Help with Error in gsvaParam(X, gs) : could not find function "gsvaParam"

[Chrisdoan9]

Hi team,

I run exactly as the vignette https://bioconductor.org/packages/devel/bioc/vignettes/GSVA/inst/doc/GSVA.html but got the error above after install and load the package. Would you please have a suggestion? Thank you so much!

gsvaPar <- gsvaParam(X, gs) Error in gsvaParam(X, gs) : could not find function "gsvaParam" R 4.2.1

[axelklenk]

Hi Chris,

parameter objects such as the one constructed by gsvaParam() are a recent addition to GSVA and were introduced in GSVA 1.50.0 in Bioconductor 3.18, released in October 2023 and matching R 4.3.

As you can see here (https://bioconductor.org/about/release-announcements/) your R version 4.2 matches Bioconductor versions 3.15 and 3.16, so BiocManager::install() in R 4.2.1 will likely install something like Bioconductor 3.16 and GSVA 1.46. You can easily check that by running packageVersion("GSVA") and/or packageVersion("BiocVersion")

For running the most recent version of the GSVA vignette you should update R to the latest version 4.3.2 and then upgrade your Bioconductor packages using BiocManager::install(version="3.18"). Other options include e.g. running the most recent R/Bioc/GSVA inside a docker container.

Hope this helps, otherwise please don't hesitate to get back to us.

[Chrisdoan9]

Thank you so much for a quick response! It takes a long time to install BiocManager::install(version="3.18"), still running after 2 hours. The console continue to print out things similar. Currently, I have R 4.3.1 on a server. Let see if it still work. Seem R 4.3.1 didn't work.

[rcastelo]

Dear Chris, if you are not succeeding to install GSVA in R 4.3.1 and you want us to help you, we need that you show us here the error messages that you are getting. Otherwise, we cannot help.

[Chrisdoan9]

Hi Robert, I can install GSVA in R 4 3.1. No error. So I plan to install R 4.3.2 to see if the error resolved.

[rcastelo]

Hi Chris, the current release version 3.18 of Bioconductor packages, including GSVA 1.50.0, should install and work fine with either R 4.3.0, 4.3.1 or 4.3.2; see https://bioconductor.org/install so any error that you may encounter with R 4.3.0 or 4.3.1 is unrelated with the R version. If installing R 4.3.2 resolves anything, it's probably more related to the fact of having a fresh new installation than the fact of changing the minor version of R. As I said in my previous message, if you encounter an error and need help to resolve it, we need you to copy & paste the error message here to be able to help you.

[Chrisdoan9]

Hi Robert, I got the same error on R 4.3.1. Bioconductor version 3.18.

gsvaPar <- gsvaParam(X, gs)
Error in gsvaParam(X, gs) : could not find function "gsvaParam"

[rcastelo]

hi Chris, could you shows us the output of the function sessionInfo() called right after the error?

[Chrisdoan9]

Hi Robert,

Sure. Not sure why it is quite long.

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: AlmaLinux 8.9 (Midnight Oncilla)

Matrix products: default
BLAS:   /share/pkg.8/r/4.3.1/install/lib64/R/lib/libRblas.so 
LAPACK: /share/pkg.8/r/4.3.1/install/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

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

other attached packages:
[1] GSVA_1.48.1

loaded via a namespace (and not attached):
  [1] DBI_1.2.1                   bitops_1.0-7                GSEABase_1.62.0             rlang_1.1.3                
  [5] magrittr_2.0.3              matrixStats_1.2.0           compiler_4.3.1              RSQLite_2.3.5              
  [9] DelayedMatrixStats_1.22.1   png_0.1-8                   vctrs_0.6.5                 stringr_1.5.1              
 [13] pkgconfig_2.0.3             crayon_1.5.2                fastmap_1.1.1               XVector_0.40.0             
 [17] utf8_1.2.4                  rmarkdown_2.22              sessioninfo_1.2.2           tzdb_0.4.0                 
 [21] graph_1.80.0                purrr_1.0.2                 bit_4.0.5                   xfun_0.42                  
 [25] zlibbioc_1.48.0             cachem_1.0.8                beachmat_2.16.0             GenomeInfoDb_1.38.6        
 [29] blob_1.2.4                  rhdf5filters_1.14.1         DelayedArray_0.26.3         Rhdf5lib_1.24.2            
 [33] BiocParallel_1.36.0         tweenr_2.0.2                irlba_2.3.5.1               parallel_4.3.1             
 [37] R6_2.5.1                    stringi_1.8.3               limma_3.58.1                GenomicRanges_1.52.0       
 [41] Rcpp_1.0.12                 SummarizedExperiment_1.30.2 knitr_1.45                  readr_2.1.4                
 [45] IRanges_2.36.0              Matrix_1.6-5                tidyselect_1.2.0            rstudioapi_0.15.0          
 [49] abind_1.4-7                 yaml_2.3.8                  codetools_0.2-19            lattice_0.22-5             
 [53] tibble_3.2.1                Biobase_2.62.0              withr_3.0.0                 KEGGREST_1.40.0            
 [57] evaluate_0.23               polyclip_1.10-6             Biostrings_2.68.1           pillar_1.9.0               
 [61] BiocManager_1.30.22         MatrixGenerics_1.14.0       stats4_4.3.1                generics_0.1.3             
 [65] RCurl_1.98-1.14             S4Vectors_0.40.2            hms_1.1.3                   ggplot2_3.4.4              
 [69] sparseMatrixStats_1.14.0    munsell_0.5.0               scales_1.3.0                xtable_1.8-6               
 [73] glue_1.7.0                  tools_4.3.1                 ScaledMatrix_1.8.1          annotate_1.78.0            
 [77] XML_3.99-0.16.1             rhdf5_2.46.1                grid_4.3.1                  tidyr_1.3.0                
 [81] AnnotationDbi_1.62.1        colorspace_2.1-1            SingleCellExperiment_1.22.0 GenomeInfoDbData_1.2.11    
 [85] BiocSingular_1.16.0         ggforce_0.4.1               HDF5Array_1.28.1            cli_3.6.2                  
 [89] rsvd_1.0.5                  fansi_1.0.6                 S4Arrays_1.2.0              dplyr_1.1.4                
 [93] gtable_0.3.4                digest_0.6.34               BiocGenerics_0.48.1         farver_2.1.1               
 [97] memoise_2.0.1               htmltools_0.5.7             lifecycle_1.0.4             httr_1.4.7                 
[101] statmod_1.5.0               bit64_4.0.5                 MASS_7.3-60.0.1          

[rcastelo]

Hi, your session information dumps information on all the packages that are loaded in your R session, including their version, which is useful to diagnose problems. In our case, The release version of GSVA is 1.50.0, however the session information indicates that you have GSVA 1.48.1, which belongs to the previous release. If you followed the instructions at https://bioconductor.org/packages/GSVA to install GSVA, you should have done:

BiocManager::install("GSVA")

and this instruction should have installed GSVA 1.50.0 on R 4.3.1. Two questions:

1. Did you use the instruction above to install GSVA?
2. Could you show us the output of BiocManager::valid()?

[Chrisdoan9]

Thank you so much! The error resolved. Not sure exactly what the cause is.