Entering edit mode
Hi all,
So I've somehow gotten my R installation in a bad state. I had been using R 3.3.2 / BioC 3.4, last installed/updated likely in late November and everything was fine. I decided to upgrade packages again using biocLite(); I thought I had closed all R other sessions and didn't have any packages loaded when I did this, but I must not have because I got lots of warnings about "unable to write to folder XXX", then the packages were unable to load. I've had this happen before and the fix has been to go manually delete the package folders from my R library, then reinstall. This seemed to work, but the next time I loaded affycoretools, I got a warning message about "vfs customization not available on this platform. Ignoring value: vfs = unix-none". I shrugged and went on. The first problem I noticed was when I tried to call plotPCA on a matrix and got the error "Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'plotPCA' for signature '"matrix"'. The same code was working fine with affycoretools 1.46.1 but after upgrading to 1.46.3 it wasn't. I don't mean to pick on affycoretools (sorry, Jim!) because I get the same warning about "vfs customization" when installing .db annotation packages (full output below), so it must be system wide.
I've even gone as far as deleting all versions of R from my computer (I only had 3.3.2 and Devel), all personal libraries, deleting my Rtools installation, everything from my path variable and even Rstudio. I also googled ""vfs customization not available on this platform" but didn't find anything useful. The outputs below are from a fresh install of R 3.3.2. Anybody have any idea of what is wrong and how I can fix it?
Thanks,
Jenny
# The first part of the output is here, but the full output makes the message too long, so I'll post the rest separately...
R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
> source("https://bioconductor.org/biocLite.R")
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
'lib = "C:/Program Files/R/R-3.3.2/library"' is not writable
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/BiocInstaller_1.24.0.zip'
Content type 'application/zip' length 126079 bytes (123 KB)
downloaded 123 KB
package ‘BiocInstaller’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘digest’, ‘memoise’, ‘Rcpp’, ‘BH’, ‘plogr’, ‘BiocGenerics’, ‘S4Vectors’, ‘DBI’, ‘RSQLite’
There is a binary version available but the source version is later:
binary source needs_compilation
digest 0.6.11 0.6.12 TRUE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/digest_0.6.11.zip'
Content type 'application/zip' length 168720 bytes (164 KB)
downloaded 164 KB
#lines deleted
package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages
installation path not writeable, unable to update packages: Matrix, mgcv, nlme,
survival
Old packages: 'digest'
Update all/some/none? [a/s/n]: a
There is a binary version available but the source version is later:
binary source needs_compilation
digest 0.6.11 0.6.12 TRUE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/digest_0.6.11.zip'
Content type 'application/zip' length 168720 bytes (164 KB)
downloaded 164 KB
package ‘digest’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages
> biocLite("affycoretools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘affycoretools’
also installing the dependencies ‘httpuv’, ‘sourcetools’, ‘backports’,
# lines deleted
package ‘affycoretools’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\drnevich\AppData\Local\Temp\RtmpMvIRxb\downloaded_packages
installing the source packages ‘GO.db’, ‘PFAM.db’
trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/GO.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 31897756 bytes (30.4 MB)
downloaded 30.4 MB
# lines deleted
* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
* DONE (GO.db)
#lines deleted
> library(affycoretools)
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 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Warning messages:
1: vfs customization not available on this platform. Ignoring value: vfs = unix-none
2: vfs customization not available on this platform. Ignoring value: vfs = unix-none
3: vfs customization not available on this platform. Ignoring value: vfs = unix-none
> setwd("D:/Statistics/Dobrucki")
> library(limma)
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
> targets <- readTargets("Targets.txt")
>
> targets$trt <- targets$Cy5
> targets$trt[targets$Cy5 == "cont"] <- targets$Cy3[targets$Cy5 == "cont"]
> f <- function(x) as.numeric(x$Flags> -99)
>
>
> #Read in the data, using the median foreground and background values
>
> RG <- read.maimages(targets$FileName,source="genepix.median",names=targets$Label,wt.fun=f,
+ annotation=c("Block", "Row", "Column", "ID", "Name", "ControlType","GeneName"))
Read 1A_588_0452.gpr
Read 1B_606_0462.gpr
Read 1C_571_0473.gpr
Read 1D_576_0475.gpr
Read 2A_571_0427.gpr
Read 2B_560_0435.gpr
Read 2C_526_0433.gpr
Read 2D_536_0448.gpr
> spottypes <- readSpotTypes()
> RG$genes$Status <- controlStatus(spottypes,RG)
Matching patterns for: ControlType
Found 45220 cDNA
Found 1224 pos
Found 153 neg
Found 823 ignore
Setting attributes: values Color
> RG.nobg <- backgroundCorrect(RG,method="none")
>
> targ2 <- data.frame(Sample = c(targets$cy5samp, targets$cy3samp),
+ group = c(targets$Cy5, targets$Cy3), FileName = rep(targets$FileName,2),
+ Array = rep(targets$array, 2), Slide = rep(targets$slide,2),
+ Dye = rep(c("R","G"), each = nrow(targets)),
+ Pair = rep(targets$pair, 2))
> #add in label
>
> targ2$Label <- paste(targ2$group, targ2$Pair, sep = ".")
> RG.quant <- RG.MA(normalizeBetweenArrays(RG.nobg,method="quantile"))
> plotPCA(log2(cbind(RG.quant$R,RG.quant$G)),groups=as.numeric(factor(targ2$group)),
+ groupnames=levels(factor(targ2$group)),addtext=targ2$Pair)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'plotPCA' for signature '"matrix"'
> affycoretools::plotPCA(log2(cbind(RG.quant$R,RG.quant$G)),groups=as.numeric(factor(targ2$group)),
+ groupnames=levels(factor(targ2$group)),addtext=targ2$Pair)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'plotPCA' for signature '"matrix"'
> biocLite("MmAgilentDesign026655.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) 'MmAgilentDesign026655.db'
also installing the dependency 'org.Mm.eg.db'
installing the source packages 'org.Mm.eg.db', 'MmAgilentDesign026655.db'
trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/org.Mm.eg.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 63616251 bytes (60.7 MB)
downloaded 60.7 MB
trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/MmAgilentDesign026655.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1479706 bytes (1.4 MB)
downloaded 1.4 MB
* installing *source* package 'org.Mm.eg.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
* DONE (org.Mm.eg.db)
* installing *source* package 'MmAgilentDesign026655.db' ...
** R
** inst
** preparing package for lazy loading
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
* DONE (MmAgilentDesign026655.db)
# the rest of the code I'll post in the thread.
