error object 'normalize_names_replacement_value' not found

[weibei43]

Hi, I encountered the problem with using SummarizedExperiment version 1.16.1. The error message is "Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'normalize_names_replacement_value' not found".

I am using R 3.6.1 on my mac system Catalina 10.15.1. The SummarizedExperiment version is 1.16.1

Thank you in advance for your support!

[weibei43]

Yes, the BiocManager::valid() output is TRUE

[LiNk-NY]

Hi WeiBei, @weibei43 In order to best help you, we would require a minimally reproducible example.

Please make sure that you are using the appropriate version of Bioconductor and are installing packages using BiocManager::install.

Please see the recommendations for a minimal reproducible example outlined in this page: https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example Best, Marcel

[hpages]

Please provide your sessionInfo(). Thanks!

[weibei43]

Hi, The sessionInfo() is R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] presto_1.0.0 Rcpp_1.0.3 gtable_0.3.0 nabor_0.5.0 Seurat_3.1.4
[6] ggrastr_0.1.7 gridExtra_2.3 Rsamtools_2.2.3 BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.54.0
[11] rtracklayer_1.46.0 Biostrings_2.54.0 XVector_0.26.0 ArchR_0.1.8 magrittr_1.5
[16] rhdf5_2.30.1 Matrix_1.2-18 data.table_1.12.8 SummarizedExperiment_1.16.1 DelayedArray_0.12.2
[21] BiocParallel_1.20.1 matrixStats_0.55.0 Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.0
[26] IRanges_2.20.2 S4Vectors_0.24.3 BiocGenerics_0.32.0 ggplot2_3.3.0

loaded via a namespace (and not attached): [1] backports_1.1.5 sn_1.5-5 plyr_1.8.6 igraph_1.2.4.2 lazyeval_0.2.2 splines_3.6.1 listenv_0.8.0
[8] usethis_1.5.1 TH.data_1.0-10 digest_0.6.25 htmltools_0.4.0 gdata_2.18.0 fansi_0.4.1 memoise_1.1.0
[15] cluster_2.1.0 ROCR_1.0-7 remotes_2.1.1 globals_0.12.5 RcppParallel_4.4.4 sandwich_2.5-1 prettyunits_1.1.1
[22] colorspace_1.4-1 ggrepel_0.8.1 dplyr_0.8.4 callr_3.4.2 crayon_1.3.4 RCurl_1.98-1.1 jsonlite_1.6.1
[29] survival_3.1-8 zoo_1.8-7 ape_5.3 glue_1.3.1 zlibbioc_1.32.0 leiden_0.3.3 pkgbuild_1.0.6
[36] Rhdf5lib_1.8.0 future.apply_1.4.0 scales_1.1.0 mvtnorm_1.1-0 bibtex_0.4.2.2 metap_1.3 plotrix_3.7-7
[43] viridisLite_0.3.0 reticulate_1.14 rsvd_1.0.3 tsne_0.1-3 htmlwidgets_1.5.1 httr_1.4.1 gplots_3.0.3
[50] RColorBrewer_1.1-2 TFisher_0.2.0 ellipsis_0.3.0 ica_1.0-2 pkgconfig_2.0.3 XML_3.99-0.3 farver_2.0.3
[57] uwot_0.1.5 tidyselect_1.0.0 labeling_0.3 rlang_0.4.5 reshape2_1.4.3 munsell_0.5.0 tools_3.6.1
[64] cli_2.0.2 devtools_2.2.2 ggridges_0.5.2 stringr_1.4.0 npsurv_0.4-0 fs_1.3.2 processx_3.4.2
[71] fitdistrplus_1.0-14 caTools_1.18.0 purrr_0.3.3 RANN_2.6.1 pbapply_1.4-2 future_1.16.0 nlme_3.1-145
[78] compiler_3.6.1 rstudioapi_0.11 plotly_4.9.2 png_0.1-7 testthat_2.3.2 lsei_1.2-0 tibble_2.1.3
[85] stringi_1.4.6 ps_1.3.2 desc_1.2.0 RSpectra_0.16-0 lattice_0.20-40 multtest_2.42.0 vctrs_0.2.3
[92] mutoss_0.1-12 pillar_1.4.3 lifecycle_0.1.0 BiocManager_1.30.10 Rdpack_0.11-1 lmtest_0.9-37 RcppAnnoy_0.0.15
[99] cowplot_1.0.0 bitops_1.0-6 irlba_2.3.3 gbRd_0.4-11 patchwork_1.0.0 R6_2.4.1 KernSmooth_2.23-16
[106] sessioninfo_1.1.1 codetools_0.2-16 pkgload_1.0.2 MASS_7.3-51.5 gtools_3.8.1 assertthat_0.2.1 rprojroot_1.3-2
[113] withr_2.1.2 GenomicAlignments_1.22.1 sctransform_0.2.1 mnormt_1.5-6 multcomp_1.4-12 GenomeInfoDbData_1.2.2 tidyr_1.0.2
[120] Cairo_1.5-10 Rtsne_0.15 numDeriv_2016.8-1.1

I figured out the error is caused by "colnames(pse) <- names(matchObj[[1]])" when I tried to assign the column names to the summarizedexperiment object "pse"

[hpages]

I figured out the error is caused by "colnames(pse) <- names(matchObj[[1]])" when I tried to assign the column names to the summarizedexperiment object "pse"

Unfortunately that is not what we call a "reproducible example". A reproducible example is a small snippet of code that we can run on our side by just copy/past'ing it in our R session and that hopefully reproduces the problem. Do you think you can provide that, or something as close as possible from that? Thanks!

[vjcitn]

my suspicion is that pse is an old serialized instance of a SummarizedExperiment. First run validObject(pse) and report result. Then see if pse2 <- updateObject(pse) leads to an object that you can use as desired.

[hpages]

Also it would be helpful if you could show the sessionInfo() you get right after running the minimal reproducible example that you come up with. That will trim the list of packages involved in the problem to its bare minimum which will probably be around 15-20 packages instead of the 140 packages you're showing above. Thx!

[hpages]

I'm saying this because normalize_names_replacement_value was replaced with normarg_names in S4Vectors in June 2019 and I don't see that any Bioconductor package is using it in BioC 3.10 (released in Oct 2019), which is what you're using. So either you still have one outdated package somewhere or the error is stemming from a non-Bioconductor package. Impossible to tell at the moment.

[weibei43]

Hi guys, It turned out that I need to update those packages by restarting the R program. Now everything is working. Thank you very much for your help!