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koustav-pal / HiCBricks

HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides a R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms.
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Error running Create_many_Bricks with H5 #21

Closed TomKellyGenetics closed 2 years ago

TomKellyGenetics commented 2 years ago

I encountered the following issue with running HiCBricks::Create_many_Bricks, following the vignette examples.

Error in h5writeDataset.data.frame(h5loc = Brick.handler, obj = object,  : 
  could not find function "h5writeDataset.data.frame"

As a workaround, the "hdf5r" package needs to be installed from CRAN separately, HiCBricks can then be called without errors and writes to disk.

dir.create(out_dir)
h5writeDataset.data.frame <- rhdf5::h5writeDataset
h5writeDataset.array <- rhdf5::h5writeDataset
Create_many_Bricks(...)

Clearly this is not ideal so if the dependencies can be installed correctly based on the DESCRIPTION and NAMESPACE that would avoid this problem.

I am using R v4.1.2 on a RHEL 8 linux server with the latest versions of packages installed from Bioconductor and CRAN.

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.5 (Ootpa)

Matrix products: default
BLAS:   /usr/local/R-4.1.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.1.2/lib64/R/lib/libRlapack.so

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       

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

other attached packages:
[1] hdf5r_1.3.5      HiCBricks_1.11.0 R6_2.5.1         rhdf5_2.38.0     curl_4.3.2      

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2       purrr_0.3.4            reshape2_1.4.4         colorspace_2.0-3      
 [5] vctrs_0.3.8            generics_0.1.2         stats4_4.1.2           viridisLite_0.4.0     
 [9] utf8_1.2.2             rlang_1.0.2            R.oo_1.24.0            pillar_1.7.0          
[13] R.utils_2.11.0         glue_1.6.2             DBI_1.1.2              BiocParallel_1.28.3   
[17] BiocGenerics_0.40.0    bit64_4.0.5            RColorBrewer_1.1-3     GenomeInfoDbData_1.2.7
[21] lifecycle_1.0.1        plyr_1.8.6             stringr_1.4.0          zlibbioc_1.40.0       
[25] munsell_0.5.0          gtable_0.3.0           R.methodsS3_1.8.1      tzdb_0.2.0            
[29] IRanges_2.28.0         GenomeInfoDb_1.30.1    parallel_4.1.2         fansi_1.0.2           
[33] Rcpp_1.0.8.3           readr_2.1.2            scales_1.1.1           S4Vectors_0.32.3      
[37] vroom_1.5.7            jsonlite_1.8.0         XVector_0.34.0         bit_4.0.4             
[41] gridExtra_2.3          hms_1.1.1              ggplot2_3.3.5          digest_0.6.29         
[45] stringi_1.7.6          dplyr_1.0.8            GenomicRanges_1.46.1   cli_3.2.0             
[49] tools_4.1.2            bitops_1.0-7           rhdf5filters_1.6.0     magrittr_2.0.2        
[53] RCurl_1.98-1.6         tibble_3.1.6           crayon_1.5.0           pkgconfig_2.0.3       
[57] ellipsis_0.3.2         data.table_1.14.2      assertthat_0.2.1       rstudioapi_0.13       
[61] viridis_0.6.2          Rhdf5lib_1.16.0        compiler_4.1.2
koustav-pal commented 2 years ago

Hi,

This is a past issue from Bioconductor 3.14. I believe this issue was fixed with Bioc 3.15 release. If you have not updated, please update your package to the latest bioconductor version

Thanks, K