Problems installing IPO

[jheaton1]

Hi,

I have some issues installing IPO. Among which include not loading 'curl' 'CAMERA' 'xcms' even though they are already installed and loaded using library. In addition I have the problem below:

Downloading github repo glibiseller/IPO@master Installing IPO Skipping 2 packages not available: CAMERA, xcms "C:/PROGRA~1/R/R-32~1.1/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore CMD INSTALL \ "C:/Users/[...]/AppData/Local/Temp/Rtmpc1yP3q/devtoolsfa041361295/glibiseller-IPO-3738d2a" \ --library="[...]/R/win-library/3.2" --install-tests

• installing source package 'IPO' ... * R * inst * tests * preparing package for lazy loading Warning: replacing previous import by 'igraph::groups' when loading 'CAMERA' \ help * installing help indices * building package indices * testing if installed package can be loaded * arch - i386 Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) : there is no package called 'IPO' Error: loading failed Execution halted *\ arch - x64 Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) : there is no package called 'IPO' Error: loading failed Execution halted ERROR: loading failed for 'i386', 'x64'
• removing '[...]/R/win-library/3.2/IPO' Error: Command failed (1)

Please advise. Thanks in advance.

[glibiseller]

Hi,

did you follow the installation description provided in the vignette? (https://github.com/glibiseller/IPO/blob/master/vignette/IPO.Rmd)

Best regards, Gunnar

[jheaton1]

Hi,

Yes, I followed the installation description. See below:

setwd("D:/") library(CAMERA) Loading required package: Biobase 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 object is masked from ‘package:stats’:

xtabs

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

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

Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: xcms Loading required package: mzR Loading required package: Rcpp Loading required package: ProtGenerics

Attaching package: ‘xcms’

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

phenoData, phenoData<-

Loading required package: igraph

Attaching package: ‘igraph’

The following object is masked from ‘package:xcms’:

groups

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

normalize, union

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

decompose, spectrum

The following object is masked from ‘package:base’:

union

Warning message: replacing previous import by ‘igraph::groups’ when loading ‘CAMERA’

library(devtools) library(xcms) library(rsm)

Attaching package: ‘rsm’

The following object is masked from ‘package:igraph’:

star

install_github("glibiseller/IPO") Downloading github repo glibiseller/IPO@master Installing IPO Skipping 2 packages not available: CAMERA, xcms "C:/PROGRA~1/R/R-32~1.1/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore CMD INSTALL \ "C:/Users/~USER /AppData/Local/Temp/RtmpKQFHVp/devtools9543ee14c62/glibiseller-IPO-3738d2a" \ --library=".../~USER/R/win-library/3.2" --install-tests

• installing source package 'IPO' ... * R * inst * tests * preparing package for lazy loading Warning: replacing previous import by 'igraph::groups' when loading 'CAMERA' \ help * installing help indices * building package indices * testing if installed package can be loaded * arch - i386 Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) : there is no package called 'IPO' Error: loading failed Execution halted *\ arch - x64 Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) : there is no package called 'IPO' Error: loading failed Execution halted ERROR: loading failed for 'i386', 'x64'
• removing '.../~USER /R/win-library/3.2/IPO' Error: Command failed (1)

From: Gunnar Libiseller [mailto:notifications@github.com] Sent: 09 July 2015 11:26 To: glibiseller/IPO Cc: Heaton, James C Subject: Re: [IPO] Problems installing IPO (#10)

Hi,

did you follow the installation description provided in the vignette? (https://github.com/glibiseller/IPO/blob/master/vignette/IPO.Rmd)

Best regards, Gunnar

— Reply to this email directly or view it on GitHubhttps://github.com/glibiseller/IPO/issues/10#issuecomment-119901111.

[glibiseller]

Hi,

Maybe someone else has an idea why it does not work :-(.

For the time beeing I could send you the R-package as zip-file and you could install it from source. Please send me a mail to gunnar.libiseller@joanneum.at.

Best regards

[raimofranke]

Hi there,

there is an issue with CAMERA and igraph, which has been addressed by a workaround by Martin Morgan on support.bioconductor.org: https://support.bioconductor.org/p/69414/

I am not sure if this is the only problem, but the warning message "replacing previous import by ‘igraph::groups’ when loading ‘CAMERA’" shows that this is at least one problem.

Best, Raimo

[glibiseller]

Thanks Raimo! That sounds plausible.

[sneumann]

It could be that CAMERA-1.25.1 has solved the issue, in that case you could close this issue.

[jheaton1]

Thanks for your help. I will see how it goes.