Question: Error in summary.DESeqResults(res) : could not find function "summary.DESeqResults"
0
gravatar for lech.kaczmarczyk
4 months ago by
lech.kaczmarczyk10 wrote:

I'm trying to run DESeq2 but got stud on this error:

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
Error in summary.DESeqResults(res) : 
  could not find function "summary.DESeqResults"

The package was fully functional on my computer before. Re-installation of the package did not solve the problem. Session info below.

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

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

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.41.6              limma_3.41.6                vsn_3.53.0                  data.table_1.12.2          
 [5] dplyr_0.8.3                 ggrepel_0.8.1               ggplot2_3.2.0               PoiClaClu_1.0.2.1          
 [9] RColorBrewer_1.1-2          pheatmap_1.0.12             DESeq2_1.25.5               SummarizedExperiment_1.15.5
[13] DelayedArray_0.11.4         BiocParallel_1.19.0         matrixStats_0.54.0          Biobase_2.45.0             
[17] GenomicRanges_1.37.14       GenomeInfoDb_1.21.1         IRanges_2.19.10             S4Vectors_0.23.17          
[21] BiocGenerics_0.31.5        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6             bit64_0.9-7              progress_1.2.2           httr_1.4.0               tools_3.6.0             
 [6] backports_1.1.4          affyio_1.55.0            R6_2.4.0                 rpart_4.1-15             Hmisc_4.2-0             
[11] DBI_1.0.0                lazyeval_0.2.2           colorspace_1.4-1         nnet_7.3-12              withr_2.1.2             
[16] tidyselect_0.2.5         gridExtra_2.3            prettyunits_1.0.2        preprocessCore_1.47.1    bit_1.1-14              
[21] curl_3.3                 compiler_3.6.0           htmlTable_1.13.1         labeling_0.3             rtracklayer_1.45.1      
[26] scales_1.0.0             checkmate_1.9.4          hexbin_1.27.3            affy_1.63.0              genefilter_1.67.1       
[31] askpass_1.1              rappdirs_0.3.1           stringr_1.4.0            digest_0.6.20            Rsamtools_2.1.2         
[36] foreign_0.8-71           XVector_0.25.0           base64enc_0.1-3          pkgconfig_2.0.2          htmltools_0.3.6         
[41] dbplyr_1.4.2             htmlwidgets_1.3          rlang_0.4.0              rstudioapi_0.10          RSQLite_2.1.1           
[46] acepack_1.4.1            RCurl_1.95-4.12          magrittr_1.5             GenomeInfoDbData_1.2.1   Formula_1.2-3           
[51] Matrix_1.2-17            Rcpp_1.0.1               munsell_0.5.0            stringi_1.4.3            zlibbioc_1.31.0         
[56] BiocFileCache_1.9.1      grid_3.6.0               blob_1.1.1               crayon_1.3.4             lattice_0.20-38         
[61] Biostrings_2.53.1        splines_3.6.0            GenomicFeatures_1.37.3   annotate_1.63.0          hms_0.4.2               
[66] locfit_1.5-9.1           knitr_1.23               pillar_1.4.2             geneplotter_1.63.0       XML_3.98-1.20           
[71] glue_1.3.1               latticeExtra_0.6-28      BiocManager_1.30.4       gtable_0.3.0             openssl_1.4             
[76] purrr_0.3.2              assertthat_0.2.1         xfun_0.8                 xtable_1.8-4             survival_2.44-1.1       
[81] tibble_2.1.3             GenomicAlignments_1.21.4 AnnotationDbi_1.47.0     memoise_1.1.0            cluster_2.1.0
deseq2 • 134 views
ADD COMMENTlink modified 4 months ago by Michael Love26k • written 4 months ago by lech.kaczmarczyk10
Answer: Error in summary.DESeqResults(res) : could not find function "summary.DESeqResu
2
gravatar for Michael Love
4 months ago by
Michael Love26k
United States
Michael Love26k wrote:

Recently, I had to change the way summary() works in DESeq2, moving it from a S3 to an S4 method, because of changes to the underlying class of DESeqResults.

Can you run:

BiocManager::valid()

?

Note that with a complete set of devel packages, DESeq2 builds (including summary() calls in the vignette) on all platforms:

http://bioconductor.org/checkResults/devel/bioc-LATEST/DESeq2/

ADD COMMENTlink written 4 months ago by Michael Love26k
> BiocManager::valid("DESeq2") 
[1] TRUE

Should I install it some other way than with BiocManager()?

ADD REPLYlink modified 4 months ago • written 4 months ago by lech.kaczmarczyk10

Tried to install it from source, but it did not solve the problem...

ADD REPLYlink written 4 months ago by lech.kaczmarczyk10

Another try, can you post your code? You didn’t post code, just messages and errors.

ADD REPLYlink modified 4 months ago • written 4 months ago by Michael Love26k
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