Cannot install Oligo package
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Entering edit mode
Anna Dvorkin ▴ 40
@anna-dvorkin-4204
Last seen 5.8 years ago

Dear All,

 

I'm trying to install the "oligo" package. Here's my session info:

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 10586)

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

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

other attached packages:
[1] BiocGenerics_0.18.0  BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] zlibbioc_1.18.0  tools_3.3.0      affyio_1.40.0    Biobase_2.32.0   S4Vectors_0.8.11
[6] stats4_3.3.0    


When I'm trying to install the "oligo" package, the following happens:

>

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
> biocLite("oligo")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘oligo’
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.3/oligo_1.34.2.zip'
Content type 'application/zip' length 57495185 bytes (54.8 MB)
downloaded 54.8 MB

package ‘oligo’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\ADG\AppData\Local\Temp\RtmpG0Od4b\downloaded_packages
Old packages: 'digest', 'mgcv', 'nlme', 'survival'
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  0.6.9 0.6.10              TRUE

Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘digest’

trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.10.tar.gz'
Content type 'application/x-gzip' length 118336 bytes (115 KB)
downloaded 115 KB

* installing *source* package 'digest' ...
** package 'digest' successfully unpacked and MD5 sums checked
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c aes.c -o aes.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crc32.c -o crc32.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c digest.c -o digest.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c md5.c -o md5.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pmurhash.c -o pmurhash.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c raes.c -o raes.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sha1.c -o sha1.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sha2.c -o sha2.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sha256.c -o sha256.o
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c xxhash.c -o xxhash.o
c:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o digest.dll tmp.def aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -Ld:/Compiler/gcc-4.9.3/local330/lib/i386 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/PROGRA~1/R/R-33~1.0/bin/i386 -lR
installing to C:/Users/ADG/Documents/R/win-library/3.3/digest/libs/i386

*** arch - x64
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c aes.c -o aes.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crc32.c -o crc32.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c digest.c -o digest.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c md5.c -o md5.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pmurhash.c -o pmurhash.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c raes.c -o raes.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sha1.c -o sha1.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sha2.c -o sha2.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sha256.c -o sha256.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/PROGRA~1/R/R-33~1.0/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c xxhash.c -o xxhash.o
c:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o digest.dll tmp.def aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/PROGRA~1/R/R-33~1.0/bin/x64 -lR
installing to C:/Users/ADG/Documents/R/win-library/3.3/digest/libs/x64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (digest)

The downloaded source packages are in
        ‘C:\Users\ADG\AppData\Local\Temp\RtmpG0Od4b\downloaded_packages’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/mgcv_1.8-13.zip'
Content type 'application/zip' length 2330918 bytes (2.2 MB)
downloaded 2.2 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/nlme_3.1-128.zip'
Content type 'application/zip' length 2146312 bytes (2.0 MB)
downloaded 2.0 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/survival_2.39-5.zip'
Content type 'application/zip' length 4814123 bytes (4.6 MB)
downloaded 4.6 MB

package ‘mgcv’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\ADG\AppData\Local\Temp\RtmpG0Od4b\downloaded_packages
> library(oligo)
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

Loading required package: oligoClasses
Error in namespaceExport(ns, exports) : undefined exports: space
In addition: Warning messages:
1: no function found corresponding to methods exports from ‘IRanges’ for: ‘elementNROWS’, ‘from’, ‘nLnode’, ‘nRnode’, ‘pcompare’, ‘pcompareRecursively’, ‘relistToClass’, ‘to’
2: multiple methods tables found for ‘unlist’
Error: package ‘oligoClasses’ could not be loaded
> biocLite("oligoClasses")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘oligoClasses’
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.3/oligoClasses_1.32.0.zip'
Content type 'application/zip' length 1770836 bytes (1.7 MB)
downloaded 1.7 MB

package ‘oligoClasses’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\ADG\AppData\Local\Temp\RtmpG0Od4b\downloaded_packages

> library(oligo)
Loading required package: oligoClasses
Error in namespaceExport(ns, exports) : undefined exports: space
In addition: Warning messages:
1: no function found corresponding to methods exports from ‘IRanges’ for: ‘elementNROWS’, ‘from’, ‘nLnode’, ‘nRnode’, ‘pcompare’, ‘pcompareRecursively’, ‘relistToClass’, ‘to’
2: multiple methods tables found for ‘unlist’
Error: package ‘oligoClasses’ could not be loaded
 

I'm not sure where the problem is - whether it is with the oligoClasses or with the oligo, but I could not find any way to fix this.

I would greatly appreciate any suggestions!

I used oligo before and I loved it, so I would prefer to use that, instead of going to the AffymetrixExpressionConsole...

 

Thank you very much for your help!

 

Regards,

Anna

 

 

 

 

oligo oligoclasses • 1.8k views
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Entering edit mode

Does BiocInstaller::biocValid() suggest that some packages are out-of-date / too new? If so, try following the instructions suggested by it.

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Entering edit mode

Hello Martin,

 

Thank you very much for your suggestion!

I've checked and although I keep the packages updated with the "update packages" menu, it turned out that some of them were still out of date. Once I've updated them - everything worked!

 

Thank you!

 

Regards,

Anna

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