Question: SCAN.UPC: exception thrown when loading GEOQuery
0
gravatar for lep
4.8 years ago by
lep90
United States
lep90 wrote:

I am using Win XP-64, have everything updated (R-3-1-2, BioC, and R-Studio).  When loading package SCAN.UPC, there is an exception being thrown regarding GEOQuery.  I checked if the .dll exist in the 64-bit library for RCurl, and it is present.  Any suggestions?

Below is the run code and error message (at very bottom):

> library("SCAN.UPC")
Loading required package: Biobase
Loading required package: BiocGenerics

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: oligo
Loading required package: oligoClasses
Welcome to oligoClasses version 1.28.0
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: XVector
=============================================================================================
Welcome to oligo version 1.30.0
=============================================================================================

Attaching package: ‘oligo’

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

    normalize

Loading required package: GEOquery
Error in inDL(x, as.logical(local), as.logical(now), ...) :
  unable to load shared object 'C:/Program Files/R/R-3.1.2/library/RCurl/libs/x64/RCurl.dll':
  LoadLibrary failure:  The specified procedure could not be found.

Error: package ‘GEOquery’ could not be loaded
geoquery scan.upc rcurl • 1.3k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by lep90

See if this is helpful: http://stackoverflow.com/questions/9429390/can-not-install-xml-package. Please let us know either way.

ADD REPLYlink written 4.8 years ago by Stephen Piccolo560

Thanks for the tip.  Downloaded windows binaries for RCurl and pasted in the folder structure.   However, the exception is still being thrown.  Was able to successfully run SCAN.UPC a while ago, so the likely issue now is a changed dependency. Any way to go back to earlier versions in order to avoid this issue?

 

Also, how about killing the GEOQuery and RCurl associations which are fired when loading SCAN.UPC?  GEOQuery is for fetching GEO data, and RCurl is for HTTP fetching.   The goal is to only normalize expression from CEL files using SCAN.UPC (I already have the data and don't need GEO or HTTP). 

 

ADD REPLYlink written 4.8 years ago by lep90

Try to simplify this. It seems like RCurl is the problem. So try just library(RCurl). Do this in a new session. If that fails, start a new session and try to remove and then install RCurl using standard R commands -- remove.packages("RCurl"); BiocInstaller::biocLite("RCurl"). 

ADD REPLYlink written 4.8 years ago by Martin Morgan ♦♦ 23k

And to follow up on Martin's suggestion, downloading the binaries and pasting into the folder structure is a recipe for disaster. There are very few R packages for which that will actually work, which is why things like install.packages() and biocLite() exist. I have the current version of SCAN.UPC installed on my 64-bit Windows box (with RCurl and XML), without any problems, so it is likely that you have a borked installation, rather than some dependency problems.

ADD REPLYlink written 4.8 years ago by James W. MacDonald51k

Thanks, I went back to R-3.0.1, and just installed RCurl in R by itself, and it loaded fine.   FYI - Using R-Studio and the syntax "library('RCurl')" works fine by itself as well.  It's only when library('SCAN.UPC') is invoked in R-Studio when the u+nsuccessful loading of GEOQuery occurs --> due to not reading the 64-bit .dll for RCurl.   A pattern is starting to emerge: GEO access and naturally HTTP are packages which are instantiated when SCAN.UPC loads.   However, isn't SCAN.UPC for computational workflow regarding normalization, without HTTP and GEO issues?  

ADD REPLYlink written 4.8 years ago by lep90

SCAN.UPC uses GEOquery to run the examples in the vignette, which is why this is a dependency (and RCurl is a dependency of GEOquery). But I don't have the same problem as you, as I can load SCAN.UPC in RStudio on Windows using R-64 bit without any problems.

> suppressPackageStartupMessages(library(SCAN.UPC))
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
============================================================================================================================
Warning messages:
1: package ‘BiocGenerics’ was built under R version 3.1.2
2: package ‘Biostrings’ was built under R version 3.1.2
3: package ‘IRanges’ was built under R version 3.1.2
4: package ‘mgcv’ was built under R version 3.1.2
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SCAN.UPC_2.8.0      sva_3.12.0          genefilter_1.48.1   mgcv_1.8-4          nlme_3.1-118        foreach_1.4.2      
 [7] affyio_1.34.0       affy_1.44.0         GEOquery_2.32.0     oligo_1.30.0        Biostrings_2.34.1   XVector_0.6.0      
[13] IRanges_2.0.1       S4Vectors_0.4.0     oligoClasses_1.28.0 Biobase_2.26.0      BiocGenerics_0.12.1

loaded via a namespace (and not attached):
 [1] affxparser_1.38.0     annotate_1.44.0       AnnotationDbi_1.28.1  BiocInstaller_1.16.1  bit_1.1-12           
 [6] bitops_1.0-6          codetools_0.2-9       DBI_0.3.1             ff_2.2-13             GenomeInfoDb_1.2.4   
[11] GenomicRanges_1.18.3  grid_3.1.1            iterators_1.0.7       lattice_0.20-29       MASS_7.3-35          
[16] Matrix_1.1-4          preprocessCore_1.28.0 RCurl_1.95-4.5        RSQLite_1.0.0         splines_3.1.1        
[21] survival_2.37-7       tools_3.1.1           XML_3.98-1.1          xtable_1.7-4          zlibbioc_1.12.0
ADD REPLYlink written 4.8 years ago by James W. MacDonald51k

A little progress, used "biocLite('SCAN.UPC') and package loading succeeded.   However, the exception can't find function 'SCAN' appears (see below):

> biocLite("SCAN.UPC")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.1.
Installing package(s) 'SCAN.UPC'
trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/SCAN.UPC_2.4.2.zip'
Content type 'application/zip' length 747141 bytes (729 Kb)
opened URL
downloaded 729 Kb

package ‘SCAN.UPC’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Documents and Settings\Administrator\Local Settings\Temp\RtmpALOYN6\downloaded_packages
> celFilePath<-  .... (this is valid without errors)
> normalized <- SCAN(celFilePath, OutFilePath="output_file.txt")
Error: could not find function "SCAN"
ADD REPLYlink written 4.8 years ago by lep90

...more progress.  Must use lower case "scan" rather than SCAN in the normalizing command syntax.  Now the only error message is:

> normalized <- scan(celFilePath)
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file 'C:....': Permission denied

 

ADD REPLYlink written 4.8 years ago by lep90

No, you don't use lower case scan(). If you look at ?scan, this is a function from base R for scanning files. You have to load the SCAN.UPC package first, and then you use SCAN().

In addition, celFilePath <- .... is NOT valid, and did not process without errors. You need to actually give the path to the celfiles, or better yet, change the working directory, and use

SCAN("*.CEL")
ADD REPLYlink written 4.8 years ago by James W. MacDonald51k

Sorry, I didn't paste my real celfilepath but rather used "...(   )"

I loaded bioC in R, then loaded SCAN.UPC and it's throwing an exception when reading the 64-bit RCurl.dll in the 64-bit library folder for the RCurl package.  (if RCurl is running via SCAN.UPC w/o issues in your win OS, why did someone give a link to a stackoverflow entry about RCurl not being available for the Win OS, which referred to Ripley's personal Windows OS packages?)

I'll uninstall everything, and then redo.   Is there a specific R version you recommend?

ADD REPLYlink written 4.8 years ago by lep90

Sorry, I didn't paste my real celfilepath but rather used "...(   )"

I loaded bioC in R, then loaded SCAN.UPC and it's throwing an exception when reading the 64-bit RCurl.dll in the 64-bit library folder for the RCurl package.  (if RCurl is running via SCAN.UPC w/o issues in your win OS, why did someone give a link to a stackoverflow entry about RCurl not being available for the Win OS, which referred to Ripley's personal Windows OS packages?)

I'll uninstall everything, and then redo.   Is there a specific R version you recommend?

ADD REPLYlink written 4.8 years ago by lep90
1

The link on stackoverflow was from 2012, at which time there were still problems getting 64-bit dlls to compile natively on Windows. So BDR was working his personal magic to get things to work.

Since R-2.12 the Rtools toolchain has included tools for both 32 and 64 bit compiling, and by R-2.15 it appears all the issues had been ironed out. See http://cran.r-project.org/bin/windows/Rtools/ for more info.

Anyway, the issues in 2012 were that trying to install RCurl or XML on 64-bit would return an error, saying that those packages weren't available. It wasn't the case that you could install something and it wouldn't work. The issues in the thread you mention had to do with installing the packages from source (where you would have to compile the dlls), rather than some borked install that couldn't find a dll that was installed from a binary package.

As for version, I recommend the latest version, R-3.1.2. You should be able to install R, then do

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

biocLite()

biocLite("SCAN.UPC")

library(SCAN.UPC)

and it should Just Work.

ADD REPLYlink written 4.8 years ago by James W. MacDonald51k
Answer: SCAN.UPC: exception thrown when loading GEOQuery
1
gravatar for lep
4.8 years ago by
lep90
United States
lep90 wrote:

RESOLVED - thanks for all of your help.  I solved the RCurl issue (not reading the 64-bit .dll file) by totally uninstalling all R versions from the Windows operating system, as well as removing R-Studio.   I think a lot of things got piled up and created the issue, because when I started with a clean reinstall of R-Studio, which installed a clean new R version (3.1.2), loading SCAN.UPC had no issues and I am up and running.   I am going to use, however, the parallel library as follows

library(doParallel)
registerDoParallel(cores=8)

when I run COMBAT after SCAN.UPC (to see how quickly the pace picks up with dual 4-core Intel Xeon processors).  Thx, L

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by lep90
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