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ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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data_frame function should be replaced #184

Closed kdgorospe closed 4 years ago

kdgorospe commented 4 years ago

This is not really a bug report, but probably something you should be aware of. I'm using the function rfishbase::synonyms, and although it works fine, I get the following warning message from R: data_frame() is deprecated as of tibble 1.1.0. Please use tibble() instead.

sckott commented 4 years ago

thanks! you're welcome to send a pull request, or we'll get to it soon

sckott commented 4 years ago

@kdgorospe i can't replicate the issue - please share your session info

kdgorospe commented 4 years ago

Sure! Here's my session info, along with the warning message when I run the rfishbase's synonyms function (but executed within another function):

data_frame() is deprecated as of tibble 1.1.0. Please use tibble() instead.This warning is displayed once every 8 hours.Call lifecycle::last_warnings() to see where this warning was generated.> sessionInfo()R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C 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] roxygen2_7.1.0 data.table_1.12.8 rfishbase_3.0.4 forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5 purrr_0.3.4 readr_1.3.1 tidyr_1.0.3 [10] tibble_3.0.1 ggplot2_3.3.0 tidyverse_1.3.0 speciesnet_0.1.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.4.6 lubridate_1.7.8 ape_5.3 lattice_0.20-41 zoo_1.8-8 foreach_1.5.0 assertthat_0.2.1 digest_0.6.25 packrat_0.5.0 plyr_1.8.6 [11] R6_2.4.1 cellranger_1.1.0 backports_1.1.6 reprex_0.3.0 httr_1.4.1 pillar_1.4.4 rlang_0.4.6 curl_4.3 readxl_1.3.1 rstudioapi_0.11 [21] taxize_0.9.95 urltools_1.7.3 triebeard_0.3.0 munsell_0.5.0 broom_0.5.6 compiler_3.6.3 modelr_0.1.7 xfun_0.13 pkgconfig_2.0.3 tidyselect_1.0.0 [31] httpcode_0.3.0 lpSolve_5.6.15 codetools_0.2-16 reshape_0.8.8 fansi_0.4.1 crayon_1.3.4 dbplyr_1.4.3 withr_2.2.0 crul_0.9.0 grid_3.6.3 [41] nlme_3.1-147 jsonlite_1.6.1 gtable_0.3.0 lifecycle_0.2.0 DBI_1.1.0 magrittr_1.5 scales_1.1.0 cli_2.0.2 stringi_1.4.6 fs_1.4.1 [51] xml2_1.3.2 ellipsis_0.3.0 generics_0.0.2 vctrs_0.2.4 gh_1.1.0 iterators_1.0.12 tools_3.6.3 bold_0.9.0 glue_1.4.0 hms_0.5.3 [61] parallel_3.6.3 colorspace_1.4-1 rvest_0.3.5 memoise_1.1.0 knitr_1.28 haven_2.2.0

On Mon, May 11, 2020 at 11:42 AM Scott Chamberlain notifications@github.com wrote:

@kdgorospe https://github.com/kdgorospe i can't replicate the issue - please share your session info

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/rfishbase/issues/184#issuecomment-626783293, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAWNY6OY4GGHNXY2MMTN6XDRRAME5ANCNFSM4MZCN5BA .

sckott commented 4 years ago

thanks, i think we fixed this in the dev version, install it remotes::install_github("ropensci/rfishbase") and try again

kdgorospe commented 4 years ago

Hi Scott,

Yup problem fixed! Sorry, I didn't even consider trying the dev version. Thanks!

On Tue, May 12, 2020 at 1:28 PM Scott Chamberlain notifications@github.com wrote:

thanks, i think we fixed this in the dev version, install it remotes::install_github("ropensci/rfishbase") and try again

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/rfishbase/issues/184#issuecomment-627484132, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAWNY6PSWHILHRTXE56MIB3RRGBLBANCNFSM4MZCN5BA .