could not find function "tcount"

ryao-mdanderson commented 2 years ago

Hello,

I followed the installation instruction and test as in the README, I hit an error, please advise, thank you!

library(venndir) setlist <- make_venn_test(100, 3) venndir(setlist) Error in tcount(sign(diff(h1h2df1$h2))) : could not find function "tcount" setlist $set_A [1] "item_067" "item_042" "item_050" "item_043" "item_014" "item_025" [7] "item_090" "item_091" "item_069" "item_093" "item_057" "item_009" [13] "item_072" "item_026" "item_007" "item_099" "item_089" "item_083" [19] "item_036" "item_078" "item_097" "item_076" "item_015" "item_032" [25] "item_086" "item_084" "item_041" "item_023" "item_027" "item_060" [31] "item_053" "item_079"

$set_B [1] "item_053" "item_027" "item_096" "item_038" "item_089" "item_034" [7] "item_093" "item_069" "item_072" "item_076" "item_063" "item_013" [13] "item_082" "item_025" "item_097" "item_021"

$set_C [1] "item_079" "item_041" "item_047" "item_090" "item_060" "item_095" [7] "item_016" "item_006" "item_072" "item_086" "item_091" "item_039" [13] "item_031" "item_081" "item_050"

venndir(setlist) Error in tcount(sign(diff(h1h2df1$h2))) : could not find function "tcount" sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] venndir_0.0.17.9000 remotes_2.4.0

loaded via a namespace (and not attached): [1] lattice_0.20-44 ps_1.6.0 prettyunits_1.1.1
[4] crayon_1.4.1 withr_2.4.2 rprojroot_2.0.2
[7] grid_4.1.0 R6_2.5.0 cli_3.0.0
[10] curl_4.3.2 data.table_1.14.0 rstudioapi_0.13
[13] sp_1.4-5 callr_3.7.0 jamba_0.0.70.900
[16] tools_4.1.0 colorjam_0.0.22.900 compiler_4.1.0
[19] processx_3.5.2 pkgbuild_1.2.0

ryao-mdanderson commented 2 years ago

@jmw86069 May you please help? Thanks!

jmw86069 commented 2 years ago

Thank you for reporting the issue, I have a quick workaround while I fix the underlying issue.

The tcount() function is provided by the jamba package, the fastest workaround is to load jamba first, then venndir will work properly:

library(jamba)
library(venndir)
venndir(...)

I need to update the colorjam package that is calling tcount() in this case, and will do so shortly. Apologies for not seeing your post sooner!

jmw86069 commented 2 years ago

Okay I have updated colorjam to use package prefix jamba::tcount(), bumped the version number. I then updated venndir to require the appropriate colorjam version. So in principle you can update venndir and see the fix.

remotes::install_github("jmw86069/venndir")

Honestly, this is a weird bug to me! I guess I'm glad to learn about it and avoid it in future.

Internally, colorjam::approx_degrees() was trying to call jamba::tcount(). (I use approx_degrees() to adjust the red-green-blue color wheel to a more dichromat-colorblindness-friendly color wheel, which is then used to define colorblindness-friendly categorical colors. approx_degrees() is like approx() for interpolation of angular degrees.)

The colorjam package imports jamba. So if someone loads library(colorjam) it also imports jamba functions. In that case, the colorjam function approx_degrees() is able to call tcount() with no error. Also, all the colorjam examples and tests work fine with no error.
However, if the function colorjam::approx_degrees() is called directly, without previously loading colorjam or jamba, then the jamba functions are not imported. The call to tcount() results in the error you reported.
The fix is to include package prefix in the function call: jamba::tcount().

Thank you for posting the error, and I apologize that I did not catch it previously.

Let me know if you have questions or feedback about venndir! I'm interested to make it useful for other people's analysis work!

ryao-mdanderson commented 2 years ago

Hello James: Thank you very much for your reply and fixes. This is a scientist in my institution asks for my help to debug with the package. I am glad to seek help from you. We will definitely try your fix version.

I appreciate.

Rong

ryao-mdanderson commented 2 years ago

@jmw86069 I am glad it works now. Thank you.

jmw86069 commented 2 years ago

Great, thank you for the feedback! And if you or the scientists at your institution have questions, feel to ask, I'm happy to help!

jmw86069 / venndir

could not find function "tcount" #2