Question

i can't find cummeRbund package

0

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Angel ▴ 40

@angel-7981

Last seen 7.7 years ago

Berlin

hi friends,

i opened rstudio and typed:

source("http://bioconductor.org/biocLite.R")

biocLite("cummeRbund")

after some time,

The downloaded source packages are in
‘/tmp/RtmpjZVbdg/downloaded_packages’
Old packages: 'actuar', 'affy', 'affyio', 'bio3d', 'Biobase', 'Biostrings', 'bitops', 'boot', 'BRugs', 'BufferedMatrix',
'BufferedMatrixMethods', 'caTools', 'class', 'cluster', 'codetools', 'foreign', 'gdata', 'GenomicRanges', 'IRanges',
'KernSmooth', 'lattice', 'maanova', 'MASS', 'Matrix', 'mgcv', 'multtest', 'nlme', 'nnet', 'preprocessCore', 'qtl',
'RCurl', 'rgdal', 'rgenoud', 'ROC', 'RODBC', 'rpart', 'Rsamtools', 'RSQLite', 'rtracklayer', 'SparseM', 'spatial',
'survival', 'tree', 'XML', 'XVector', 'abind', 'affydata', 'ALL', 'AnnotationDbi', 'BiocGenerics', 'biomaRt', 'BSgenome',
'BSgenome.Celegans.UCSC.ce2', 'car', 'DBI', 'DynDoc', 'fibroEset', 'GenomeInfoDb', 'GenomicFeatures', 'hgu133acdf',
'hgu95av2cdf', 'hgu95av2probe', 'pls', 'qcc', 'qvalue', 'RUnit', 'sandwich', 'statmod', 'systemfit', 'TH.data',
'timeDate', 'tkWidgets', 'widgetTools', 'xtable'
Update all/some/none? [a/s/n]:
n
There were 29 warnings (use warnings() to see them)

then i went to tool option and searched cummeRbund package and press install but

install.packages("cummerbund")
Installing package into ‘/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘cummerbund’ is not available (for R version 3.2.1)

what is the reason please? if you were me how install this package in rstudio? im in fedora 64 bit

software error cuumeRbund rna-seq • 2.4k views

ADD COMMENT • link updated 9.3 years ago by Martin Morgan 25k • written 9.3 years ago by Angel ▴ 40

Martin Morgan · Answer 1 · 2015-09-06

1

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

Follow the directions for installation of Bioconductor packages, printed on each package landing page, e.g., for cummeRbund. Edit: Answer 'a' when asked if you would like to update old packages.

ADD COMMENT • link 9.3 years ago Martin Morgan 25k

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thank you but i cant find ‘/tmp/RtmpjZVbdg folder

ADD REPLY • link 9.3 years ago Angel ▴ 40

1

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That is not relevant to your problem, The directory is temporary and removed after the end of the R session. You have an old version of many packages. Answer 'a' (edit: previously said 'y', but that was incorrect) to the question about updating.

ADD REPLY • link 9.3 years ago Martin Morgan 25k

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there is no R installed on my computer just rstudio, maybe this is the reason that cummRbund package cant be find in rstudio?

ADD REPLY • link 9.3 years ago Angel ▴ 40

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Rstudio includes a version of R (otherwise how could it work???). In a new Rstudio session, enter the lines

source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

and respond 'a' (edit: previously said 'y', but that is not a valid response) when asked if you want to update all old packages.

ADD REPLY • link 9.3 years ago Martin Morgan 25k

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sorry Martin,

i tried

source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

then,

Update all/some/none? [a/s/n]:
y
Update all/some/none? [a/s/n]:
s
actuar :
 Version 1.1-8 installed in /usr/lib64/R/library
 Version 1.1-10 available at http://cran.rstudio.com
Update (y/N/c)?  y
affy :
 Version 1.40.0 installed in /usr/lib64/R/library
 Version 1.46.1 available at http://bioconductor.org/packages/3.1/bioc
Update (y/N/c)?

am i right please?

ADD REPLY • link updated 9.3 years ago by Martin Morgan 25k • written 9.3 years ago by Angel ▴ 40

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I am wrong. You should answer 'a' the first time, to update all old packages.

ADD REPLY • link 9.3 years ago Martin Morgan 25k

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i tried many y but again asked for another package and infinite y...when i typed a, told whould you have a personal library and i typed y...still runing something

ADD REPLY • link 9.3 years ago Angel ▴ 40

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good, it is updating your old packages. Pay attention to the output, especially if there are warnings or errors. Usually the _first_ warning or error is the problem, with later warnings or errors coming from that, so pay particular attention to that.

ADD REPLY • link 9.3 years ago Martin Morgan 25k