[Bioc-devel] orthogene: evolving dependencies
Hervé Pagès
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Tue Apr 5 07:30:54 CEST 2022
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/>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.github using gmail.com
More information about the Bioc-devel
mailing list