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GabrielHoffman / variancePartition

Quantify and interpret divers of variation in multilevel gene expression experiments
http://gabrielhoffman.github.io/variancePartition/
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Possible function namespace related error #14

Closed combiz closed 4 years ago

combiz commented 4 years ago

The voomWithDreamWeights function fails after successfully running: -

> vobjDream <- variancePartition::voomWithDreamWeights( mat, model_formula, as.data.frame(SummarizedExperiment::colData(sce)) )
Memory usage to store result: >724.3 Mb
Dividing work into 100 chunks...
iteration: 100

Total:85 s
Error in variancePartition::voomWithDreamWeights(mat, model_formula, as.data.frame(SummarizedExperiment::colData(sce))) : 
  object 'design' not found

The error can be resolved by first loading the library with library(variancePartition). Seems like a possible namespace issue with design.

GabrielHoffman commented 4 years ago

Thanks for the bug report. Can you give me 1) a minimal reproducible example and 2) sessionInfo()

Cheers, Gabriel

combiz commented 4 years ago

Thanks for the quick reply. I've included the sessionInfo() below but will have to get back to you on the reproducible example. That said, the source code at https://github.com/GabrielHoffman/variancePartition/blob/master/R/voomWithDreamWeights.R references an out of scope 'design' object so this should be reproducible for anyone running the function with a namespace prefix without loading the library. Cheers.

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
[1] variancePartition_1.16.1 Biobase_2.46.0           BiocGenerics_0.32.0      scales_1.1.1             foreach_1.5.0            limma_3.42.2            
[7] ggplot2_3.3.0            magrittr_1.5             scFlow_0.5.0            

loaded via a namespace (and not attached):
  [1] rgl_0.100.54                rsvd_1.0.3                  Hmisc_4.4-0                 ica_1.0-2                   svglite_1.2.3              
  [6] class_7.3-15                lmtest_0.9-37               crayon_1.3.4                jcolors_0.0.4               MASS_7.3-51.6              
 [11] MAST_1.13.6                 nlme_3.1-144                backports_1.1.7             monocle3_0.2.1.1            rlang_0.4.6                
 [16] caret_6.0-86                XVector_0.26.0              bib2df_1.1.1                ROCR_1.0-11                 readxl_1.3.1               
 [21] irlba_2.3.3                 nloptr_1.2.2.1              scater_1.14.6               apcluster_1.4.8             qs_0.21.2                  
 [26] BiocParallel_1.20.1         rjson_0.2.20                manipulateWidget_0.10.1     bit64_0.9-7                 glue_1.4.1                 
 [31] rngtools_1.5                sctransform_0.2.1           pbkrtest_0.4-8.6            vipor_0.4.5                 AnnotationDbi_1.48.0       
 [36] UpSetR_1.4.0                HGNChelper_0.8.1            haven_2.2.0                 tidyselect_1.1.0            SummarizedExperiment_1.16.1
 [41] liger_0.5.0.9000            rio_0.5.16                  fitdistrplus_1.0-14         XML_3.99-0.3                tidyr_1.0.3                
 [46] zoo_1.8-8                   packrat_0.5.0               ggpubr_0.3.0                xtable_1.8-4                orthopolynom_1.0-5         
 [51] formattable_0.2.0.1         evaluate_0.14               gdtools_0.2.2               cli_2.0.2                   zlibbioc_1.32.0            
 [56] rstudioapi_0.11             doRNG_1.8.2                 miniUI_0.1.1.1              whisker_0.4                 rpart_4.1-15               
 [61] maps_3.3.0                  shiny_1.4.0.2               BiocSingular_1.2.2          xfun_0.13                   askpass_1.1                
 [66] cluster_2.1.0               caTools_1.18.0              doSNOW_1.0.18               KEGGREST_1.26.1             tibble_3.0.1               
 [71] ggrepel_0.8.2               threejs_0.3.3               ape_5.3                     listenv_0.8.0               Biostrings_2.54.0          
 [76] png_0.1-7                   future_1.17.0               withr_2.2.0                 ipred_0.9-9                 bitops_1.0-6               
 [81] plyr_1.8.6                  cellranger_1.1.0            nVennR_0.2.2                pROC_1.16.2                 dqrng_0.2.1                
 [86] pillar_1.4.4                RcppParallel_5.0.1          gplots_3.0.3                graphite_1.32.0             paletteer_1.1.0            
 [91] DelayedMatrixStats_1.8.0    vctrs_0.3.0                 ellipsis_0.3.1              generics_0.0.2              lava_1.6.7                 
 [96] RApiSerialize_0.1.0         tools_3.6.3                 foreign_0.8-75              beeswarm_0.2.3              munsell_0.5.0              
[101] DelayedArray_0.12.3         fastmap_1.0.1               compiler_3.6.3              abind_1.4-5                 httpuv_1.5.2               
[106] scico_1.1.0                 plotly_4.9.2.1              prodlim_2019.11.13          GenomeInfoDbData_1.2.2      gridExtra_2.3              
[111] enrichR_2.1                 edgeR_3.28.1                riverplot_0.6               lattice_0.20-40             snow_0.4-3                 
[116] later_1.0.0                 dplyr_0.8.5                 recipes_0.1.12              BiocFileCache_1.10.2        humaniformat_0.6.0         
[121] jsonlite_1.6.1              kBET_0.99.6                 graph_1.64.0                pbapply_1.4-2               carData_3.0-3              
[126] genefilter_1.68.0           lazyeval_0.2.2              promises_1.1.0              car_3.0-7                   doParallel_1.0.15          
[131] latticeExtra_0.6-29         R.utils_2.9.2               reticulate_1.15             checkmate_2.0.0             rmarkdown_2.1              
[136] openxlsx_4.1.5              sandwich_2.5-1              cowplot_1.0.0               statmod_1.4.34              webshot_0.5.2              
[141] Rtsne_0.15                  forcats_0.5.0               dichromat_2.0-0             uwot_0.1.8                  igraph_1.2.5               
[146] HDF5Array_1.14.4            survival_3.1-11             systemfonts_0.2.2           htmltools_0.4.0             memoise_1.1.0              
[151] Seurat_3.1.5                locfit_1.5-9.4              IRanges_2.20.2              viridisLite_0.3.0           digest_0.6.25              
[156] assertthat_0.2.1            mime_0.9                    rappdirs_0.3.1              npsurv_0.4-0.1              palr_0.2.0                 
[161] pals_1.6                    RSQLite_2.2.0               future.apply_1.5.0          lsei_1.2-0.1                mapproj_1.2.7              
[166] data.table_1.12.8           blob_1.2.1                  S4Vectors_0.24.4            R.oo_1.23.0                 splines_3.6.3              
[171] Formula_1.2-3               rematch2_2.1.2              Rhdf5lib_1.8.0              RCurl_1.98-1.2              broom_0.5.6                
[176] hms_0.5.3                   rhdf5_2.30.1                colorspace_1.4-1            DropletUtils_1.6.1          base64enc_0.1-3            
[181] WebGestaltR_0.4.3           ggbeeswarm_0.6.0            GenomicRanges_1.38.0        maxLik_1.3-8                nnet_7.3-13                
[186] Rcpp_1.0.4.6                mclust_5.4.6                RANN_2.6.1                  fansi_0.4.1                 ModelMetrics_1.2.2.2       
[191] R6_2.4.1                    grid_3.6.3                  acepack_1.4.1               ggridges_0.5.2              lifecycle_0.2.0            
[196] DoubletFinder_2.0.2         oompaBase_3.2.9             zip_2.0.4                   miscTools_0.6-26            curl_4.3                   
[201] ggsignif_0.6.0              minqa_1.2.4                 gdata_2.18.0                leiden_0.3.3                leaflet_2.0.3              
[206] Matrix_1.2-18               uniftest_1.1                RcppAnnoy_0.0.16            RColorBrewer_1.1-2          iterators_1.0.12           
[211] ROntoTools_2.14.0           gower_0.2.1                 stringr_1.4.0               htmlwidgets_1.5.1           biomaRt_2.42.1             
[216] purrr_0.3.4                 DirichletReg_0.6-3.1        crosstalk_1.1.0.1           globals_0.12.5              openssl_1.4.1              
[221] htmlTable_1.13.3            patchwork_1.0.0.9000        KEGGgraph_1.46.0            lubridate_1.7.8             codetools_0.2-16           
[226] matrixStats_0.56.0          FNN_1.1.3                   gtools_3.8.2                EWCE_0.99.2                 prettyunits_1.1.1          
[231] SingleCellExperiment_1.8.0  dbplyr_1.4.3                R.methodsS3_1.8.0           GenomeInfoDb_1.22.1         gtable_0.3.0               
[236] tsne_0.1-3                  DBI_1.1.0                   stats4_3.6.3                httr_1.4.1                  KernSmooth_2.23-16         
[241] stringi_1.4.6               progress_1.2.2              reshape2_1.4.4              english_1.2-5               annotate_1.64.0            
[246] viridis_0.5.1               Rgraphviz_2.30.0            timeDate_3043.102           colorRamps_2.3              ggdendro_0.1-20            
[251] boot_1.3-24                 BiocNeighbors_1.4.2         lme4_1.1-23                 geneplotter_1.64.0          readr_1.3.1                
[256] DESeq2_1.26.0               bit_1.1-15.2                jpeg_0.1-8.1                pkgconfig_2.0.3             rstatix_0.5.0              
[261] knitr_1.28
GabrielHoffman commented 4 years ago

You are using v1.16.1. Looking at my notes, I fixed this in v1.17.2. The current version is v1.19.1 from an hour ago. Can you try that?

I am working on fixing a few small bugs in the Bioconductor release

combiz commented 4 years ago

All working fine in the latest github (1.19.1). Thanks again, and great work on the package and documentation.