> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq2_1.16.1 SummarizedExperiment_1.4.0 Biobase_2.34.0 GenomicRanges_1.26.3
[5] GenomeInfoDb_1.10.3 IRanges_2.8.1 S4Vectors_0.12.0 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] genefilter_1.56.0 locfit_1.5-9.1 splines_3.4.0 lattice_0.20-35 colorspace_1.3-2
[6] htmltools_0.3.6 base64enc_0.1-3 blob_1.1.0 survival_2.41-3 XML_3.98-1.9
[11] rlang_0.1.1 foreign_0.8-69 DBI_0.7 BiocParallel_1.8.2 bit64_0.9-7
[16] RColorBrewer_1.1-2 matrixStats_0.52.2 plyr_1.8.4 stringr_1.2.0 zlibbioc_1.20.0
[21] munsell_0.4.3 gtable_0.2.0 htmlwidgets_0.9 memoise_1.1.0 latticeExtra_0.6-28
[26] knitr_1.16 geneplotter_1.52.0 AnnotationDbi_1.36.2 htmlTable_1.9 Rcpp_0.12.12
[31] acepack_1.4.1 xtable_1.8-2 scales_0.4.1 backports_1.1.0 checkmate_1.8.3
[36] DelayedArray_0.3.16 Hmisc_4.0-3 annotate_1.52.1 XVector_0.14.0 bit_1.1-12
[41] gridExtra_2.2.1 ggplot2_2.2.1 digest_0.6.12 stringi_1.1.5 grid_3.4.0
[46] bitops_1.0-6 tools_3.4.0 magrittr_1.5 lazyeval_0.2.0 RCurl_1.95-4.8
[51] tibble_1.3.3 RSQLite_2.0 Formula_1.2-2 cluster_2.0.6 Matrix_1.2-10
[56] data.table_1.10.4 rpart_4.1-11 nnet_7.3-12 compiler_3.4.0
> countData <- matrix(1:100,ncol=4)
> condition <- factor(c("A","A","B","B"))
> dds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), ~ condition)
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class “NULL” is not valid for slot ‘NAMES’ in an object of class “DESeqDataSet”; is(value, "character_OR_NULL") is not TRUE
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("DelayedArray")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘DelayedArray’
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4:
can not open URL'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4:
can not open URL'https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4:
can not open URL'https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4/PACKAGES'
Old packages: 'AnnotationHub', 'curl', 'fgsea', 'GenomicAlignments', 'GenomicRanges', 'GOSemSim', 'IRanges', 'limma', 'Rsamtools', 'S4Vectors',
'VariantAnnotation', 'XVector'
Update all/some/none? [a/s/n]:
can anyone know the reason why DESeqDataSetFromMatrix {DESeq2} is wrong and I can not install DelayedArray package??
I have tried what you said, but there is another question?
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && :
missing value where TRUE/FALSE needed
I think something about the version of R or bioconductor is wrong.
I have just tried edgeR today with R 3.4.0 successfully, so I will choose edgeR for bioinformatics.Thanks a lot for your answer.
That's fine :)
If you continue to have problems installing Bioc packages, you can post this latest error and get some help. Usually the issue is that Bioc packages were installed in multiple locations or not using biocLite.