Question: can not install "ChIPpeakAnno"
0
gravatar for tarek.mohamed
23 months ago by
tarek.mohamed240
tarek.mohamed240 wrote:

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 • 1.2k views
ADD COMMENTlink written 23 months ago by tarek.mohamed240
1
gravatar for h.mon
23 months ago by
h.mon24k
Brazil
h.mon24k wrote:

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

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

ADD COMMENTlink modified 22 months ago • written 23 months ago by h.mon24k

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

Please install the package "shiny" and try again!

ADD REPLYlink written 23 months ago by YaGalbi1.4k
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