Fixed bug in get_ereefs_ts() in mmp check.

[BarbaraRobson]

@ #34

[dbarneche]

Hi Barbara, I just installed ncdf4 1.19 and ereefsfrom your fix, but it still seems to be failing.

> get_ereefs_ts('Chl_a_sum', location_latlon=data.frame(latitide=c(-23.39189,-18), longitude=c(150.88852, 147.5)), layer='surface', start_date=c(2010,12,31),end_date=c(2011,1,5), input_file=2)

  |                                                                                                                                  |   0%oc_open: server error retrieving url: code=403 message="Request too big=69895.440656 Mbytes, max=500.0"Error in Rsx_nc4_get_vara_double: NetCDF: Authorization failure
Var: Chl_a_sum  Ndims: 4   Start: 30,46,46,268 Count: 1,1,11,167
Error in ncvar_get_inner(ncid2use, varid2use, nc$var[[li]]$missval, addOffset,  : 
  C function R_nc4_get_vara_double returned error
In addition: Warning message:
In get_ereefs_ts("Chl_a_sum", location_latlon = data.frame(latitide = c(-23.39189,  :
  Assuming that the first column of location_latlon is latitude and the second column is longitude
...

And it keeps trying with the same error over and over.

Also, the function warn on this line does not exist, it needs to be warning

[dbarneche]

The third example mentioned in #34 also failed

> get_ereefs_ts(var_names=c('ZooL_N', 'ZooS_N'), location_latlon=data.frame(latitide=c(-23.39189,-18), longitude=c(150.88852, 147.5)), layer=45, start_date=c(2010,12,31),end_date=c(2011,1,5), input_file="http://dapds00.nci.org.au/thredds/dodsC/fx3/gbr4_bgc_GBR4_H2p0_B2p0_Cpre_Dcrt/gbr4_bgc_simple_2016-06.nc")

  |                                                                                                                                  |   0%oc_open: server error retrieving url: code=403 message="Request too big=69895.440656 Mbytes, max=500.0"Error in Rsx_nc4_get_vara_double: NetCDF: Authorization failure
Var: ZooL_N  Ndims: 4   Start: 30,44,46,268 Count: 1,1,11,167
Error in ncvar_get_inner(ncid2use, varid2use, nc$var[[li]]$missval, addOffset,  : 
  C function R_nc4_get_vara_double returned error
In addition: Warning message:
In get_ereefs_ts(var_names = c("ZooL_N", "ZooS_N"), location_latlon = data.frame(latitide = c(-23.39189,  :
  Assuming that the first column of location_latlon is latitude and the second column is longitude
[1] "retrying in  1 second(s)"

[BarbaraRobson]

Hi Diego, That seems to be a problem with ncdf 1.19. Can you revert to the version of ncdf4 that you had working previously? Barbara Dr Barbara Robson Research Team Leader - Tropical Marine Ecosystems and Impacts Australian Institute of Marine Science PMB 3 | Townsville MC QLD 4810 | Australia Tel. (+61) 7 4753 4324 | Mob. (+61) 422 175 792 ***@***.******@***.***> | www.aims.gov.au<http://www.aims.gov.au/> Zoom https://aims.zoom.us/j/989-010-9890 ***@***.******@***.******@***.***<https://www.facebook.com/australianmarinescience> ***@***.***<http://www.aims.gov.au/> From: Diego Barneche ***@***.***> Sent: Monday, May 22, 2023 4:24 PM To: open-AIMS/ereefs ***@***.***> Cc: Barbara Robson ***@***.***>; Author ***@***.***> Subject: Re: [open-AIMS/ereefs] Fixed bug in get_ereefs_ts() in mmp check. (PR #35) CAUTION: This email originated from outside of AIMS. DO NOT click links or open attachments in unsolicited emails, call and confirm the content is safe with the sender first. To report any suspicious emails, use the Report Message outlook add-in or send to ***@***.******@***.***>. Hi Barbara, I just installed ncdf4 1.19 and ereefsfrom your fix, but it still seems to be failing.

get_ereefs_ts('Chl_a_sum', location_latlon=data.frame(latitide=c(-23.39189,-18), longitude=c(150.88852, 147.5)), layer='surface', start_date=c(2010,12,31),end_date=c(2011,1,5), input_file=2)

| | 0%oc_open: server error retrieving url: code=403 message="Request too big=69895.440656 Mbytes, max=500.0"Error in Rsx_nc4_get_vara_double: NetCDF: Authorization failure Var: Chl_a_sum Ndims: 4 Start: 30,46,46,268 Count: 1,1,11,167 Error in ncvar_get_inner(ncid2use, varid2use, nc$var[[li]]$missval, addOffset, : C function R_nc4_get_vara_double returned error In addition: Warning message: In get_ereefs_ts("Chl_a_sum", location_latlon = data.frame(latitide = c(-23.39189, : Assuming that the first column of location_latlon is latitude and the second column is longitude ... And it keeps trying with the same error over and over. Also, the function warn on this line<https://github.com/open-AIMS/ereefs/blob/747371b100f88430cf6f6f8d9be779d8dc0f4049/R/data_extraction_functions.R#L557> does not exist, it needs to be warning - Reply to this email directly, view it on GitHub<#35 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIT3CIPC4QY2CKCSWY5WZHTXHMBAFANCNFSM6AAAAAAYJ5QCWM>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[dbarneche]

Trying with current ncdf 1.21 also fails. I'm not sure which one is the desired version?

[BarbaraRobson]

I'm still using the github mdsumner version. Try using the current version (compiled from source) Barbara [1520817071662_PastedImage]

…

________________________________ From: Diego Barneche ***@***.***> Sent: 22 May 2023 17:09 To: open-AIMS/ereefs ***@***.***> Cc: Barbara Robson ***@***.***>; Author ***@***.***> Subject: Re: [open-AIMS/ereefs] Fixed bug in get_ereefs_ts() in mmp check. (PR #35) CAUTION: This email originated from outside of AIMS. DO NOT click links or open attachments in unsolicited emails, call and confirm the content is safe with the sender first. To report any suspicious emails, use the Report Message outlook add-in or send to ***@***.*** Trying with current ncdf 1.21 also fails. I'm not sure which one is the desired version? — Reply to this email directly, view it on GitHub<#35 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIT3CII3QAFZ53BQDX3GC6LXHMGK3ANCNFSM6AAAAAAYJ5QCWM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[dbarneche]

I just tried with devtools::install_github("mdsumner/ncdf4") but no luck.