import from GDS fails

[cmatKhan]

Hi all. I am trying to import data from a VCF produced by GATK Haplotypecaller. The VarientExperiment constructor fails from both VCF or GDS. Reproduced with the GDS:

ve = VariantExperiment::makeVariantExperimentFromGDS(
  'all_recomb_results_all_wg_c8_minimal.gds'
)

Error in vapply(nds, function(x) .get_gdsnode_desp(file, x, "dim"), integer(1)) : 
  values must be length 1,
 but FUN(X[[15]]) result is length 2

I get the same error when I use showAvailable.

NOTE: This is a .gds file. But, github requires it has one of a set of extensions, hence the .txt. Just ignore that. I think it works just to add the extension, but I'm happy to share via email if it doesn't.

all_recomb_results_all_wg_c8_minimal.gds.txt

[Liubuntu]

Hello Chase,

Thanks for using VariantExperiment and sorry for the inconvenience!

The fact is that I've just made some changes to GDSArray on which VariantExperiment depends. Consequently, I'll need to fix VariantExperiment to be consistent with the GDSArray changes. I'm in the process of fixing it right now and hopefully to have it done today, but it could also be a few days... I'll have you posted.

Have a great day!

Best, Qian

On Tue, Apr 16, 2024 at 9:28 AM Chase Mateusiak @.***> wrote:

Hi all. I am trying to import data from a VCF produced by GATK Haplotypecaller. The VarientExperiment constructor fails from both VCF or GDS. Reproduced with the GDS:

ve = VariantExperiment::makeVariantExperimentFromGDS( 'all_recomb_results_all_wg_c8_minimal.gds' )

Error in vapply(nds, function(x) .get_gdsnode_desp(file, x, "dim"), integer(1)) : values must be length 1, but FUN(X[[15]]) result is length 2

I get the same error when I use showAvailable.

NOTE: This is a .gds file. But, github requires it has one of a set of extensions, hence the .txt. Just ignore that. I think it works just to add the extension, but I'm happy to share via email if it doesn't.

all_recomb_results_all_wg_c8_minimal.gds.txt https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FVariantExperiment%2Ffiles%2F14997437%2Fall_recomb_results_all_wg_c8_minimal.gds.txt&data=05%7C02%7Cqliu7%40g-mail.buffalo.edu%7C2019b9ce599842e0f72e08dc5e19281f%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638488709336601948%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=jrd5LZsIMkB8iV10gPEmdYqEH3oM%2BNz0tlkQpUYt7q4%3D&reserved=0

— Reply to this email directly, view it on GitHub https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FVariantExperiment%2Fissues%2F5&data=05%7C02%7Cqliu7%40g-mail.buffalo.edu%7C2019b9ce599842e0f72e08dc5e19281f%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638488709336758164%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=ilvVhcGzf1GlCgJDmo2L3ZPAWeIjfq%2FLE9Imf0NBb6A%3D&reserved=0, or unsubscribe https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADAYVSMXAV742ZEQ4J7GTETY5URRHAVCNFSM6AAAAABGJLUYM6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGI2DMMBXGE3TKMQ&data=05%7C02%7Cqliu7%40g-mail.buffalo.edu%7C2019b9ce599842e0f72e08dc5e19281f%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638488709336758164%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Hq22XoUS4lUR%2Bnk%2FqkIc4BYo0%2BinYmHCi2B7WnXr7UQ%3D&reserved=0 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[cmatKhan]

I see -- so is a temporary solution to downgrade GDSArray?

[Liubuntu]

If you go back to the release version of both VE and GDSArray, I think it should work.

On Tue, Apr 16, 2024 at 11:32 AM Chase Mateusiak @.***> wrote:

I see -- so is a temporary solution to downgrade GDSArray?

— Reply to this email directly, view it on GitHub https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FVariantExperiment%2Fissues%2F5%23issuecomment-2059375885&data=05%7C02%7Cqliu7%40g-mail.buffalo.edu%7Cfdb32a5ef622421cce9108dc5e2a609e%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638488783301244741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=877OSFZDctf8tGbpi7GoafUuQS2OsYb%2BjPsdUhwl7ic%3D&reserved=0, or unsubscribe https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADAYVSMVYDZQSPTPLAZFD7DY5U77PAVCNFSM6AAAAABGJLUYM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJZGM3TKOBYGU&data=05%7C02%7Cqliu7%40g-mail.buffalo.edu%7Cfdb32a5ef622421cce9108dc5e2a609e%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638488783301244741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=UqiOoUgntQxNL31EXFmiQlhayZChKZoI4qGO4paBxU0%3D&reserved=0 . You are receiving this because you commented.Message ID: @.***>

[Liubuntu]

Hi Chase,

The error for VE should be fixed. Please allow 24-48 hours when the changes to kick into the Bioc building system.

Best, Qian

On Tue, Apr 16, 2024 at 12:55 PM Qian Liu @.***> wrote:

If you go back to the release version of both VE and GDSArray, I think it should work.

On Tue, Apr 16, 2024 at 11:32 AM Chase Mateusiak @.***> wrote:

I see -- so is a temporary solution to downgrade GDSArray?

— Reply to this email directly, view it on GitHub https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FVariantExperiment%2Fissues%2F5%23issuecomment-2059375885&data=05%7C02%7Cqliu7%40g-mail.buffalo.edu%7Cfdb32a5ef622421cce9108dc5e2a609e%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638488783301244741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=877OSFZDctf8tGbpi7GoafUuQS2OsYb%2BjPsdUhwl7ic%3D&reserved=0, or unsubscribe https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADAYVSMVYDZQSPTPLAZFD7DY5U77PAVCNFSM6AAAAABGJLUYM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJZGM3TKOBYGU&data=05%7C02%7Cqliu7%40g-mail.buffalo.edu%7Cfdb32a5ef622421cce9108dc5e2a609e%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638488783301244741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=UqiOoUgntQxNL31EXFmiQlhayZChKZoI4qGO4paBxU0%3D&reserved=0 . You are receiving this because you commented.Message ID: @.***>

[cmatKhan]

I'm getting the same error. I have 1.18.0 installed, which biocmanager seems to think is the current version.

> BiocManager::install('VariantExperiment', version = '3.19', Ncpus=10)
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    codetools, lattice, MASS, Matrix, nlme, spatial, survival
Warning message:
package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'VariantExperiment' 

R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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       

time zone: America/Chicago
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] lubridate_1.9.3             forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                
 [5] purrr_1.0.2                 readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1               
 [9] ggplot2_3.5.1               tidyverse_2.0.0             VariantExperiment_1.18.0    SummarizedExperiment_1.34.0
[13] Biobase_2.64.0              GenomicRanges_1.56.0        GenomeInfoDb_1.40.0         IRanges_2.38.0             
[17] MatrixGenerics_1.16.0       matrixStats_1.3.0           S4Vectors_0.42.0            BiocGenerics_0.50.0        

loaded via a namespace (and not attached):
 [1] gtable_0.3.5            SeqArray_1.44.0         lattice_0.22-5          tzdb_0.4.0              vctrs_0.6.5            
 [6] tools_4.4.0             generics_0.1.3          parallel_4.4.0          fansi_1.0.6             pkgconfig_2.0.3        
[11] Matrix_1.6-5            lifecycle_1.0.4         GenomeInfoDbData_1.2.12 compiler_4.4.0          Biostrings_2.72.0      
[16] munsell_0.5.1           pillar_1.9.0            crayon_1.5.2            DelayedArray_0.30.0     abind_1.4-5            
[21] DelayedDataFrame_1.20.0 digest_0.6.35           tidyselect_1.2.1        stringi_1.8.4           grid_4.4.0             
[26] colorspace_2.1-0        cli_3.6.2               SparseArray_1.4.1       magrittr_2.0.3          S4Arrays_1.4.0         
[31] utf8_1.2.4              SNPRelate_1.38.0        withr_3.0.0             scales_1.3.0            UCSC.utils_1.0.0       
[36] bit64_4.0.5             timechange_0.3.0        GDSArray_1.24.0         XVector_0.44.0          httr_1.4.7             
[41] bit_4.0.5               hms_1.1.3               rlang_1.1.3             glue_1.7.0              gdsfmt_1.40.0          
[46] vroom_1.6.5             rstudioapi_0.16.0       jsonlite_1.8.8          R6_2.5.1                zlibbioc_1.50.0