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Question: Error installing Annaffy
0
gravatar for naokotblues
8 months ago by
naokotblues0 wrote:

## Hello everyone!

## I've been trying to install annaffy for a while and it doesn't work. It's the only one from 'affy' package that doesn't work. It says it is due to an error on installing 'Go.db' and 'KEGG.db'. I've tried to install those packages before and after annaffy, but it keeps on going on error. Thank you. - A.

 

 

 

> biocLite("annaffy")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘annaffy’
also installing the dependencies ‘GO.db’, ‘KEGG.db’

trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/annaffy_1.46.0.zip'
Content type 'application/zip' length 783907 bytes (765 KB)
downloaded 765 KB

package ‘annaffy’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\AppData\Local\Temp\Rtmp2FQ3E8\downloaded_packages
installing the source packages ‘GO.db’, ‘KEGG.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

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1976342 bytes (1.9 MB)
downloaded 1.9 MB

* installing *source* package 'GO.db' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Documents/R/win-library/3.3/GO.db/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  no se puede abrir la conexión
ERROR: installing package DESCRIPTION failed for package 'GO.db'
* removing 'C:/Users/Documents/R/win-library/3.3/GO.db'
* installing *source* package 'KEGG.db' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Documents/R/win-library/3.3/KEGG.db/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  no se puede abrir la conexión
ERROR: installing package DESCRIPTION failed for package 'KEGG.db'
* removing 'C:/Users/Documents/R/win-library/3.3/KEGG.db'

The downloaded source packages are in
    ‘C:\Users\AppData\Local\Temp\Rtmp2FQ3E8\downloaded_packages’
installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme,
  survival
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\Rtmp2FQ3E8/downloaded_packages/GO.db_3.4.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status
3: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\Rtmp2FQ3E8/downloaded_packages/KEGG.db_3.2.3.tar.gz' had status 1 
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘KEGG.db’ had non-zero exit status
> library("annaffy")
Error: package ‘GO.db’ required by ‘annaffy’ could not be found
ADD COMMENTlink modified 8 months ago by James W. MacDonald45k • written 8 months ago by naokotblues0

The unusual thing about the output above is that the path "C:\Users\Documents" does not contain a user name, for instance I have "c:\Users\mtmorgan\Documents", so I wonder if there is a basic mis-configuration in either the R installation or elsewhere?

ADD REPLYlink written 8 months ago by Martin Morgan ♦♦ 21k

Sorry for the misunderstood. I deleted that info when I copied it due to personal information.

ADD REPLYlink written 8 months ago by naokotblues0
1
gravatar for James W. MacDonald
8 months ago by
United States
James W. MacDonald45k wrote:

It's the Á in your name. See here, particularly Martin Maechler's response and Francois Rousseu's solution, which may be useful, although I am not completely clear as to what Francois did to fix the problem

Probably the best idea is to use a different personal library dir that uses only standard ASCII characters.

 

ADD COMMENTlink written 8 months ago by James W. MacDonald45k

Thanks for your answer. How can I change library dir on R? 

ADD REPLYlink written 8 months ago by naokotblues0

What is the first hit you get if you google that?

ADD REPLYlink written 8 months ago by James W. MacDonald45k

https://support.rstudio.com/hc/en-us/community/posts/200698036-Changing-Default-packages-instalation-directory-in-R-studio

There are different ways to change dir on R, as I am new to omics I did not want to mess up and end up deleting Rstudio by mistake. Anyway, thank you!  

ADD REPLYlink written 8 months ago by naokotblues0
0
gravatar for naokotblues
8 months ago by
naokotblues0 wrote:

Here it is completed:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("affy")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘affy’
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/affy_1.52.0.zip'
Content type 'application/zip' length 2889519 bytes (2.8 MB)
downloaded 2.8 MB

package ‘affy’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Ángela.NAOKO\AppData\Local\Temp\RtmpUV489t\downloaded_packages
installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme,
  survival
> library("affy")
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

Loading required package: Biobase
Welcome to Bioconductor

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

> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘GO.db’
installing the source package ‘GO.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

* installing *source* package 'GO.db' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Angela.NAOKO/Documents/R/win-library/3.3/GO.db/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  no se puede abrir la conexión
ERROR: installing package DESCRIPTION failed for package 'GO.db'
* removing 'C:/Users/Ángela.NAOKO/Documents/R/win-library/3.3/GO.db'

 

ADD COMMENTlink written 8 months ago by naokotblues0

The downloaded source packages are in
    ‘C:\Users\Ángela.NAOKO\AppData\Local\Temp\RtmpUV489t\downloaded_packages’
installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme,
  survival
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Ángela.NAOKO\Documents\R\win-library\3.3" C:\Users\NGELA~1.NAO\AppData\Local\Temp\RtmpUV489t/downloaded_packages/GO.db_3.4.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status
> library("GO.db")
Error in library("GO.db") : there is no package called ‘GO.db’
> biocLite("KEGG.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘KEGG.db’
installing the source package ‘KEGG.db’

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1976342 bytes (1.9 MB)
downloaded 1.9 MB

* installing *source* package 'KEGG.db' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Angela.NAOKO/Documents/R/win-library/3.3/KEGG.db/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  no se puede abrir la conexión
ERROR: installing package DESCRIPTION failed for package 'KEGG.db'
* removing 'C:/Users/Ángela.NAOKO/Documents/R/win-library/3.3/KEGG.db'

The downloaded source packages are in
    ‘C:\Users\Ángela.NAOKO\AppData\Local\Temp\RtmpUV489t\downloaded_packages’
installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme,
  survival
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Ángela.NAOKO\Documents\R\win-library\3.3" C:\Users\NGELA~1.NAO\AppData\Local\Temp\RtmpUV489t/downloaded_packages/KEGG.db_3.2.3.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘KEGG.db’ had non-zero exit status
> library("KEGG.db")
Error in library("KEGG.db") : there is no package called ‘KEGG.db’

ADD REPLYlink written 8 months ago by naokotblues0

> biocLite("affyPLM")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘affyPLM’
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/affyPLM_1.50.0.zip'
Content type 'application/zip' length 5310077 bytes (5.1 MB)
downloaded 5.1 MB

package ‘affyPLM’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Ángela.NAOKO\AppData\Local\Temp\RtmpUV489t\downloaded_packages
installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme,
  survival
> library("affyPLM")
Loading required package: gcrma
Loading required package: preprocessCore
> biocLite("limma")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘limma’
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/limma_3.30.13.zip'
Content type 'application/zip' length 4275869 bytes (4.1 MB)
downloaded 4.1 MB

package ‘limma’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Ángela.NAOKO\AppData\Local\Temp\RtmpUV489t\downloaded_packages
installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme,
  survival
> library("limma")

Attaching package: ‘limma’

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

    plotMA

Warning message:
package ‘limma’ was built under R version 3.3.3 
> biocLite("simpleaffy")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘simpleaffy’
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/simpleaffy_2.50.0.zip'
Content type 'application/zip' length 856151 bytes (836 KB)
downloaded 836 KB

package ‘simpleaffy’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Ángela.NAOKO\AppData\Local\Temp\RtmpUV489t\downloaded_packages
installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme,
  survival
> library("simpleaffy")
Loading required package: genefilter
> biocLite("annaffy")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘annaffy’
also installing the dependencies ‘GO.db’, ‘KEGG.db’

trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/annaffy_1.46.0.zip'
Content type 'application/zip' length 783907 bytes (765 KB)
downloaded 765 KB

package ‘annaffy’ successfully unpacked and MD5 sums checked

ADD REPLYlink written 8 months ago by naokotblues0

The downloaded binary packages are in
    C:\Users\Ángela.NAOKO\AppData\Local\Temp\RtmpUV489t\downloaded_packages
installing the source packages ‘GO.db’, ‘KEGG.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

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1976342 bytes (1.9 MB)
downloaded 1.9 MB

* installing *source* package 'GO.db' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Angela.NAOKO/Documents/R/win-library/3.3/GO.db/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  no se puede abrir la conexión
ERROR: installing package DESCRIPTION failed for package 'GO.db'
* removing 'C:/Users/Ángela.NAOKO/Documents/R/win-library/3.3/GO.db'
* installing *source* package 'KEGG.db' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Angela.NAOKO/Documents/R/win-library/3.3/KEGG.db/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  no se puede abrir la conexión
ERROR: installing package DESCRIPTION failed for package 'KEGG.db'
* removing 'C:/Users/Ángela.NAOKO/Documents/R/win-library/3.3/KEGG.db'

The downloaded source packages are in
    ‘C:\Users\Ángela.NAOKO\AppData\Local\Temp\RtmpUV489t\downloaded_packages’
installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme,
  survival
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Ángela.NAOKO\Documents\R\win-library\3.3" C:\Users\NGELA~1.NAO\AppData\Local\Temp\RtmpUV489t/downloaded_packages/GO.db_3.4.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status
3: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Ángela.NAOKO\Documents\R\win-library\3.3" C:\Users\NGELA~1.NAO\AppData\Local\Temp\RtmpUV489t/downloaded_packages/KEGG.db_3.2.3.tar.gz' had status 1 
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘KEGG.db’ had non-zero exit status
> library("annaffy")
Error: package ‘GO.db’ required by ‘annaffy’ could not be found

ADD REPLYlink written 8 months ago by naokotblues0
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