错误信息：
：validObject(.Object) 中的错误：无效类“ScalarCharacter” 对象：超类“characterORconnection”未在 对象类的环境
我通过 biocManager 下载了dada2。
代码如下（所有的参数都是之前定义的）：
out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=250,
maxN=0, maxEE=1, truncQ=2, rm.phix=TRUE,
compress=TRUE, multithread=TRUE)
【问题讨论】：
我也遇到了同样的问题，也是通过 biocManager 安装包的。
在阅读了 GitHub 上的this long thread 后，他们也提到了dada2，我尝试将R 更新到最新版本，然后我重新安装了BiocManager 和dada2。之后一切都很顺利。
我遇到问题时的会话信息：
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
没有问题的会话信息：
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
【讨论】：