Possible function namespace related error

[combiz]

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]

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

Cheers,
Gabriel

[combiz]

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]

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]

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