Error invalid class object

Error invalid class object 780)?780:this.scrollWidth); max-width:780px; height: expression((parseInt(this.scrollHeight)>300)?300:this.scrollHeight); overflow: hidden; max-height:300px;»> Do not ask me about online cheats. I don’t know any and wont help finding them. Like my help? Join me on Patreon so i can keep helping Back to top omax Newbie cheater Joined: 29 May 2014Posts: 14Location: Jupiter Posted: Wed Sep […]
Instead of no_railgun_inaccuracy give sender and see if that works

Also, it’s most likely you haven’t defined a global variable named no_railgun_inaccuracy and assigned it the checkbox object, so i suggest getting the checkbox from the form it is on
E.g myformname.no_railgun_inaccuracy
_________________

780)?780:this.scrollWidth); max-width:780px; height: expression((parseInt(this.scrollHeight)>300)?300:this.scrollHeight); overflow: hidden; max-height:300px;»> Do not ask me about online cheats. I don’t know any and wont help finding them.

Like my help? Join me on Patreon so i can keep helping

Источник

FindNeighbors() error: invalid class “Graph” object: superclass «Mnumeric» not defined.. #4436

Initially ran into this error on a small 1k pbmc dataset, but was able to reproduce it using the dataset given for the Guided Clustering Tutorial using the exact same Rmd file. IIRC, the error popped up when attempting to knit the document (however, when assembling my custom Rmd file, the code chunks ran perfectly fine). Since attempting to knit the document, the error has persisted — even after restarts of both RStudio and Ubuntu. Perhaps worth mentioning that I recently updated Ubuntu and did a fresh install of R, RStudio, perhaps I am missing a package but it is not obvious to me with my limited experience with Seurat.

Error in validObject(.Object) : invalid class “Graph” object: superclass «Mnumeric» not defined in the environment of the object’s class

The text was updated successfully, but these errors were encountered:

HI! Same issue appeared on my macOS Catalina 10.15.7. not recalling if I updated anything. Perhaps just restarted my MAC.

Computing nearest neighbor graph Computing SNN Error in validObject(.Object) : invalid class “Graph” object: superclass «Mnumeric» not defined in the environment of the object’s class

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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 stats graphics grDevices utils datasets methods base

other attached packages:
[1] Signac_1.2.0 RColorBrewer_1.1-2 gtools_3.8.2 cowplot_1.1.1
[5] gridExtra_2.3 gplots_3.1.1 ggplot2_3.3.3 pheatmap_1.0.12
[9] SeuratObject_4.0.0 Seurat_4.0.1 dplyr_1.0.5

loaded via a namespace (and not attached):
[1] fastmatch_1.1-0 plyr_1.8.6 igraph_1.2.6
[4] lazyeval_0.2.2 splines_4.0.3 BiocParallel_1.24.1
[7] listenv_0.8.0 SnowballC_0.7.0 scattermore_0.7
[10] GenomeInfoDb_1.26.7 digest_0.6.27 htmltools_0.5.1.1
[13] fansi_0.4.2 magrittr_2.0.1 tensor_1.5
[16] cluster_2.1.2 ROCR_1.0-11 limma_3.46.0
[19] globals_0.14.0 Biostrings_2.58.0 matrixStats_0.58.0
[22] docopt_0.7.1 spatstat.sparse_2.0-0 colorspace_2.0-1
[25] ggrepel_0.9.1 sparsesvd_0.2 crayon_1.4.1
[28] RCurl_1.98-1.3 jsonlite_1.7.2 spatstat.data_2.1-0
[31] survival_3.2-11 zoo_1.8-9 ape_5.5
[34] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0
[37] zlibbioc_1.36.0 XVector_0.30.0 leiden_0.3.7
[40] future.apply_1.7.0 BiocGenerics_0.36.1 abind_1.4-5
[43] scales_1.1.1 DBI_1.1.1 edgeR_3.32.1
[46] miniUI_0.1.1.1 Rcpp_1.0.6 viridisLite_0.4.0
[49] xtable_1.8-4 tidytree_0.3.3 reticulate_1.20
[52] spatstat.core_2.1-2 stats4_4.0.3 htmlwidgets_1.5.3
[55] httr_1.4.2 ellipsis_0.3.2 ica_1.0-2
[58] pkgconfig_2.0.3 farver_2.1.0 ggseqlogo_0.1
[61] uwot_0.1.10 deldir_0.2-10 locfit_1.5-9.4
[64] utf8_1.2.1 labeling_0.4.2 tidyselect_1.1.1
[67] rlang_0.4.11 reshape2_1.4.4 later_1.2.0
[70] munsell_0.5.0 tools_4.0.3 generics_0.1.0
[73] ggridges_0.5.3 stringr_1.4.0 fastmap_1.1.0
[76] goftest_1.2-2 ggtree_2.4.2 fitdistrplus_1.1-3
[79] caTools_1.18.2 purrr_0.3.4 RANN_2.6.1
[82] pbapply_1.4-3 future_1.21.0 nlme_3.1-152
[85] mime_0.10 slam_0.1-48 RcppRoll_0.3.0
[88] aplot_0.0.6 compiler_4.0.3 rstudioapi_0.13
[91] plotly_4.9.3 png_0.1-7 spatstat.utils_2.1-0
[94] treeio_1.14.4 tibble_3.1.1 tweenr_1.0.2
[97] stringi_1.5.3 lattice_0.20-44 Matrix_1.3-3
[100] vctrs_0.3.8 pillar_1.6.0 lifecycle_1.0.0
[103] BiocManager_1.30.12 spatstat.geom_2.1-0 lmtest_0.9-38
[106] RcppAnnoy_0.0.18 data.table_1.14.0 bitops_1.0-7
[109] irlba_2.3.3 httpuv_1.6.0 patchwork_1.1.1
[112] GenomicRanges_1.42.0 R6_2.5.0 promises_1.2.0.1
[115] lsa_0.73.2 KernSmooth_2.23-20 IRanges_2.24.1
[118] parallelly_1.25.0 codetools_0.2-18 MASS_7.3-54
[121] assertthat_0.2.1 withr_2.4.2 qlcMatrix_0.9.7
[124] sctransform_0.3.2 Rsamtools_2.6.0 S4Vectors_0.28.1
[127] GenomeInfoDbData_1.2.4 mgcv_1.8-35 parallel_4.0.3
[130] rpart_4.1-15 tidyr_1.1.3 rvcheck_0.1.8
[133] Rtsne_0.15 ggforce_0.3.3 shiny_1.6.0

Hi, I’m also encountering the same issue, exact same command and error message. I installed Seurat in a fresh conda environment around 8 hours ago, and it worked fine. I then installed Scater, and suddenly I’m getting this error message. Perhaps there’s specific dependency causing an issue?

R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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

other attached packages:
[1] SeuratObject_4.0.0 Seurat_4.0.1

loaded via a namespace (and not attached):
[1] nlme_3.1-152 spatstat.sparse_2.0-0 matrixStats_0.58.0
[4] RcppAnnoy_0.0.18 RColorBrewer_1.1-2 httr_1.4.2
[7] repr_1.1.3 sctransform_0.3.2 tools_4.0.3
[10] utf8_1.2.1 R6_2.5.0 irlba_2.3.3
[13] rpart_4.1-15 KernSmooth_2.23-20 uwot_0.1.10
[16] mgcv_1.8-35 DBI_1.1.1 lazyeval_0.2.2
[19] colorspace_2.0-1 tidyselect_1.1.1 gridExtra_2.3
[22] compiler_4.0.3 plotly_4.9.3 scales_1.1.1
[25] spatstat.data_2.1-0 lmtest_0.9-38 ggridges_0.5.3
[28] pbapply_1.4-3 goftest_1.2-2 pbdZMQ_0.3-5
[31] stringr_1.4.0 digest_0.6.27 spatstat.utils_2.1-0
[34] base64enc_0.1-3 pkgconfig_2.0.3 htmltools_0.5.1.1
[37] parallelly_1.25.0 fastmap_1.1.0 htmlwidgets_1.5.3
[40] rlang_0.4.11 shiny_1.6.0 generics_0.1.0
[43] zoo_1.8-9 jsonlite_1.7.2 ica_1.0-2
[46] dplyr_1.0.5 magrittr_2.0.1 patchwork_1.1.1
[49] Matrix_1.3-3 Rcpp_1.0.6 IRkernel_1.1.1
[52] munsell_0.5.0 fansi_0.4.2 abind_1.4-5
[55] reticulate_1.20 lifecycle_1.0.0 stringi_1.5.3
[58] MASS_7.3-54 Rtsne_0.15 plyr_1.8.6
[61] grid_4.0.3 parallel_4.0.3 listenv_0.8.0
[64] promises_1.2.0.1 ggrepel_0.9.1 crayon_1.4.1
[67] deldir_0.2-10 miniUI_0.1.1.1 lattice_0.20-44
[70] IRdisplay_1.0 cowplot_1.1.1 splines_4.0.3
[73] tensor_1.5 pillar_1.6.0 igraph_1.2.6
[76] uuid_0.1-4 spatstat.geom_2.1-0 future.apply_1.7.0
[79] reshape2_1.4.4 codetools_0.2-18 leiden_0.3.7
[82] glue_1.4.2 evaluate_0.14 data.table_1.14.0
[85] png_0.1-7 vctrs_0.3.8 httpuv_1.6.0
[88] polyclip_1.10-0 spatstat.core_2.1-2 gtable_0.3.0
[91] RANN_2.6.1 purrr_0.3.4 tidyr_1.1.3
[94] scattermore_0.7 future_1.21.0 assertthat_0.2.1
[97] ggplot2_3.3.3 mime_0.10 xtable_1.8-4
[100] later_1.2.0 viridisLite_0.4.0 survival_3.2-11
[103] tibble_3.1.1 cluster_2.1.2 globals_0.14.0
[106] fitdistrplus_1.1-3 ellipsis_0.3.2 ROCR_1.0-11

I believe it’s a problem related to the latest version of the Matrix package (1.3-3). I updated my packages today and ran into the same error message. Searching the web, I found this issue associating a similar error with the Matrix package. Downgrading for version 1.3-2 solved the problem.

A modification related to ‘Mnumeric’ is mentioned in the description of the update (https://cloud.r-project.org/web/packages/Matrix/news.html):
«removed the nowhere used (and unexported but still active) class union «Mnumeric» which actually trickled into many base classes properties. Notably would it break validity of factor with a proposed change in validity checking, as factors were also «Mnumeric» but did not fulfill its validity method.»

Super detective work @ftencaten 😎

Very useful, thanks! And do not forget to restart your Rstudio. 😎

Источник

Error: invalid class»otu_table» object #1225

I ran this command — ps.ctrls

The text was updated successfully, but these errors were encountered:

I have figured this out. It worked after some trials

Hello,
I am experiencing the same issue. Can you provide some insight into what the problem was/what you changed?

I have to provide the correct variable in which I stored my OTU_table. So when I put the right variable in the above code, it ran successfully .

I have it working now also. Thank you so much for the help.

Hi
I am doing some microbiome analysis I am in the filtering step after the decontam and I got to this error that I can’t find any solution. Could you help me with that? After the following code, I get the error

filter for relative abundance

transform to relative abundance

pst 1e-5, TRUE)
Error in validObject(.Object) : invalid class “otu_table” object:
OTU abundance data must have non-zero dimensions.

I thought there was a problem in my pst but here is the info of it:
phyloseq-class experiment-level object
otu_table() OTU Table: [ 3377 taxa and 51 samples ]
sample_data() Sample Data: [ 51 samples by 3 sample variables ]
tax_table() Taxonomy Table: [ 3377 taxa by 6 taxonomic ranks ]

Any help would be very appreciatted.
Thank you

@aff30 This looks like an issue with the phyloseq package rather than the dada2 package, you might want to look at the phyloseq site.

I don’t know what is going on, but I’d start by taking a look at the logical vector that filter_taxa makes, to see if it sensible or if perhaps every taxa is being removed or something.

Источник

Invalid class dgCMatrix object #2

Trying to load a MAT file with objects of two classes — double & cell.

The variables shown in the image belong to the following classes:

  • X , Y , Y2 — double (sparse matrices)
  • all_sentiments — double (vector)
  • all_genres — cell

Hi,

Initially ran into this error on a small 1k pbmc dataset, but was able to reproduce it using the dataset given for the Guided Clustering Tutorial using the exact same Rmd file. IIRC, the error popped up when attempting to knit the document (however, when assembling my custom Rmd file, the code chunks ran perfectly fine). Since attempting to knit the document, the error has persisted — even after restarts of both RStudio and Ubuntu. Perhaps worth mentioning that I recently updated Ubuntu and did a fresh install of R, RStudio, perhaps I am missing a package but it is not obvious to me with my limited experience with Seurat.

line 267:

pbmc <- FindNeighbors(pbmc, dims = 1:10) # <- problem line
pbmc <- FindClusters(pbmc, resolution = 0.5)

# Look at cluster IDs of the first 5 cells
head(Idents(pbmc), 5)

Error:

Error in validObject(.Object) : invalid class “Graph” object: superclass «Mnumeric» not defined in the environment of the object’s class

Traceback:

13. stop(msg, ": ", errors, domain = NA)
12. validObject(.Object)
11. .nextMethod(.Object = .Object, ... = ...)
10. callNextMethod()
9. initialize(value, ...)
8. initialize(value, ...)
7. new(Class = "Graph", i = c(0L, 6L, 102L, 203L, 292L, 421L, 451L, 511L, 547L, 618L, 651L, 767L, 963L, 978L, 1005L, 1043L, 1148L, 1156L, 1264L, 1337L, 1338L, 1385L, 1504L, 1554L, 1573L, 1620L, 1695L, 1851L, 1904L, 1991L, 2079L, 2136L, 2187L, 2296L, 2317L, ...
6. do.call(what = "new", args = object.list)
5. UpdateSlots(object = object)
4. `DefaultAssay<-.Graph`(object = `*tmp*`, value = assay)
3. `DefaultAssay<-`(object = `*tmp*`, value = assay)
2. FindNeighbors.Seurat(pbmc, dims = 1:10)
1. FindNeighbors(pbmc, dims = 1:10)

> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
[1] SeuratObject_4.0.0 dplyr_1.0.5        patchwork_1.1.1    Seurat_4.0.1      

loaded via a namespace (and not attached):
  [1] nlme_3.1-152          spatstat.sparse_2.0-0 matrixStats_0.58.0    RcppAnnoy_0.0.18      RColorBrewer_1.1-2    httr_1.4.2            sctransform_0.3.2    
  [8] tools_4.0.5           utf8_1.2.1            R6_2.5.0              irlba_2.3.3           rpart_4.1-15          KernSmooth_2.23-20    uwot_0.1.10          
 [15] mgcv_1.8-35           DBI_1.1.1             lazyeval_0.2.2        colorspace_2.0-1      withr_2.4.2           tidyselect_1.1.1      gridExtra_2.3        
 [22] compiler_4.0.5        cli_2.5.0             plotly_4.9.3          labeling_0.4.2        scales_1.1.1          spatstat.data_2.1-0   lmtest_0.9-38        
 [29] ggridges_0.5.3        pbapply_1.4-3         goftest_1.2-2         stringr_1.4.0         digest_0.6.27         spatstat.utils_2.1-0  rmarkdown_2.7        
 [36] pkgconfig_2.0.3       htmltools_0.5.1.1     parallelly_1.25.0     fastmap_1.1.0         htmlwidgets_1.5.3     rlang_0.4.11          rstudioapi_0.13      
 [43] shiny_1.6.0           farver_2.1.0          generics_0.1.0        zoo_1.8-9             jsonlite_1.7.2        ica_1.0-2             magrittr_2.0.1       
 [50] Matrix_1.3-3          Rcpp_1.0.6            munsell_0.5.0         fansi_0.4.2           abind_1.4-5           reticulate_1.20       lifecycle_1.0.0      
 [57] stringi_1.5.3         yaml_2.2.1            MASS_7.3-54           Rtsne_0.15            plyr_1.8.6            grid_4.0.5            parallel_4.0.5       
 [64] listenv_0.8.0         promises_1.2.0.1      ggrepel_0.9.1         crayon_1.4.1          deldir_0.2-10         miniUI_0.1.1.1        lattice_0.20-44      
 [71] cowplot_1.1.1         splines_4.0.5         tensor_1.5            knitr_1.33            pillar_1.6.0          igraph_1.2.6          spatstat.geom_2.1-0  
 [78] future.apply_1.7.0    reshape2_1.4.4        codetools_0.2-18      leiden_0.3.7          glue_1.4.2            evaluate_0.14         data.table_1.14.0    
 [85] png_0.1-7             vctrs_0.3.8           httpuv_1.6.0          polyclip_1.10-0       gtable_0.3.0          RANN_2.6.1            purrr_0.3.4          
 [92] spatstat.core_2.1-2   tidyr_1.1.3           scattermore_0.7       future_1.21.0         assertthat_0.2.1      ggplot2_3.3.3         xfun_0.22            
 [99] mime_0.10             xtable_1.8-4          later_1.2.0           survival_3.2-11       viridisLite_0.4.0     tibble_3.1.1          tinytex_0.31         
[106] cluster_2.1.2         globals_0.14.0        fitdistrplus_1.1-3    ellipsis_0.3.2        ROCR_1.0-11  

I’m currently working on some code that needs to get some properties from the Win32_OperatingSystem class and have some code that looks like the following:

var managmentObject = new System.Management.ManagementObject("Win32_OperatingSystem.Name='TotalVirtualMemorySize'");
var memory = (ulong) managmentObject["TotalVirtualMemorySize"]*1024ul;

This code is more or less the same as the sample provided in this answer, but I have been getting a System.Managment.ManagmentException with the message «Invalid class» when I run it. Any ideas what might be going on?

Community's user avatar

asked Feb 27, 2015 at 20:10

rjzii's user avatar

Use "Win32_OperatingSystem=@" to get the current instance of the Win32_OperatingSystem class. @ means that an object is singleton, which is mentioned towards the bottom of the MSDN documentation in the «Remarks» section.

For info about paths in WMI please read Describing an Instance Object Path.

rjzii's user avatar

rjzii

14.1k12 gold badges83 silver badges119 bronze badges

answered Feb 27, 2015 at 20:59

Yoh Deadfall's user avatar

Yoh DeadfallYoh Deadfall

2,7037 gold badges29 silver badges32 bronze badges

3

As Yoh Deadfall said and also mentioned here,Win32_OperatingSystem is a singleton class. To get the single instance, use «@» for the key.

var managmentObject = new ManagementObject("Win32_OperatingSystem=@");
var memory = (ulong)managmentObject["TotalVirtualMemorySize"] * 1024ul;

answered Feb 27, 2015 at 21:41

Vinkal's user avatar

VinkalVinkal

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DESeq2: error invalid class SummarizedExperiment object when creating DESeqDataSetFromMatrix

@jillianwaters-14491

Last seen 2.8 years ago

Hello,

I am trying to create the DESeqDataSetFromMatrix, and am receiving an error that there is an invalid class «summarizedExperiment» object. I initially thought there was something wrong with my input files, but I receive the same errors when I use the Pasilla dataset and enter in all code as outlined in the instructions here (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#quick-start)

I have entered the input and full error below, as well as the sessionInfo().

Thank you for any help with this!

library("DESeq2")

dds <- DESeqDataSetFromMatrix(countData = cts,

                              colData = coldata,

                              design = ~ condition)

dds
Error in validObject(.Object): invalid class “SummarizedExperiment” object: undefined class for slot "NAMES" ("characterORNULL")
Traceback:

1. DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~condition)
2. SummarizedExperiment(assays = SimpleList(counts = countData),
.     colData = colData, ...)
3. SummarizedExperiment(assays = SimpleList(counts = countData),
.     colData = colData, ...)
4. .local(assays, ...)
5. new_SummarizedExperiment(assays, ans_rownames, rowData, colData,
.     metadata)
6. new("SummarizedExperiment", NAMES = names, elementMetadata = rowData,
.     colData = colData, assays = assays, metadata = as.list(metadata))
7. initialize(value, ...)
8. initialize(value, ...)
9. validObject(.Object)
10. stop(msg, ": ", errors, domain = NA)
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /ebio/abt3_projects/Christensenella_Project/anaconda3/envs/R_DEseq2/lib/R/lib/libRblas.so
LAPACK: /ebio/abt3_projects/Christensenella_Project/anaconda3/envs/R_DEseq2/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
 [1] BiocInstaller_1.28.0       BiocParallel_1.12.0       
 [3] DESeq2_1.18.1              SummarizedExperiment_1.4.0
 [5] Biobase_2.38.0             GenomicRanges_1.30.0      
 [7] GenomeInfoDb_1.14.0        IRanges_2.12.0            
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0       
[11] ggplot2_2.2.1              tidyr_0.6.3               
[13] dplyr_0.7.0               

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1          Rcpp_0.12.13            lattice_0.20-34        
 [4] assertthat_0.2.0        digest_0.6.12           IRdisplay_0.4.4        
 [7] R6_2.2.1                plyr_1.8.4              repr_0.10              
[10] acepack_1.4.1           RSQLite_1.1-2           evaluate_0.10          
[13] zlibbioc_1.24.0         rlang_0.1.2             lazyeval_0.2.0         
[16] uuid_0.1-2              annotate_1.56.0         rpart_4.1-10           
[19] Matrix_1.2-7.1          splines_3.4.1           geneplotter_1.56.0     
[22] stringr_1.2.0           foreign_0.8-67          RCurl_1.95-4.8         
[25] munsell_0.4.3           compiler_3.4.1          nnet_7.3-12            
[28] tibble_1.3.3            GenomeInfoDbData_0.99.1 Hmisc_3.14-6           
[31] XML_3.98-1.6            crayon_1.3.2            bitops_1.0-6           
[34] grid_3.4.1              jsonlite_1.5            xtable_1.8-2           
[37] gtable_0.2.0            DBI_0.6-1               magrittr_1.5           
[40] scales_0.4.1            stringi_1.1.2           XVector_0.18.0         
[43] genefilter_1.60.0       latticeExtra_0.6-28     IRkernel_0.7.1         
[46] Formula_1.2-1           RColorBrewer_1.1-2      tools_3.4.1            
[49] glue_1.1.1              survival_2.40-1         AnnotationDbi_1.40.0   
[52] colorspace_1.3-2        cluster_2.0.6           memoise_1.1.0          
[55] pbdZMQ_0.2-6 

deseq2

• 3.5k views

@martin-morgan-1513

Last seen 3 days ago

United States

Usually this is a problem associated with package versions from different Bioconductor releases; what does BiocInstaller::biocValid() say? If it looks clean, I’d suggest re-installing the packages (via biocLite()) SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, XVector.

@mikelove

Last seen 1 hour ago

United States

Can you run biocLite() and update all packages until you get no errors from biocValid()? 

I can see you have an old version of SummarizedExperiment (the current version is 1.8). Bioconductor packages are designed to work all together based on consistent releases.

In the past, this error came up when there were mixed versions of software on the machine:

DESeqDataSetFromTximport: Error in checkSlotAssignment

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355 votes

1 answers

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I am new to PHP and I’m trying to make a function that can insert any arguments given in the param into a table specified also as a param of the function, but when I execute my code it says:

call_user_func_array() expects parameter 1 to be a valid callback, first array member is not a valid class name or object

here is my code:

function insert($table, $args){
    
    $Query = "INSERT INTO ? VALUES(";
    $types="";
    foreach($args as $arg){
        $Query=$Query."?,";
        $type = gettype($arg);
        switch ($type) {
            case "string": 
                $types = $types."s";
                break;
            case "integer": 
            case "double": 
                $types = $types."d";
                break; 
        }
    }
    $Query=substr($Query, 0, -1);
    $Query=$Query.")";
    global $mysqli;
    $stmt=$mysqli->prepare($Query);
    echo $stmt;
    array_unshift($args, $table);
    array_unshift($args, $types);

    call_user_func_array(array($stmt, "bind_param"), $args);
    $stmt->execute();
}

so what’s wrong here and thank you?

2021-11-24

Write your answer


710

votes

Answer

Solution:

Why, oh why would you want to create such function?

Don’t even think about creating such complex and utterly useless function. This will be your nightmare. Trust my advice and stop what you are doing right now.

If you are only starting with PHP then forget about mysqli. It is missing a lot of functionality and is very complex. Start learning PDO.

With PDO you do not need such functions.

Start by opening PDO connection:

$pdo = new PDO("mysql:host=localhost;dbname=db_name;charset=utf8mb4", 'username', 'password', [
    PDO::ATTR_ERRMODE => PDO::ERRMODE_EXCEPTION,
    PDO::ATTR_EMULATE_PREPARES => false
]);

Then you can execute a simple statement like this:

$pdo->prepare('INSERT INTO tableA(col1, col2) VALUES(?,?)')
    ->execute(['val1', 'val2']);

Binding unknown number of parameters is also quite simple.

$stmt = $pdo->prepare('SELECT * FROM TableA WHERE Id IN ('.implode(',', array_fill(0, count($ids), '?')).')');
$stmt->execute($ids);
$data = $stmt->fetchAll();

Just take a look how much simpler it is compared to your custom function.


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Date the issue was resolved:

2021-11-24

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 — I am purging inactive userprofiles from 2012r2 RDS Collection host servers using powershell. 

 — Out of six servers, the command I’m using works on all but one.

 — All servers are Windows Server 2012r2 and have the exact same patching level, and are running Powershell 4.0

Here is the full syntax:    Get-CimInstance -Class Win32_UserProfile | Where-Object { $_.LocalPath.split(»)[-1] -eq ‘USERPROFILE’ } | Remove-CimInstance

Here is the resulting output: 

Get-CimInstance : Invalid class
At line:1 char:1
+ Get-CimInstance -Class Win32_UserProfile | Where-Object { $_.LocalPath.split(» …
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : MetadataError: (rootcimv2:Win32_UserProfile:String) [Get-CimInstance], CimException
    + FullyQualifiedErrorId : HRESULT 0x80041010,Microsoft.Management.Infrastructure.CimCmdlets.GetCimInstanceCommand

NOTE:  If I just strip everything out and simply type «Get-CimInstance -Class Win32_UserProfile», I get the same error, so it’s not the Object, it’s the class.  

NOTE:  If I switch to Get-WMIObject, I get the same «Invalid Class» error, see below:

Get-WmiObject : Invalid class «Win32_Userprofile»
At line:1 char:1
+ Get-WmiObject Win32_Userprofile
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : InvalidType: (:) [Get-WmiObject], ManagementException
    + FullyQualifiedErrorId : GetWMIManagementException,Microsoft.PowerShell.Commands.GetWmiObjectCommand

___________________________________________________________________________________________

Here are my questions:

1.)  Has anyone seen this before, and if so, what did you do to resolve it?

2.)  Does anyone know if there is a way to rebuild/reinstall the WMI Classes?

3.)  As the same thing happens between Get-CimInstance and Get-WmiObject, can anyone point me toward what the underlying source/cause of the problem might be? 

I consider myself somewhat unskilled Powershell user, as I don’t use it much.   Regardless, these commands work fine on 5 out of 6 other identical servers.  

Any help is appreciated!, thanks.

-sMh-

Недавно столкнулся с ошибкой, которая не давала запустить скрипты, и некоторые командлеты:

PS C:UsersUsers> Get-ExecutionPolicy
Get-ExecutionPolicy : Invalid class
At line:1 char:20
+ Get-ExecutionPolicy <<<<
+ CategoryInfo          : NotSpecified: (:) [Get-ExecutionPolicy],
ManagementException
+ FullyQualifiedErrorId :
System.Management.ManagementException,Microsoft.PowerShell.Commands.GetExecutionPolicyCommand

Ошибка оказалась в проблемах с базой wmi. Которая очень быстро восстанавливается следующей коммандой, запущенная из под администратора:

PS C:> cd C:WindowsSystem32wbem;MOFcomp CIMWIN32.MOF

Microsoft (R) MOF Compiler Version 6.1.7600.16385

Copyright (c) Microsoft Corp. 1997-2006. All rights reserved.

Parsing MOF file: CIMWIN32.MOF

MOF file has been successfully parsed

Storing data in the repository...

Done!

PS C:WindowsSystem32wbem>

Но, если у вас проблема таким образом не решилась или возможно у вас они возникли с другими командлетами, можно запустить следующий скрипт, который перерегистрирует все библиотеки WMI.

PowerShell:

Set-Service winmgmt -StartupType Disabled

stop-Service winmgmt -Force

Set-Location $env:windirsystem32wbem

Get-ChildItem *.dll | ForEach-Object {regsvr32 /s $_}

wmiprvse /regserver

Set-Service winmgmt -StartupType Automatic

Start-Service winmgmt

Get-ChildItem *.mof,*.mfl | ForEach-Object {mofcomp $_}

Set-Location $env:windirsystem32wbemAutoRecover

Get-ChildItem *.mof,*.mfl | ForEach-Object {mofcomp $_}

Тоже самое для командной строки(воз):

sc config winmgmt start= disabled

net stop winmgmt

cd %windir%system32wbem

for /f %s in (‘dir /b *.dll’) do regsvr32 /s %s

wmiprvse /regserver

sc config winmgmt start= auto

net start winmgmt

for /f %s in (‘dir /b *.mof’) do mofcomp %s

for /f %s in (‘dir /b *.mfl’) do mofcomp %s

cd %windir%system32wbemAutoRecover

for /f %s in (‘dir /b *.mof’) do mofcomp %s

for /f %s in (‘dir /b *.mfl’) do mofcomp %s

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