Documentation #10
Comments
meztez
added this to To do
in R package for downscaled monthly climate normals
via automation
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@cmahony start poking around |
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@meztez great to see the progress. i'm out of commission for the next couple of days, but can have a look on friday. Is there a way for me to test the package yet? |
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@cmahony https://github.com/bcgov/climR-pnw, check README. |
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@meztez
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Wondering if it is a missing dependency from another package. Do you have the full log? > remotes::install_github("bcgov/climR-pnw")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo bcgov/climR-pnw@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: rlang (1.0.1 -> 1.0.2 ) [CRAN]
5: Rcpp (1.0.8 -> 1.0.8.3) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 3
✓ checking for file ‘/tmp/RtmpJ12RPH/remotes4eeb45760d67/bcgov-climR-pnw-e8cb238/DESCRIPTION’ ...
─ preparing ‘climRpnw’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘climRpnw_0.0.0.9000.tar.gz’
Installing package into ‘/home/bruno/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
* installing *source* package ‘climRpnw’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (climRpnw)Will post Windows results, in a bit |
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Windows > remotes::install_github("bcgov/climR-pnw")
Downloading GitHub repo bcgov/climR-pnw@HEAD
Installing 23 packages: fastmap, rlang, sys, askpass, R6, openssl, mime, jsonlite, curl, glue, Rcpp, cachem, ini, httr, gitcreds, cli, terra, sp, memoise, gh, data.table, ncdf4, raster
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/fastmap_1.1.0.zip'
Content type 'application/zip' length 215411 bytes (210 KB)
downloaded 210 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/rlang_1.0.2.zip'
Content type 'application/zip' length 1719584 bytes (1.6 MB)
downloaded 1.6 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/sys_3.4.zip'
Content type 'application/zip' length 59816 bytes (58 KB)
downloaded 58 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/askpass_1.1.zip'
Content type 'application/zip' length 243690 bytes (237 KB)
downloaded 237 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/R6_2.5.1.zip'
Content type 'application/zip' length 84256 bytes (82 KB)
downloaded 82 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/openssl_2.0.0.zip'
Content type 'application/zip' length 3994824 bytes (3.8 MB)
downloaded 3.8 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/mime_0.12.zip'
Content type 'application/zip' length 48094 bytes (46 KB)
downloaded 46 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/jsonlite_1.8.0.zip'
Content type 'application/zip' length 1155893 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/curl_4.3.2.zip'
Content type 'application/zip' length 4322463 bytes (4.1 MB)
downloaded 4.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/glue_1.6.2.zip'
Content type 'application/zip' length 171998 bytes (167 KB)
downloaded 167 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/Rcpp_1.0.8.3.zip'
Content type 'application/zip' length 3356433 bytes (3.2 MB)
downloaded 3.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/cachem_1.0.6.zip'
Content type 'application/zip' length 79002 bytes (77 KB)
downloaded 77 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/ini_0.3.1.zip'
Content type 'application/zip' length 15750 bytes (15 KB)
downloaded 15 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/httr_1.4.2.zip'
Content type 'application/zip' length 518572 bytes (506 KB)
downloaded 506 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/gitcreds_0.1.1.zip'
Content type 'application/zip' length 97514 bytes (95 KB)
downloaded 95 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/cli_3.2.0.zip'
Content type 'application/zip' length 1256437 bytes (1.2 MB)
downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/terra_1.5-21.zip'
Content type 'application/zip' length 41915570 bytes (40.0 MB)
downloaded 40.0 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/sp_1.4-6.zip'
Content type 'application/zip' length 2200739 bytes (2.1 MB)
downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/memoise_2.0.1.zip'
Content type 'application/zip' length 50284 bytes (49 KB)
downloaded 49 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/gh_1.3.0.zip'
Content type 'application/zip' length 141809 bytes (138 KB)
downloaded 138 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/data.table_1.14.2.zip'
Content type 'application/zip' length 2599534 bytes (2.5 MB)
downloaded 2.5 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/ncdf4_1.19.zip'
Content type 'application/zip' length 3271923 bytes (3.1 MB)
downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/raster_3.5-15.zip'
Content type 'application/zip' length 4123748 bytes (3.9 MB)
downloaded 3.9 MB
package ‘fastmap’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘sys’ successfully unpacked and MD5 sums checked
package ‘askpass’ successfully unpacked and MD5 sums checked
package ‘R6’ successfully unpacked and MD5 sums checked
package ‘openssl’ successfully unpacked and MD5 sums checked
package ‘mime’ successfully unpacked and MD5 sums checked
package ‘jsonlite’ successfully unpacked and MD5 sums checked
package ‘curl’ successfully unpacked and MD5 sums checked
package ‘glue’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘cachem’ successfully unpacked and MD5 sums checked
package ‘ini’ successfully unpacked and MD5 sums checked
package ‘httr’ successfully unpacked and MD5 sums checked
package ‘gitcreds’ successfully unpacked and MD5 sums checked
package ‘cli’ successfully unpacked and MD5 sums checked
package ‘terra’ successfully unpacked and MD5 sums checked
package ‘sp’ successfully unpacked and MD5 sums checked
package ‘memoise’ successfully unpacked and MD5 sums checked
package ‘gh’ successfully unpacked and MD5 sums checked
package ‘data.table’ successfully unpacked and MD5 sums checked
package ‘ncdf4’ successfully unpacked and MD5 sums checked
package ‘raster’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\gen01914\AppData\Local\Temp\RtmpED1ofq\downloaded_packages
Running `R CMD build`...
* checking for file 'C:\Users\gen01914\AppData\Local\Temp\RtmpED1ofq\remotes2ed853f469e\bcgov-climR-pnw-e8cb238/DESCRIPTION' ... OK
* preparing 'climRpnw':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'climRpnw_0.0.0.9000.tar.gz'
* installing *source* package 'climRpnw' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'climRpnw'
finding HTML links ... done
append_calc html
baseline html
cache_exists html
cache_path html
calc_DD_above_18 html
calc_DD_above_5 html
calc_DD_below_0 html
calc_DD_below_18 html
calc_EMT html
calc_EXT html
calc_FFP html
calc_NFFD html
calc_PAS html
calc_RH html
calc_bFFP html
calc_eFFP html
content_get html
data_delete html
data_download html
data_get html
data_path html
data_update html
downscale html
future html
lapse_rate html
lapse_rate_mem html
list_data html
list_dem html
list_gcm html
list_normal html
list_parse html
list_period html
list_ssp html
list_unique html
list_variables html
variables html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (climRpnw) |
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@meztez it's tripping up on package 'curl'. i'm troubleshooting it but see below in bold.
1: All Enter one or more numbers, or an empty line to skip updates:1 trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/glue_1.6.2.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/Rcpp_1.0.8.3.zip' Content type 'application/zip' length 3355085 bytes (3.2 MB) trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cachem_1.0.6.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cli_3.2.0.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/sp_1.4-6.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/memoise_2.0.1.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/gh_1.3.0.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/data.table_1.14.2.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/ncdf4_1.19.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/raster_3.5-15.zip' package ‘curl’ successfully unpacked and MD5 sums checked |
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@meztez i got it to work by restarting r |
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That's a classic on windows. It fails because remotes is already using curl to download packages. On Windows, packages with C dll object cannot be replaced while they are used, unlike linux. What I suggest is just installing climRpnw, without updating your existing packages. You can always do that with update.packages(). |
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roger that. something for documentation. |
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That's a classic on windows. It fails because remotes is already using curl to download packages. On Windows, packages with C dll object cannot be replaced while they are used, unlike linux. What I suggest is just installing climRpnw, without updating your existing packages. You can always do that with update.packages(). |
Wondering if there was a hiccup during data_update(). Could you send me a copy the file at the location: C:\Users\CMAHONY\AppData\Local\R\cache\R\climRpnw\inputs\gcm\BCC-CSM2-MR\gcmData.BCC-CSM2-MR.pr.nc |
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sent by email |
I was able to reproduce the problem on Windows. Give me a second. |
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@cmahony do a data_delete(), reinstall climRpnw, reload session, load climRpnw and redo data_update(). Sorry for the delays, depending on machine configuration, Windows does not always download file in binary mode. I've explicitly configured it this time. |
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@cmahony All right. Let me test some more on Windows. I'll circle back to you. |
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@cmahony It works with the latest commit. Still investigating performance issue on Windows. Also you might get Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x) : attempt to apply non-function
Error in (function (x) : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-functionThese messages can be ignored per terra package maintainer comments. But they are annoying and I'm not done shusing them all. |
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@meztez wow you are a true magic man. running well and with the test i did it was 25x faster than climateBC. I will send this to Will and Kiri and do a more thorough review on Friday. what is the best way for us to provide you with itemized feedback? |
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@cmahony keep them in a separate. I'm not done with speed up. Most of the time was spent on computing lapse rate. I'm moving that somewhere as the caching does not want to cooperate due to Error mentioned in my previous comment. |
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