Giters

grimbough / FITfileR

R package for reading data from FIT files using only native R code, rather than relying on external libraries.

Home Page:https://msmith.de/FITfileR

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Read error

mkln opened this issue · comments

commented

Hi, cool package!
I'm getting an error when attempting to read a .fit file from a Hammerhead Karoo 2 device:

>library(FITfileR)
>test <- readFitFile("~/Downloads/testfile.fit")

Error in `filter()`:
! Problem while computing `..1 = key == tmp@fields[[manufacturer_id_idx]][1]`.
Caused by error in `tmp@fields[[manufacturer_id_idx]]`:
! attempt to select less than one element in get1index
Run `rlang::last_error()` to see where the error occurred.

Here's the file: testfile.fit.zip

commented

Do you have the latest version of the package? Perhaps you could share the output of sessionInfo() so I can see if there's any differences. Reading the the file works for me e.g.:

library(FITfileR)

## download and extract the example file
destfile = tempfile(fileext = ".zip")
url = "https://github.com/grimbough/FITfileR/files/10086014/testfile.fit.zip"
dl = download.file(url = url, destfile = destfile)
example_file = unzip(destfile, files = "testfile.fit", exdir = tempdir())

## read the file
fitFile <- readFitFile(example_file)

## display the device information
getMessagesByType(fitFile, message_type = "device_info")
#> $device_info_1
#> # A tibble: 2 × 9
#>   timestamp           device_index manufacturer      produ…¹ sourc…² ant_d…³ product seria…⁴ devic…⁵
#>   <dttm>              <chr>        <chr>             <chr>   <chr>     <int>   <int>   <dbl>   <int>
#> 1 2022-11-23 19:48:52 <NA>         favero_electroni… 12      antplus   27489      12  1.80e9      11
#> 2 2022-11-23 19:48:52 <NA>         fitcare           4       antplus   18623       4  0          120
#> # … with abbreviated variable names ¹​product_name, ²​source_type, ³​ant_device_number,
#> #   ⁴​serial_number, ⁵​device_type
#> 
#> $device_info_2
#> # A tibble: 1 × 8
#>   timestamp           device_index manufacturer product_name product serial_number source_…¹ devic…²
#>   <dttm>              <chr>        <chr>        <chr>          <int>         <dbl> <chr>       <int>
#> 1 2022-11-23 16:33:24 creator      hammerhead   Karoo 2            2     102500513 local           4
#> # … with abbreviated variable names ¹​source_type, ²​device_type
#> 
#> $device_info_3
#> # A tibble: 19 × 11
#>    timestamp           device_index manufa…¹ produ…² product seria…³ sourc…⁴ devic…⁵ batte…⁶ batte…⁷
#>    <dttm>              <chr>        <chr>    <chr>     <int>   <dbl> <chr>     <int> <chr>     <dbl>
#>  1 2022-11-23 17:07:31 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.99
#>  2 2022-11-23 17:21:11 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.91
#>  3 2022-11-23 17:34:02 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.94
#>  4 2022-11-23 17:41:16 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.95
#>  5 2022-11-23 17:46:05 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.93
#>  6 2022-11-23 18:05:21 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.93
#>  7 2022-11-23 18:06:58 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.91
#>  8 2022-11-23 18:19:49 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.90
#>  9 2022-11-23 18:20:42 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.90
#> 10 2022-11-23 18:25:26 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.89
#> 11 2022-11-23 18:39:05 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.85
#> 12 2022-11-23 18:43:06 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.85
#> 13 2022-11-23 18:52:45 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.84
#> 14 2022-11-23 19:02:23 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.82
#> 15 2022-11-23 19:12:01 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.84
#> 16 2022-11-23 19:20:03 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.82
#> 17 2022-11-23 19:28:05 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.80
#> 18 2022-11-23 19:36:07 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.82
#> 19 2022-11-23 19:43:21 creator      hammerh… Karoo 2       2  1.03e8 local         4 ok         3.81
#> # … with 1 more variable: charge <int>, and abbreviated variable names ¹​manufacturer,
#> #   ²​product_name, ³​serial_number, ⁴​source_type, ⁵​device_type, ⁶​battery_status, ⁷​battery_voltage

Here's my session info:

sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Linux Mint 20.3
#> 
#> Matrix products: default
#> BLAS:   /home/msmith/Applications/R/R-4.2.2/lib/libRblas.so
#> LAPACK: /home/msmith/Applications/R/R-4.2.2/lib/libRlapack.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
#>  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
#> [10] LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] FITfileR_0.1.5
#> 
#> loaded via a namespace (and not attached):
#>  [1] rstudioapi_0.14  knitr_1.41       magrittr_2.0.3   tidyselect_1.2.0 R6_2.5.1        
#>  [6] rlang_1.0.6      fastmap_1.1.0    fansi_1.0.3      stringr_1.4.1    highr_0.9       
#> [11] dplyr_1.0.10     tools_4.2.2      xfun_0.35        utf8_1.2.2       DBI_1.1.3       
#> [16] cli_3.4.1        withr_2.5.0      htmltools_0.5.3  assertthat_0.2.1 yaml_2.3.6      
#> [21] digest_0.6.30    tibble_3.1.8     lifecycle_1.0.3  vctrs_0.5.1      fs_1.5.2        
#> [26] glue_1.6.2       evaluate_0.18    rmarkdown_2.18   reprex_2.0.2     stringi_1.7.8   
#> [31] compiler_4.2.2   pillar_1.8.1     generics_0.1.3   pkgconfig_2.0.3
commented

I installed via devtools::install_github, I think that's version 0.1.6.
Here's sessionInfo() for two machines both of which give me the same error

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.0.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2   

> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_rt.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_1.0.10   FITfileR_0.1.6

loaded via a namespace (and not attached):
 [1] fansi_1.0.3      assertthat_0.2.1 utf8_1.2.2       R6_2.5.1         DBI_1.1.3        lifecycle_1.0.3 
 [7] magrittr_2.0.3   pillar_1.8.1     rlang_1.0.6      cli_3.4.1        rstudioapi_0.14  vctrs_0.5.1     
[13] generics_0.1.3   tools_4.2.2      glue_1.6.2       compiler_4.2.2   pkgconfig_2.0.3  tidyselect_1.2.0
[19] tibble_3.1.8
commented

Thanks. Looks like I'm the one running an old version of FITfileR 🤦‍♂️I guess I've got the latest version under R-devel but not R-4.2 I'll take a look at the issue later.

For now you could install version 0.1.5, but you'll probably have to pick through the git log to find the right commit to install from.

commented

Ok, I'm currently on May 25 (https://github.com/grimbough/FITfileR/tree/a3b70fedb60de8555a7eb94cd99f13d257b2e242) which seems to be the last one that works without error. On the July 1 commit I get this:

> FITfileR::readFitFile("~/Downloads/testfile.fit")
Error in tmp@fields[[2]] : subscript out of bounds

Hope this helps!

commented

Thanks for digging through the history. I made an assumption in my changes to address #20 that any developer messages would have a 'manufacturer' field. however that isn't the case in your files. Hopefully it's been fixed in the latest set of updates.