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DOI-USGS / streamMetabolizer

streamMetabolizer uses inverse modeling to estimate aquatic metabolism (photosynthesis and respiration) from time series data on dissolved oxygen, water temperature, depth, and light.
http://usgs-r.github.io/streamMetabolizer/
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package is not available (for R version 3.3.2) #416

Closed mlbrooks closed 1 year ago

mlbrooks commented 2 years ago

Brief problem description

Believe this is an entirely new problem on the forum. When I try to run the package using the following

install.packages("streamMetabolizer", dependencies=TRUE, repos=c("https://owi.usgs.gov/R","https://cran.rstudio.com"))

What you saw on your computer

I receive the message:

Warning in install.packages : package ‘streamMetabolizer’ is not available (for R version 3.3.2) Warning in install.packages : unable to access index for repository https://cran.rstudio.com/bin/windows/contrib/3.3: cannot open URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/PACKAGES'

I received this same message using the most recent 4.2.1 version of R.

A colleague also tried to install the package and received the same message. Both of us were able to download Lake Metabolizer.

Any suggestions are most appreciated.

mlbrooks

mlbrooks commented 1 year ago

Bob Hall was good enough to point out that I likely needed to install the "remote' package, which I did from the cran mirror.

Following that step, I followed his advice below: First install the unitted dependency:

remotes::install_github('appling/unitted')

You can then install the most cutting edge version of streamMetabolizer with this command:

remotes::install_github("USGS-R/streamMetabolizer")

Thanks, Bob.

sasindug commented 1 year ago

I also have the same problem. I installed "remote' package using remotes::install_github('appling/unitted') and the tried to install streamMetabolizer using the following code. remotes::install_github("USGS-R/streamMetabolizer")

I keep getting following error ERROR: dependency 'LakeMetabolizer' is not available for package 'streamMetabolizer'

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 2: In i.p(...) : installation of package ‘C:/Users/sasin/AppData/Local/Temp/RtmpQVMMtp/file2804513054a0/streamMetabolizer_0.12.0.tar.gz’ had non-zero exit status

Please let me know what to do Thanks

mlbrooks commented 1 year ago

Greetings,

Last week, I continued my efforts to load streamMetabolizer on a second laptop. Since the instructions on USGS-R/streamMetabolizer produced the error message described below, I spent some time searching for a means to download LakeMetabolizer. As a result, I found that it has been removed from the cran mirror as of 10/3/2022.

Before that date, I downloaded the LakeMetabolizer package on the one laptop on which I can run streamMetabolizer. Thus, my conclusion is that it would be helpful if the LakeMetabolizer package were made available again despite it's apparent flaws. Seems essential.

Best regards, Marj Dr. Marjorie L Brooks Biogeochemistry and Aquatic Ecology 1125 Lincoln Dr, MC 6501 Carbondale, IL 62901

Office: Life Science II Building, Room 317 Laboratory: Life Science II Building, Room 311 Cell: 307-399-0576 Tel: 618-453-7639

From: sasindug @.> Sent: Wednesday, October 26, 2022 9:28 AM To: USGS-R/streamMetabolizer @.> Cc: mlbrooks @.>; Author @.> Subject: Re: [USGS-R/streamMetabolizer] package is not available (for R version 3.3.2) (Issue #416)

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I also have the same problem. I installed "remote' package using remotes::install_github('appling/unitted') and the tried to install streamMetabolizer using the following code. remotes::install_github("USGS-R/streamMetabolizer")

I keep getting following error ERROR: dependency 'LakeMetabolizer' is not available for package 'streamMetabolizer'

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packageshttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fdoc%2Fmanuals%2Fr-patched%2FR-admin.html%23Installing-packages&data=05%7C01%7Cmlbrooks%40siu.edu%7Cf93d7e28468441d6834408dab766b09b%7Cd57a98e7744d43f9bc9108de1ff3710d%7C0%7C0%7C638023948922686624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nsvGBk%2F%2Fz%2BfA2bKGnU1ZoYCs8FhysJzR%2FS5i1KZgnPo%3D&reserved=0 2: In i.p(...) : installation of package 'C:/Users/sasin/AppData/Local/Temp/RtmpQVMMtp/file2804513054a0/streamMetabolizer_0.12.0.tar.gz' had non-zero exit status

Please let me know what to do Thanks

- Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FUSGS-R%2FstreamMetabolizer%2Fissues%2F416%23issuecomment-1292224363&data=05%7C01%7Cmlbrooks%40siu.edu%7Cf93d7e28468441d6834408dab766b09b%7Cd57a98e7744d43f9bc9108de1ff3710d%7C0%7C0%7C638023948922686624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Nj%2Fk%2FiltLnQu01eEI2gSyvMT255JznDad4YPAThQ71Y%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FA3M5LUOEHJ24KLSGOT5772LWFFEYPANCNFSM6AAAAAAQ3XRSA4&data=05%7C01%7Cmlbrooks%40siu.edu%7Cf93d7e28468441d6834408dab766b09b%7Cd57a98e7744d43f9bc9108de1ff3710d%7C0%7C0%7C638023948922686624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jkZAPB0Ujj9IQwN%2F%2BnZ0v5BfQwXclx%2FlYmq5H15rvFc%3D&reserved=0. You are receiving this because you authored the thread.Message ID: @.**@.>>

sasindug commented 1 year ago

Thanks for letting me know.

nmarzolf91 commented 1 year ago

LakeMetabolizer is available via devtools::install_github('GLEON/LakeMetabolizer')

and should be run in addition to: 

remotes::install_github('appling/unitted')
remotes::install_github("USGS-R/streamMetabolizer")
sasindug commented 1 year ago

LakeMetabolizer is available via devtools::install_github('GLEON/LakeMetabolizer')

and should be run in addition to:

remotes::install_github('appling/unitted')
remotes::install_github("USGS-R/streamMetabolizer")

Thank you so much it worked

jordansread commented 1 year ago

Oh wow, I didn't realize LakeMetabolizer was removed from CRAN. I created an issue. https://github.com/GLEON/LakeMetabolizer/issues/147

In the meantime, the solution from @sasindug should work. I'd slightly revise that to 

remotes::install_github('GLEON/LakeMetabolizer')
remotes::install_github('appling/unitted')
remotes::install_github('USGS-R/streamMetabolizer')

So you can do it all with remotes

mlbrooks commented 1 year ago

Thank you.

Dr. Marjorie L Brooks, Associate Professor Biogeochemistry and Aquatic Ecology 1125 Lincoln Dr, MC 6501 Carbondale, IL 62901

Office: Life Science II Building, Room 317 Laboratory: Life Science II Building, Room 311 Cell: 307-399-0576 Tel: 618-453-7639

From: Jordan S Read @.> Sent: Wednesday, October 26, 2022 11:08 AM To: USGS-R/streamMetabolizer @.> Cc: mlbrooks @.>; Author @.> Subject: Re: [USGS-R/streamMetabolizer] package is not available (for R version 3.3.2) (Issue #416)

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Oh wow, I didn't realize LakeMetabolizer was removed from CRAN. I created an issue. GLEON/LakeMetabolizer#147https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FGLEON%2FLakeMetabolizer%2Fissues%2F147&data=05%7C01%7Cmlbrooks%40siu.edu%7C532ba5ff27a4464117f808dab774b495%7Cd57a98e7744d43f9bc9108de1ff3710d%7C0%7C0%7C638024009316734752%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TtusfZr4NLezVJcyLXdcbJxFMkimfVWnKKmE6hvORiI%3D&reserved=0

In the meantime, the solution from @sasindughttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsasindug&data=05%7C01%7Cmlbrooks%40siu.edu%7C532ba5ff27a4464117f808dab774b495%7Cd57a98e7744d43f9bc9108de1ff3710d%7C0%7C0%7C638024009316734752%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lhqRHrCqe137iZhj5c%2F4%2FYPIWM32otSE2b7ObKFc8io%3D&reserved=0 should work. I'd slightly revise that to

remotes::install_github('GLEON/LakeMetabolizer')

remotes::install_github('appling/unitted')

remotes::install_github('USGS-R/streamMetabolizer')

So you can do it all with remotes

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jzwart commented 1 year ago

LakeMetabolizer is back on CRAN https://cran.r-project.org/web/packages/LakeMetabolizer/index.html

mlbrooks commented 1 year ago

Good to hear!

Dr. Marjorie L Brooks Biogeochemistry and Aquatic Ecology 1125 Lincoln Dr, MC 6501 Carbondale, IL 62901

Office: Life Science II Building, Room 317 Laboratory: Life Science II Building, Room 311 Cell: 307-399-0576 Tel: 618-453-7639

From: Jake Zwart @.> Sent: Wednesday, November 16, 2022 6:11 AM To: USGS-R/streamMetabolizer @.> Cc: mlbrooks @.>; Author @.> Subject: Re: [USGS-R/streamMetabolizer] package is not available (for R version 3.3.2) (Issue #416)

[EXTERNAL EMAIL ALERT]: Verify sender before opening links or attachments.

LakeMetabolizer is back on CRAN https://cran.r-project.org/web/packages/LakeMetabolizer/index.htmlhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2FLakeMetabolizer%2Findex.html&data=05%7C01%7Cmlbrooks%40siu.edu%7C5dc6018e60bc49f5a19208dac7cb9e36%7Cd57a98e7744d43f9bc9108de1ff3710d%7C0%7C0%7C638041974628160681%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=DuVSfeA6fDn%2Fwuxq5nejP5ERW7LA9CKYsX7QyaqaO2M%3D&reserved=0

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jordansread commented 1 year ago

Thanks @jzwart !

aappling-usgs commented 1 year ago

Yay for community debugging! Thanks, everyone.

mlbrooks commented 1 year ago

Thanks, Alison.

Dr. Marjorie L Brooks Biogeochemistry and Aquatic Ecology 1125 Lincoln Dr, MC 6501 Carbondale, IL 62901

Office: Life Science II Building, Room 317 Laboratory: Life Science II Building, Room 311 Cell: 307-399-0576 Tel: 618-453-7639

From: Alison Appling @.> Sent: Sunday, July 2, 2023 3:17 PM To: USGS-R/streamMetabolizer @.> Cc: mlbrooks @.>; Author @.> Subject: Re: [USGS-R/streamMetabolizer] package is not available (for R version 3.3.2) (Issue #416)

[EXTERNAL EMAIL ALERT]: Verify sender before opening links or attachments.

Yay for community debugging! Thanks, everyone.

- Reply to this email directly, view it on GitHubhttps://github.com/USGS-R/streamMetabolizer/issues/416#issuecomment-1616806747, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A3M5LUO25NDDB3SM4XE4FLLXOHJMJANCNFSM6AAAAAAQ3XRSA4. You are receiving this because you authored the thread.Message ID: @.**@.>>