can not install "ChIPpeakAnno"
1
0
Entering edit mode
5.1 years ago
tarek.mohamed ▴ 320

Hi there,

I am having problems with installing "ChIPpeakAnno" package.

biocLite("ChIPpeakAnno") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘ChIPpeakAnno’ also installing the dependency ‘Rsamtools’

trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/Rsamtools_1.26.2.zip' Content type 'application/zip' length 8763232 bytes (8.4 MB) downloaded 8.4 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/ChIPpeakAnno_3.8.9.zip' Content type 'application/zip' length 34178441 bytes (32.6 MB) downloaded 32.6 MB

package ‘Rsamtools’ successfully unpacked and MD5 sums checked package ‘ChIPpeakAnno’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\tmm447\AppData\Local\Temp\Rtmp4q7hI1\downloaded_packages installation path not writeable, unable to update packages: boot, cluster, foreign, lattice, MASS, rpart, survival Old packages: 'curl', 'formatR', 'markdown', 'memoise', 'rmarkdown' Update all/some/none? [a/s/n]: a

There is a binary version available but the source version is later: binary source needs_compilation curl 2.5 2.6 TRUE

Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/curl_2.5.zip' Content type 'application/zip' length 3092334 bytes (2.9 MB) downloaded 2.9 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/formatR_1.5.zip' Content type 'application/zip' length 126108 bytes (123 KB) downloaded 123 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/markdown_0.8.zip' Content type 'application/zip' length 168617 bytes (164 KB) downloaded 164 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/memoise_1.1.0.zip' Content type 'application/zip' length 29608 bytes (28 KB) downloaded 28 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/rmarkdown_1.5.zip' Content type 'application/zip' length 2274347 bytes (2.2 MB) downloaded 2.2 MB

package ‘curl’ successfully unpacked and MD5 sums checked package ‘formatR’ successfully unpacked and MD5 sums checked package ‘markdown’ successfully unpacked and MD5 sums checked package ‘memoise’ successfully unpacked and MD5 sums checked package ‘rmarkdown’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\tmm447\AppData\Local\Temp\Rtmp4q7hI1\downloaded_packages

library(ChIPpeakAnno) Loading required package: grid Loading required package: IRanges Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply,
parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Biostrings Loading required package: XVector Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: VennDiagram Loading required package: futile.logger

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called ‘shiny’ Error: package or namespace load failed for ‘ChIPpeakAnno’

ChIPpeakAnno • 2.6k views
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1
Entering edit mode
5.1 years ago
h.mon 34k

Try install.packages("shiny"), then try loading ChIPpeakAnno again.

edit: moved from comment to answer, as solved OP problem.

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0
Entering edit mode

lol ... R gives such long errors....why not just the last line or better still....

Please install the package "shiny" and try again!

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