Setting authorization key matR

[Djeppschmidt]

I used matR a couple years ago with no problem. I'm now trying to use it again to access another MG-Rast dataset, and I'm getting a peculiar error when I'm trying to set up my authorization key. I've noticed that the package has changed a lot since I last used it, and I'm wondering if this feature has changed. Here's the code with the error:

library(matR)
msession$setAuth("~/Downloads/MGRastAuth.txt")
Error: object 'msession' not found

I've tried reinstalling matR a couple times in case it was a compilation error. I'm running OSX 10.13.4, and R 3.4.4.

Any insight is greatly appreciated!

-Dietrich

[wltrimbl]

The syntax for specifying the authentication token has changed.

auth.MGRAST(file="~/Downloads/MGRastAuth.txt")

will do what you want.

[Djeppschmidt]

Thanks; now I get this error:

library(matR) auth.MGRAST()

Error in auth.MGRAST() : could not find function "auth.MGRAST" *Dietrich Epp Schmidt, PhD Candidate* *Graduate Research Assistant* *UMD Environmental Science and Technology* *www.humaneecology.com <http://www.humaneecology.com>* *“Whether we and our politicians know it or not, Nature is party to all our deals and decisions, and she has more votes, a longer memory, and a sterner sense of justice than we do.” * Wendell Berry <http://www.goodreads.com/author/show/8567.Wendell_Berry>

…

On Fri, Oct 12, 2018 at 10:34 AM Will Trimble ***@***.***> wrote: The syntax for specifying the authentication token has changed. auth.MGRAST(file="~/Downloads/MGRastAuth.txt") will do what you want. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#82 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASZbjCO67AyUVonUZ2B50TXdLC4UR_ktks5ukKh_gaJpZM4XZkBk> .

[wltrimbl]

You have a version of matR that is too old. Reinstall 0.9.1 from CRAN or use the instructions at
https://github.com/MG-RAST/matR

sessionInfo(matR)
other attached packages:
[1] matR_0.9

[Djeppschmidt]

I've tried both approaches, still same problem.

library(matR)

Loading required package: BIOM.utils BIOM.utils (0.9 dbcb27) matR: metagenomics analysis tools for R (0.9.1)

auth.MGRAST()

Error in auth.MGRAST() : could not find function "auth.MGRAST" Installation from GitHub: matR * 0.9.1 2018-10-12 Github (MG-RAST/matR@0c0b556) MGRASTer * 0.9 2014-08-02 CRAN (R 3.4.0) Installation from CRAN: matR * 0.9.1 2018-05-04 CRAN (R 3.4.4) MGRASTer * 0.9 2014-08-02 CRAN (R 3.4.0) I have also run an update through bioconductor to make sure the dependencies are up to date. Thanks, *Dietrich Epp Schmidt, PhD Candidate* *Graduate Research Assistant* *UMD Environmental Science and Technology* *www.humaneecology.com <http://www.humaneecology.com>* *“Whether we and our politicians know it or not, Nature is party to all our deals and decisions, and she has more votes, a longer memory, and a sterner sense of justice than we do.” * Wendell Berry <http://www.goodreads.com/author/show/8567.Wendell_Berry>

…

On Fri, Oct 12, 2018 at 11:18 AM Will Trimble ***@***.***> wrote: You have a version of matR that is too old. Reinstall 0.9.1 from CRAN or use the instructions at https://github.com/MG-RAST/matR sessionInfo(matR) other attached packages: [1] matR_0.9 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#82 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASZbjLuEQstieFa4jCIbn5NZWYYmPJz4ks5ukLLVgaJpZM4XZkBk> .

[Djeppschmidt]

Do you have the auth.MGRAST() function code in github? I didn't see it but I could try writing it into the environment manually for a quick fix. Thanks, *Dietrich Epp Schmidt, PhD Candidate* *Graduate Research Assistant* *UMD Environmental Science and Technology* *www.humaneecology.com <http://www.humaneecology.com>* *“Whether we and our politicians know it or not, Nature is party to all our deals and decisions, and she has more votes, a longer memory, and a sterner sense of justice than we do.” * Wendell Berry <http://www.goodreads.com/author/show/8567.Wendell_Berry> On Fri, Oct 12, 2018 at 11:44 AM Dietrich Epp Schmidt < djeppschmidt@gmail.com> wrote:

…

I've tried both approaches, still same problem. > library(matR) Loading required package: BIOM.utils BIOM.utils (0.9 dbcb27) matR: metagenomics analysis tools for R (0.9.1) > auth.MGRAST() Error in auth.MGRAST() : could not find function "auth.MGRAST" Installation from GitHub: matR * 0.9.1 2018-10-12 Github ***@***.***) MGRASTer * 0.9 2014-08-02 CRAN (R 3.4.0) Installation from CRAN: matR * 0.9.1 2018-05-04 CRAN (R 3.4.4) MGRASTer * 0.9 2014-08-02 CRAN (R 3.4.0) I have also run an update through bioconductor to make sure the dependencies are up to date. Thanks, *Dietrich Epp Schmidt, PhD Candidate* *Graduate Research Assistant* *UMD Environmental Science and Technology* *www.humaneecology.com <http://www.humaneecology.com>* *“Whether we and our politicians know it or not, Nature is party to all our deals and decisions, and she has more votes, a longer memory, and a sterner sense of justice than we do.” * Wendell Berry <http://www.goodreads.com/author/show/8567.Wendell_Berry> On Fri, Oct 12, 2018 at 11:18 AM Will Trimble ***@***.***> wrote: > You have a version of matR that is too old. Reinstall 0.9.1 from CRAN or > use the instructions at > https://github.com/MG-RAST/matR > > sessionInfo(matR) > other attached packages: > [1] matR_0.9 > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#82 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ASZbjLuEQstieFa4jCIbn5NZWYYmPJz4ks5ukLLVgaJpZM4XZkBk> > . >

[wltrimbl]

The source is here:
https://github.com/MG-RAST/MGRASTer/blob/master/R/source.R

So the auth function requires MGRASTer 0.9.1, which isn't in CRAN at the moment.

Sorry to have inconvenienced you with unclearly-versioned dependencies.

[Djeppschmidt]

Ok progress! Version 0.9 of call.MGRAST was not appending the key to the URL, so I had to manually load all the updated functions so they were consistent. It seems to at least partially be working; it is granted initial access and downloads 33.1 MB of data, but somehow also isn't granted access to the data and doesn't write the data to the specified file. Here's the error: ### call.MGRAST("annot", "seq", id=4679418.3, eval=10, type="ont", source="Sub", destfile = "~/Desktop/006.biom") trying URL ' http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4679418.3?evalue=10&type=ontology&source=Subsystems&auth=gbdwiyCZqACamvn8fG59aTs3Z ' downloaded 33.1 MB Error retrieving URL: simpleWarning in download.file(call.url, destfile = destfile, quiet = FALSE): URL ' http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4679418.3?evalue=10&type=ontology&source=Subsystems&auth=gbdwiyCZqACamvn8fG59aTs3Z': status was 'Failure when receiving data from the peer' URL requested: http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4679418.3?evalue=10&type=ontology&source=Subsystems&auth=gbdwiyCZqACamvn8fG59aTs3Z HTTP Response: 2: {"ERROR":"insufficient permissions to view this data"} 1: download.file call.url destfile FALSE [1] "~/Desktop/006.biom" Warning message: MGRASTer: saving to file unimplemented with 'parse' and 'verify'; ignoring these ### I know the key is correct because I can access the data via a web interface using the same URL that matR uses to query e.g. http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4679418.3?evalue=10&type=ontology&source=Subsystems&auth=gbdwiyCZqACamvn8fG59aTs3Z so it seems to me that there is something in reading and writing the data that isn't working for me now. Any thoughts? Thanks, *Dietrich Epp Schmidt, PhD Candidate* *Graduate Research Assistant* *UMD Environmental Science and Technology* *www.humaneecology.com <http://www.humaneecology.com>* *“Whether we and our politicians know it or not, Nature is party to all our deals and decisions, and she has more votes, a longer memory, and a sterner sense of justice than we do.” * Wendell Berry <http://www.goodreads.com/author/show/8567.Wendell_Berry>

…

On Fri, Oct 12, 2018 at 12:03 PM Will Trimble ***@***.***> wrote: The source is here: https://github.com/MG-RAST/MGRASTer/blob/master/R/source.R So the auth function requires MGRASTer 0.9.1, which isn't in CRAN at the moment. Sorry to have inconvenienced you with unclearly-versioned dependencies. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#82 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASZbjHKXXQFRkXtPy8v5TYpuQjSupz1iks5ukL1ugaJpZM4XZkBk> .

[Djeppschmidt]

Never mind... I can download just fine with your code. It just wasn't able to write over old versions of the file 006.biom. Once I deleted, it worked just fine. Thanks, *Dietrich Epp Schmidt, PhD Candidate* *Graduate Research Assistant* *UMD Environmental Science and Technology* *www.humaneecology.com <http://www.humaneecology.com>* *“Whether we and our politicians know it or not, Nature is party to all our deals and decisions, and she has more votes, a longer memory, and a sterner sense of justice than we do.” * Wendell Berry <http://www.goodreads.com/author/show/8567.Wendell_Berry> On Fri, Oct 12, 2018 at 2:52 PM Dietrich Epp Schmidt <djeppschmidt@gmail.com> wrote:

…

Ok progress! Version 0.9 of call.MGRAST was not appending the key to the URL, so I had to manually load all the updated functions so they were consistent. It seems to at least partially be working; it is granted initial access and downloads 33.1 MB of data, but somehow also isn't granted access to the data and doesn't write the data to the specified file. Here's the error: ### call.MGRAST("annot", "seq", id=4679418.3, eval=10, type="ont", source="Sub", destfile = "~/Desktop/006.biom") trying URL ' http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4679418.3?evalue=10&type=ontology&source=Subsystems&auth=gbdwiyCZqACamvn8fG59aTs3Z ' downloaded 33.1 MB Error retrieving URL: simpleWarning in download.file(call.url, destfile = destfile, quiet = FALSE): URL ' http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4679418.3?evalue=10&type=ontology&source=Subsystems&auth=gbdwiyCZqACamvn8fG59aTs3Z': status was 'Failure when receiving data from the peer' URL requested: http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4679418.3?evalue=10&type=ontology&source=Subsystems&auth=gbdwiyCZqACamvn8fG59aTs3Z HTTP Response: 2: {"ERROR":"insufficient permissions to view this data"} 1: download.file call.url destfile FALSE [1] "~/Desktop/006.biom" Warning message: MGRASTer: saving to file unimplemented with 'parse' and 'verify'; ignoring these ### I know the key is correct because I can access the data via a web interface using the same URL that matR uses to query e.g. http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4679418.3?evalue=10&type=ontology&source=Subsystems&auth=gbdwiyCZqACamvn8fG59aTs3Z so it seems to me that there is something in reading and writing the data that isn't working for me now. Any thoughts? Thanks, *Dietrich Epp Schmidt, PhD Candidate* *Graduate Research Assistant* *UMD Environmental Science and Technology* *www.humaneecology.com <http://www.humaneecology.com>* *“Whether we and our politicians know it or not, Nature is party to all our deals and decisions, and she has more votes, a longer memory, and a sterner sense of justice than we do.” * Wendell Berry <http://www.goodreads.com/author/show/8567.Wendell_Berry> On Fri, Oct 12, 2018 at 12:03 PM Will Trimble ***@***.***> wrote: > The source is here: > https://github.com/MG-RAST/MGRASTer/blob/master/R/source.R > > So the auth function requires MGRASTer 0.9.1, which isn't in CRAN at the > moment. > > Sorry to have inconvenienced you with unclearly-versioned dependencies. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#82 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ASZbjHKXXQFRkXtPy8v5TYpuQjSupz1iks5ukL1ugaJpZM4XZkBk> > . >