the package, as follows: > > > # Old function (in the current release branch) > > getHpa(id, hpadata = "NormalTissue") > > > #New function (in the current devel branch) > > getHpa(id, hpadata = "hpaNormalTissue") > > > A function of my package (MetaboSignal) uses this function from the > hpar package, so today I had to update my code according to this > modification of the getHpa function. I just wanted to confirm that the > next release version of hpar is going to keep this new version of the > getHpa function. Otherwise, I guess this might cause trouble with the > upcoming release version of MetaboSignal. Would it be worthy to write > my own getHpa function to avoid this kind of problems ? > > > Thanks very much in advance, > > > Andrea > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/