migrateR will not install on R 3.5.2

[dhondorp]

Hello,

I'm trying to install migrateR, but the installation always fails and R reports that:

'migrateR_1.0.7.tar.gz’ is not available (for R version 3.5.2)'

I've tried both the manual install and installing directly from gitHub-- neither works.

Help!

-Darryl

[dbspitz]

Hi Darryl,

Thanks for the email. What are you working on?

Hmmm: the first hurdle. Installation errors can be a bit tricky as they're often system specific. Devtools is usually the easier path to troubleshoot here. Can you try running the following and then send me the output?

sessionInfo() packageDescription("devtools")

Might take a little back-and-forth to pin this down. My guess is an issue with updates within one of the package dependencies, but R can be full of surprises!

Best,

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 10:53 AM dhondorp notifications@github.com wrote:

Hello,

I'm trying to install migrateR, but the installation always fails and R reports that:

'migrateR_1.0.7.tar.gz’ is not available (for R version 3.5.2)'

I've tried both the manual install and installing directly from gitHub-- neither works.

Help!

-Darryl

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/dbspitz/migrateR/issues/4, or mute the thread https://github.com/notifications/unsubscribe-auth/ACTZKURXITVSRNA4B56LFB3PURQJTANCNFSM4HL4VNRQ .

[dhondorp]

dHi Derek,

Thanks for the quick response. I'm analyzing the behavior of acoustic-tagged lake sturgeon in lakes huron and erie (and their connecting waters). Just curious about how NSD models might fit the telemetry data.

Attached is the output from those two function calls. Let me know if something jumps out at you. sessionInfo.docx

Hi Darryl, Thanks for the email. What are you working on? Hmmm: the first hurdle. Installation errors can be a bit tricky as they're often system specific. Devtools is usually the easier path to troubleshoot here. Can you try running the following and then send me the output? sessionInfo() packageDescription("devtools") Might take a little back-and-forth to pin this down. My guess is an issue with updates within one of the package dependencies, but R can be full of surprises! Best, Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology … On Thu, May 9, 2019 at 10:53 AM dhondorp @.***> wrote: Hello, I'm trying to install migrateR, but the installation always fails and R reports that: 'migrateR_1.0.7.tar.gz’ is not available (for R version 3.5.2)' I've tried both the manual install and installing directly from gitHub-- neither works. Help! -Darryl — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or mute the thread https://github.com/notifications/unsubscribe-auth/ACTZKURXITVSRNA4B56LFB3PURQJTANCNFSM4HL4VNRQ .

[dhondorp]

Hi Derek,

Thanks for the quick response. I'm analyzing the behavior of acoustic-tagged lake sturgeon in lakes huron and erie (and their connecting waters). Just curious about how NSD models might fit the telemetry data.

Attached is the output from those two function calls. Let me know if something jumps out at you.

Darryl W. Hondorp
Research Fish Biologist
USGS--Great Lakes Science Center
1451 Green Road
Ann Arbor, MI  48105
Office:  (734) 214-7241
Cell:  (734) 545-6258
Fax:  (734) 994-8780
Email: dhondorp@usgs.gov
USGS Professional Page: https://profile.usgs.gov/dhondorp

On Thu, May 9, 2019 at 2:45 PM Derek Spitz notifications@github.com wrote:

Hi Darryl,

Thanks for the email. What are you working on?

Hmmm: the first hurdle. Installation errors can be a bit tricky as they're often system specific. Devtools is usually the easier path to troubleshoot here. Can you try running the following and then send me the output?

sessionInfo() packageDescription("devtools")

Might take a little back-and-forth to pin this down. My guess is an issue with updates within one of the package dependencies, but R can be full of surprises!

Best,

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab < http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 10:53 AM dhondorp notifications@github.com wrote:

Hello,

I'm trying to install migrateR, but the installation always fails and R reports that:

'migrateR_1.0.7.tar.gz’ is not available (for R version 3.5.2)'

I've tried both the manual install and installing directly from gitHub-- neither works.

Help!

-Darryl

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/dbspitz/migrateR/issues/4, or mute the thread < https://github.com/notifications/unsubscribe-auth/ACTZKURXITVSRNA4B56LFB3PURQJTANCNFSM4HL4VNRQ

.

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[dbspitz]

Has Spring reached Ann Arbor? Really curious to hear more about application of NSD models to aquatic species. Once you get the packages working you'll have to let me know what you think. I've been in touch with a couple researchers in FL who have run into issues with increasing coastline complexity; we'd discussed some possible solutions but ultimately issue appeared to be unusual/infrequent.

Appreciate the code, but unfortunately nothing jumps out at me as obvious so far. Is there any other information you can give me on the errors you're seeing--e.g., any warnings, etc. before the 'not available' message or is that the only output you're seeing?

If there's any more output leading up to the instillation failure, sending me that code could be helpful. Otherwise, the only other obvious suggestion for the moment would be the good ol' turn it off and on again 'trick': close R, open with a fresh workspace, reinstall 'devtools', attempt the instillation and see if you trigger the same error. A more aggressive form of this could include reopening R to a fresh workspace and running through 'update.packages()'. If the issue is indeed with package versioning, these approaches have a good chance of solving the problem.

I'm in meetings most of the rest of the day, but can take another look at the code you sent tomorrow a.m. In the meantime, let me know if you run into any other clues or hunches about the hang up. Unfortunately these sorts of delays are sometimes the price of doing business in R, but we'll get this figured out.

Good luck and keep me posted!

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 12:00 PM dhondorp notifications@github.com wrote:

Hi Derek,

Thanks for the quick response. I'm analyzing the behavior of acoustic-tagged lake sturgeon in lakes huron and erie (and their connecting waters). Just curious about how NSD models might fit the telemetry data.

Attached is the output from those two function calls. Let me know if something jumps out at you.

Darryl W. Hondorp
Research Fish Biologist
USGS--Great Lakes Science Center
1451 Green Road
Ann Arbor, MI 48105
Office: (734) 214-7241
Cell: (734) 545-6258
Fax: (734) 994-8780
Email: dhondorp@usgs.gov
USGS Professional Page: https://profile.usgs.gov/dhondorp

On Thu, May 9, 2019 at 2:45 PM Derek Spitz notifications@github.com wrote:

Hi Darryl,

Thanks for the email. What are you working on?

Hmmm: the first hurdle. Installation errors can be a bit tricky as they're often system specific. Devtools is usually the easier path to troubleshoot here. Can you try running the following and then send me the output?

sessionInfo() packageDescription("devtools")

Might take a little back-and-forth to pin this down. My guess is an issue with updates within one of the package dependencies, but R can be full of surprises!

Best,

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab <

http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 10:53 AM dhondorp notifications@github.com wrote:

Hello,

I'm trying to install migrateR, but the installation always fails and R reports that:

'migrateR_1.0.7.tar.gz’ is not available (for R version 3.5.2)'

I've tried both the manual install and installing directly from gitHub-- neither works.

Help!

-Darryl

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/dbspitz/migrateR/issues/4, or mute the thread <

https://github.com/notifications/unsubscribe-auth/ACTZKURXITVSRNA4B56LFB3PURQJTANCNFSM4HL4VNRQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dbspitz/migrateR/issues/4#issuecomment-491021054, or mute the thread < https://github.com/notifications/unsubscribe-auth/AIZHVKYMU3UO27LCHKKMYXDPURWJ3ANCNFSM4HL4VNRQ

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[dhondorp]

Hey Derek,

Yes, we're into spring here. Has been really wet, though.

Thanks for looking at the output. I'll try a set another set of installations after closing and restarting R and let you know what I find.

Darryl W. Hondorp
Research Fish Biologist
USGS--Great Lakes Science Center
1451 Green Road
Ann Arbor, MI  48105
Office:  (734) 214-7241
Cell:  (734) 545-6258
Fax:  (734) 994-8780
Email: dhondorp@usgs.gov
USGS Professional Page: https://profile.usgs.gov/dhondorp

On Thu, May 9, 2019 at 3:41 PM Derek Spitz notifications@github.com wrote:

Has Spring reached Ann Arbor? Really curious to hear more about application of NSD models to aquatic species. Once you get the packages working you'll have to let me know what you think. I've been in touch with a couple researchers in FL who have run into issues with increasing coastline complexity; we'd discussed some possible solutions but ultimately issue appeared to be unusual/infrequent.

Appreciate the code, but unfortunately nothing jumps out at me as obvious so far. Is there any other information you can give me on the errors you're seeing--e.g., any warnings, etc. before the 'not available' message or is that the only output you're seeing?

If there's any more output leading up to the instillation failure, sending me that code could be helpful. Otherwise, the only other obvious suggestion for the moment would be the good ol' turn it off and on again 'trick': close R, open with a fresh workspace, reinstall 'devtools', attempt the instillation and see if you trigger the same error. A more aggressive form of this could include reopening R to a fresh workspace and running through 'update.packages()'. If the issue is indeed with package versioning, these approaches have a good chance of solving the problem.

I'm in meetings most of the rest of the day, but can take another look at the code you sent tomorrow a.m. In the meantime, let me know if you run into any other clues or hunches about the hang up. Unfortunately these sorts of delays are sometimes the price of doing business in R, but we'll get this figured out.

Good luck and keep me posted!

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab < http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 12:00 PM dhondorp notifications@github.com wrote:

Hi Derek,

Thanks for the quick response. I'm analyzing the behavior of acoustic-tagged lake sturgeon in lakes huron and erie (and their connecting waters). Just curious about how NSD models might fit the telemetry data.

Attached is the output from those two function calls. Let me know if something jumps out at you.

Darryl W. Hondorp
Research Fish Biologist
USGS--Great Lakes Science Center
1451 Green Road
Ann Arbor, MI 48105
Office: (734) 214-7241
Cell: (734) 545-6258
Fax: (734) 994-8780
Email: dhondorp@usgs.gov
USGS Professional Page: https://profile.usgs.gov/dhondorp

On Thu, May 9, 2019 at 2:45 PM Derek Spitz notifications@github.com wrote:

Hi Darryl,

Thanks for the email. What are you working on?

Hmmm: the first hurdle. Installation errors can be a bit tricky as they're often system specific. Devtools is usually the easier path to troubleshoot here. Can you try running the following and then send me the output?

sessionInfo() packageDescription("devtools")

Might take a little back-and-forth to pin this down. My guess is an issue with updates within one of the package dependencies, but R can be full of surprises!

Best,

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab <

http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 10:53 AM dhondorp notifications@github.com wrote:

Hello,

I'm trying to install migrateR, but the installation always fails and R reports that:

'migrateR_1.0.7.tar.gz’ is not available (for R version 3.5.2)'

I've tried both the manual install and installing directly from gitHub-- neither works.

Help!

-Darryl

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/dbspitz/migrateR/issues/4, or mute the thread <

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[dbspitz]

Hi Darryl,

Any updates? Would be interested in any added info. Hope you've had better luck getting the package installed.

Best,

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 12:48 PM dhondorp notifications@github.com wrote:

Hey Derek,

Yes, we're into spring here. Has been really wet, though.

Thanks for looking at the output. I'll try a set another set of installations after closing and restarting R and let you know what I find.

Darryl W. Hondorp
Research Fish Biologist
USGS--Great Lakes Science Center
1451 Green Road
Ann Arbor, MI 48105
Office: (734) 214-7241
Cell: (734) 545-6258
Fax: (734) 994-8780
Email: dhondorp@usgs.gov
USGS Professional Page: https://profile.usgs.gov/dhondorp

On Thu, May 9, 2019 at 3:41 PM Derek Spitz notifications@github.com wrote:

Has Spring reached Ann Arbor? Really curious to hear more about application of NSD models to aquatic species. Once you get the packages working you'll have to let me know what you think. I've been in touch with a couple researchers in FL who have run into issues with increasing coastline complexity; we'd discussed some possible solutions but ultimately issue appeared to be unusual/infrequent.

Appreciate the code, but unfortunately nothing jumps out at me as obvious so far. Is there any other information you can give me on the errors you're seeing--e.g., any warnings, etc. before the 'not available' message or is that the only output you're seeing?

If there's any more output leading up to the instillation failure, sending me that code could be helpful. Otherwise, the only other obvious suggestion for the moment would be the good ol' turn it off and on again 'trick': close R, open with a fresh workspace, reinstall 'devtools', attempt the instillation and see if you trigger the same error. A more aggressive form of this could include reopening R to a fresh workspace and running through 'update.packages()'. If the issue is indeed with package versioning, these approaches have a good chance of solving the problem.

I'm in meetings most of the rest of the day, but can take another look at the code you sent tomorrow a.m. In the meantime, let me know if you run into any other clues or hunches about the hang up. Unfortunately these sorts of delays are sometimes the price of doing business in R, but we'll get this figured out.

Good luck and keep me posted!

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab <

http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 12:00 PM dhondorp notifications@github.com wrote:

Hi Derek,

Thanks for the quick response. I'm analyzing the behavior of acoustic-tagged lake sturgeon in lakes huron and erie (and their connecting waters). Just curious about how NSD models might fit the telemetry data.

Attached is the output from those two function calls. Let me know if something jumps out at you.

Darryl W. Hondorp
Research Fish Biologist
USGS--Great Lakes Science Center
1451 Green Road
Ann Arbor, MI 48105
Office: (734) 214-7241
Cell: (734) 545-6258
Fax: (734) 994-8780
Email: dhondorp@usgs.gov
USGS Professional Page: https://profile.usgs.gov/dhondorp

On Thu, May 9, 2019 at 2:45 PM Derek Spitz notifications@github.com wrote:

Hi Darryl,

Thanks for the email. What are you working on?

Hmmm: the first hurdle. Installation errors can be a bit tricky as they're often system specific. Devtools is usually the easier path to troubleshoot here. Can you try running the following and then send me the output?

sessionInfo() packageDescription("devtools")

Might take a little back-and-forth to pin this down. My guess is an issue with updates within one of the package dependencies, but R can be full of surprises!

Best,

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab <

http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Thu, May 9, 2019 at 10:53 AM dhondorp notifications@github.com wrote:

Hello,

I'm trying to install migrateR, but the installation always fails and R reports that:

'migrateR_1.0.7.tar.gz’ is not available (for R version 3.5.2)'

I've tried both the manual install and installing directly from gitHub-- neither works.

Help!

-Darryl

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/dbspitz/migrateR/issues/4, or mute the thread <

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[SimonePirrello]

Hi Derek, I reopen this discussion as I am running in the same issue of Darryl, as I am trying to install migrateR version 1.0.9 on R version 3.5.3 but it doesn't work. All my R packages are updated and the version of devtools is 2.2.1

I ran the following code: install_github("dbspitz/migrateR/migrateR", build_vignettes = T) also tried with (...build_vignettes = F) but returns the following error:

Downloading GitHub repo dbspitz/migrateR@master ✓ checking for file ‘/private/var/folders/5y/0msbszcj3rx4t9pnptq9bjyh0000gq/T/RtmpDBm4DP/remotes23cc33bc760d/dbspitz-migrateR-6e5c413/migrateR/DESCRIPTION’ ... ─ preparing ‘migrateR’: ✓ checking DESCRIPTION meta-information ─ installing the package to build vignettes ✓ creating vignettes (11.1s) ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘migrateR_1.0.9.tar.gz’

Errore: Failed to install 'migrateR' from GitHub: (contertito da avviso) incomplete final line found on '/Users/pirrello/.Rprofile'

Please, can you help me out with this issue? Best, Simone

[dbspitz]

Hi Simone,

Thanks for the email. Appreciate your including output. I wasn't able to recreate the error, which makes tracking the problem down a bit tricky. Here's my best guess, with links to stackoverflow:

The error looks like it may be a response to your .Rprofile, rather than the package code. This error is typically caused if the last line of A file is missing a return. https://stackoverflow.com/questions/5990654/incomplete-final-line-warning-when-trying-to-read-a-csv-file-into-r If this is the issue you should be able to fix the problem by rerunning the install after manually adding a return at the end of your .Rprofile (tips on finding your .Rprofile here https://stackoverflow.com/questions/13735745/locate-the-rprofile-file-generating-default-options). Alternatively, if you haven't already, the manual install instructions might be worth trying (i.e., downloading the tarball and installing from source). Finally, you could also try installing an earlier version of the package with, e.g.: devtools::install_github("dbspitz/migrateR/migrateR@Version 1.0.8", build_vignettes = T)

Hopefully one of these approaches does the trick. If so, please let me know. I'd also be very interested in any new error messages you encounter. Happy to help more with troubleshooting, but without being able to recreate the issue myself, I'll be depending on you for more info.

Keep me posted and good luck!

Derek Spitz Postdoc, UCSC Bishop, CA (831) 737-3120 CityOfKitesAndCrows.com http://cityofkitesandcrows.com Wilmers Lab http://wildlife.ucsc.edu // Wittmer Lab http://cms.victoria.ac.nz/sbs/research/ecology-biodiversity-research/ecology-and-conservation-biology

On Mon, Feb 17, 2020 at 8:09 AM SimonePirrello notifications@github.com wrote:

Hi Derek, I reopen this discussion as I am running in the same issue of Darryl, as I am trying to install migrateR version 1.0.9 on R version 3.5.3 but it doesn't work. All my R packages are updated and the version of devtools is 2.2.1

I ran the following code: install_github("dbspitz/migrateR/migrateR", build_vignettes = T) also tried with (...build_vignettes = F) but returns the following error:

Downloading GitHub repo dbspitz/migrateR@master ✓ checking for file ‘/private/var/folders/5y/0msbszcj3rx4t9pnptq9bjyh0000gq/T/RtmpDBm4DP/remotes23cc33bc760d/dbspitz-migrateR-6e5c413/migrateR/DESCRIPTION’ ... ─ preparing ‘migrateR’: ✓ checking DESCRIPTION meta-information ─ installing the package to build vignettes ✓ creating vignettes (11.1s) ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘migrateR_1.0.9.tar.gz’

Errore: Failed to install 'migrateR' from GitHub: (contertito da avviso) incomplete final line found on '/Users/pirrello/.Rprofile'

Please, can you help me out with this issue? Best, Simone

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[SimonePirrello]

Hey Derek,

it was really a trivial error...I have just added a return at the end of my .Rprofile and then the installation of your package worked smoothly. Thank you for your help!

Best, Simone