[Bioc-devel] orthogene: evolving dependencies

Sun Apr 10 13:06:05 CEST 2022

Thanks, Herve, that all makes sense to me. 

I’ve contacted the babelgene <https://github.com/igordot/babelgene/issues/2> author and managed to resolve the issues in a way that doesn’t require me to download data via piggyback anymore. piggyback <https://github.com/ropensci/piggyback/issues/49> (in the current CRAN release) required a valid GitHub Personal Access Token <https://docs.github.com/en/enterprise-server@3.4/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token> to be stored as a global variable. Thus why I was unable to replicate the errors locally or on GitHub Actions, but they were appearing on Bioc’s VMs.

Fingers crossed that these updates I pushed on Friday all pass before the freeze on Monday!

Thanks again for all your help, 
Brian

> On 7 Apr 2022, at 14:07, Hervé Pagès <hpages.on.github using gmail.com> wrote:
> 
> Hi Brian,
> 
> On 06/04/2022 06:25, Brian Schilder wrote:
> 
>> Hi Herve,
>> 
>> Thanks for checking this. I’ve managed to go through and fix the issues on Bioc 3.14 (now orthogene 1.0.1).
> Great, thanks!
>> However, the larger question is at hand is: after the Bioc 3.14 release is frozen, how do I prevent this version of orthogene from breaking when there’s changes to its dependencies that I’m unable to control?
> 
> Unfortunately you can't prevent that. The only way you could maybe try to solve this is by convincing the author of the breaking change to revert the change.
> 
>> 
>> I’ll try tackling the errors on 3.15 next.
> 
> Sounds good.
> 
> Cheers,
> 
> H.
> 
>> 
>> Best,
>> Brian
>> 
>>> On 5 Apr 2022, at 06:30, Hervé Pagès <hpages.on.github using gmail.com> wrote:
>>> 
>>> Hi Brian,
>>> 
>>> Let's start by taking care of orthogene's failure in BioC 3.14 (this is orthogene 1.0.0):
>>> 
>>> https://bioconductor.org/checkResults/3.14/bioc-LATEST/orthogene/
>>> 
>>> The error we see there is different from what we see in devel for orthogene 1.1.4. In release the tests in 'test-map_orthologs_babelgene.R' fail at line 18. I can reproduce this on my laptop with:
>>> 
>>> library(testthat)
>>> 
>>> library(orthogene)
>>> 
>>> data("exp_mouse")
>>> 
>>> #### mouse ==> human ####
>>> gene_map1 <- orthogene:::map_orthologs_babelgene(
>>> genes = rownames(exp_mouse),
>>> input_species = "mouse",
>>> output_species = "human"
>>> )
>>> testthat::expect_gte(nrow(gene_map1), 13000)
>>> 
>>> #### human ==> mouse ####
>>> gene_map2 <- orthogene:::map_orthologs_babelgene(
>>> genes = gene_map1$ortholog_gene,
>>> input_species = "human",
>>> output_species = "mouse"
>>> )
>>> testthat::expect_gte(nrow(gene_map2), 13000)
>>> 
>>> This last line produces:
>>> 
>>> Error: nrow(gene_map2) is not more than 13000. Difference: -1.3e+04
>>> 
>>> See my sessionInfo() below.
>>> 
>>> Best,
>>> 
>>> H.
>>> 
>>>> sessionInfo()
>>> R version 4.1.1 (2021-08-10)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: Ubuntu 21.10
>>> 
>>> Matrix products: default
>>> BLAS: /home/hpages/R/R-4.1.1/lib/libRblas.so
>>> LAPACK: /home/hpages/R/R-4.1.1/lib/libRlapack.so
>>> 
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_GB 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] orthogene_1.0.0 testthat_3.1.3
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] tidyselect_1.1.2 purrr_0.3.4
>>> [3] lattice_0.20-45 carData_3.0-5
>>> [5] colorspace_2.0-3 gprofiler2_0.2.1
>>> [7] vctrs_0.4.0 generics_0.1.2
>>> [9] htmltools_0.5.2 viridisLite_0.4.0
>>> [11] utf8_1.2.2 plotly_4.10.0
>>> [13] rlang_1.0.2 ggpubr_0.4.0
>>> [15] pillar_1.7.0 glue_1.6.2
>>> [17] DBI_1.1.2 GenomeInfoDbData_1.2.7
>>> [19] lifecycle_1.0.1 munsell_0.5.0
>>> [21] ggsignif_0.6.3 gtable_0.3.0
>>> [23] htmlwidgets_1.5.4 fastmap_1.1.0
>>> [25] parallel_4.1.1 fansi_1.0.3
>>> [27] broom_0.7.12 scales_1.1.1
>>> [29] backports_1.4.1 jsonlite_1.8.0
>>> [31] abind_1.4-5 brio_1.1.3
>>> [33] babelgene_22.3 ggplot2_3.3.5
>>> [35] digest_0.6.29 rstatix_0.7.0
>>> [37] dplyr_1.0.8 grid_4.1.1
>>> [39] cli_3.2.0 tools_4.1.1
>>> [41] magrittr_2.0.3 patchwork_1.1.1
>>> [43] lazyeval_0.2.2 tibble_3.1.6
>>> [45] crayon_1.5.1 tidyr_1.2.0
>>> [47] car_3.0-12 pkgconfig_2.0.3
>>> [49] ellipsis_0.3.2 Matrix_1.4-1
>>> [51] data.table_1.14.2 homologene_1.4.68.19.3.27
>>> [53] assertthat_0.2.1 httr_1.4.2
>>> [55] R6_2.5.1 compiler_4.1.1
>>> 
>>> On 04/04/2022 10:28, Brian Schilder wrote:
>>>> Hello everyone,
>>>> 
>>>> I’m the developer of orthogene <https://github.com/neurogenomics/orthogene>, a package for inter-species gene mapping.
>>>> 
>>>> Despite orthogene passing all CRAN and Bioc checks on GitHub Actions <https://github.com/neurogenomics/orthogene/actions/runs/2079508299> (including when using the official Bioc devel Docker container <https://github.com/neurogenomics/orthogene/runs/5794025048?check_suite_focus=true> with Bioc 3.15 and R 4.2), it is consistently failing on Bioc’s VMs <http://bioconductor.org/checkResults/devel/bioc-LATEST/orthogene/>. Most if not all of these errors seem to be due to corrupted .rda files from babelgene (a central dependency of orthogene):
>>>> Error in `load(filename)`: bad restore file magic number (file may be corrupted) -- no data loaded
>>>> The developer of babelgene <https://github.com/igordot/babelgene/> has recently been making quite a few changes/updates to their package. They last submitted an update to CRAN on March 30th 2022 <https://cran.r-project.org/web/packages/babelgene/index.html>. Hopefully these will be complete soon so I can make any necessary adjustments to orthogene. Still, I’m not sure why I’ve been unable to replicate the errors seen on Bioc’s VMs over the past several weeks.
>>>> 
>>>> In addition, I just received a message that the old version of orthogene on Bioc 3.14 is now failing <https://master.bioconductor.org/checkResults/3.14/bioc-LATEST/orthogene/nebbiolo2-checksrc.html> for the first time because of these changes. I hadn’t specified a version of babelgene in 3.14 because I designed my unit tests to pass after slight changes (e.g. varying numbers of mapped orthologs between mouse and human) but not failures (e.g. corrupted .rda files).
>>>> 
>>>> So my questions are two-fold:
>>>> Why am I unable to replicate the errors seen on Bioc’s VMs on my local machine (both within a Bioc 3.15 Docker container and outside of it) or on GHA (both within a Bioc 3.15 Docker container and outside of it).
>>>> Since Bioc 3.14 is now frozen, how can I prevent orthogene from failing Bioc checks <https://master.bioconductor.org/checkResults/3.14/bioc-LATEST/orthogene/nebbiolo2-checksrc.html>failing <https://master.bioconductor.org/checkResults/3.14/bioc-LATEST/orthogene/nebbiolo2-checksrc.html> Bioc checks due to the changes to babelgene?
>>>> 
>>>> Many thanks in advance,
>>>> Brian
>>>> 
>>>> ___________
>>>> Brian Schilder
>>>> PhD Candidate
>>>> UK Dementia Research Institute at Imperial College London
>>>> Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
>>>> Profile | bit.ly/imperial_profile <https://bit.ly/imperial_profile>
>>>> LinkedIn | linkedin.com/in/brian-schilder <https://www.linkedin.com/in/brian-schilder/>
>>>> Twitter | twitter.com/BMSchilder <http://www.twitter.com/BMSchilder>
>>>> Lab | neurogenomics.co.uk <http://neurogenomics.co.uk/>
>>>> UK DRI | www.ukdri.ac.uk <http://www.ukdri.ac.uk/>
>>>> 
>>>> 
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>>>> 
>>>> _______________________________________________
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>>> -- 
>>> Hervé Pagès
>>> 
>>> Bioconductor Core Team
>>> hpages.on.github using gmail.com
>>> 
> -- 
> Hervé Pagès
> 
> Bioconductor Core Team
> hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>

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