在R(4.0.2)中使用dada2中的filterandTrim函数时出现错误消息



错误信息:

: validObject(.Object)中的错误:无效类" ScalarCharacter "对象:超类characterORconnection"没有定义在对象类

的环境

我通过biocManager下载了dada2。

代码如下(其中所有参数都是预先定义的):

out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=250,
maxN=0, maxEE=1, truncQ=2, rm.phix=TRUE,
compress=TRUE, multithread=TRUE)

我遇到了同样的问题,也通过biocManager安装包。

在GitHub上阅读这个长线程后,他们也提到dada2,我试图将R更新到最新版本,然后我重新安装了BiocManager和dada2。从那以后一切都很顺利。

Session info WHEN I HAD PROBLEMS:

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] dada2_1.16.0 Rcpp_1.0.6  
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.18.2 tidyselect_1.1.1            purrr_0.3.4                
[4] reshape2_1.4.4              lattice_0.20-41             colorspace_2.0-1           
[7] vctrs_0.3.8                 generics_0.1.0              stats4_4.0.3               
[10] utf8_1.2.1                  rlang_0.4.11                pillar_1.6.1               
[13] glue_1.4.2                  DBI_1.1.1                   BiocParallel_1.22.0        
[16] BiocGenerics_0.38.0         RColorBrewer_1.1-2          matrixStats_0.59.0         
[19] jpeg_0.1-8.1                GenomeInfoDbData_1.2.4      lifecycle_1.0.0            
[22] plyr_1.8.6                  stringr_1.4.0               zlibbioc_1.36.0            
[25] Biostrings_2.58.0           munsell_0.5.0               gtable_0.3.0               
[28] hwriter_1.3.2               labeling_0.4.2              latticeExtra_0.6-29        
[31] Biobase_2.48.0              IRanges_2.24.1              GenomeInfoDb_1.26.7        
[34] parallel_4.0.3              fansi_0.5.0                 scales_1.1.1               
[37] BiocManager_1.30.16         DelayedArray_0.14.1         S4Vectors_0.28.1           
[40] RcppParallel_5.1.4          XVector_0.30.0              ShortRead_1.46.0           
[43] farver_2.1.0                Rsamtools_2.4.0             digest_0.6.27              
[46] ggplot2_3.3.5               png_0.1-7                   stringi_1.5.3              
[49] dplyr_1.0.7                 GenomicRanges_1.40.0        grid_4.0.3                 
[52] tools_4.0.3                 bitops_1.0-7                magrittr_2.0.1             
[55] RCurl_1.98-1.3              tibble_3.1.2                crayon_1.4.1               
[58] pkgconfig_2.0.3             ellipsis_0.3.2              Matrix_1.2-18              
[61] assertthat_0.2.1            rstudioapi_0.13             R6_2.5.0                   
[64] GenomicAlignments_1.24.0    compiler_4.0.3

Session info WITHOUT PROBLEMS:

R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] dada2_1.20.0 Rcpp_1.0.6  
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.22.0 tidyselect_1.1.1            reshape2_1.4.4              purrr_0.3.4                
[5] lattice_0.20-44             colorspace_2.0-2            vctrs_0.3.8                 generics_0.1.0             
[9] stats4_4.1.0                utf8_1.2.1                  rlang_0.4.11                pillar_1.6.1               
[13] glue_1.4.2                  DBI_1.1.1                   BiocParallel_1.26.1         BiocGenerics_0.38.0        
[17] RColorBrewer_1.1-2          plyr_1.8.6                  matrixStats_0.59.0          jpeg_0.1-8.1               
[21] GenomeInfoDbData_1.2.6      lifecycle_1.0.0             stringr_1.4.0               zlibbioc_1.38.0            
[25] MatrixGenerics_1.4.0        Biostrings_2.60.1           munsell_0.5.0               gtable_0.3.0               
[29] hwriter_1.3.2               latticeExtra_0.6-29         Biobase_2.52.0              IRanges_2.26.0             
[33] GenomeInfoDb_1.28.1         parallel_4.1.0              fansi_0.5.0                 scales_1.1.1               
[37] DelayedArray_0.18.0         S4Vectors_0.30.0            RcppParallel_5.1.4          XVector_0.32.0             
[41] ShortRead_1.50.0            Rsamtools_2.8.0             ggplot2_3.3.5               png_0.1-7                  
[45] stringi_1.6.2               dplyr_1.0.7                 GenomicRanges_1.44.0        grid_4.1.0                 
[49] tools_4.1.0                 bitops_1.0-7                magrittr_2.0.1              RCurl_1.98-1.3             
[53] tibble_3.1.2                crayon_1.4.1                pkgconfig_2.0.3             ellipsis_0.3.2             
[57] Matrix_1.3-4                assertthat_0.2.1            rstudioapi_0.13             R6_2.5.0                   
[61] GenomicAlignments_1.28.0    compiler_4.1.0

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