This do not help either:
> BiocInstaller::biocLite("limma", type="source")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
Installing package(s) 'limma'
trying URL '
http://bioconductor.org/packages/3.0/bioc/src/contrib/limma_3.21.10.tar.gz'
Content type 'application/x-gzip' length 1215791 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb
* installing *source* package âlimmaâ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R-3.1.1/include -DNDEBUG
-I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o
gcc -std=gnu99 -I/usr/local/lib/R-3.1.1/include -DNDEBUG
-I/usr/local/include -fpic -g -O2 -c weighted_lowess.c -o
weighted_lowess.o
gcc -std=gnu99 -shared -L/usr/local/lib -o limma.so normexp.o
weighted_lowess.o -L/usr/local/lib/R-3.1.1/lib -lR
installing to /usr/local/lib/R-3.1.1/library/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (limma)
The downloaded source packages are in
â/tmp/RtmpjACGfx/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> BiocInstaller::biocLite("affycoretools")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
Installing package(s) 'affycoretools'
trying URL '
http://bioconductor.org/packages/3.0/bioc/src/contrib/affycoretools_1.37.1.tar.gz
'
Content type 'application/x-gzip' length 6909574 bytes (6.6 Mb)
opened URL
==================================================
downloaded 6.6 Mb
* installing *source* package âaffycoretoolsâ ...
** R
** inst
** preparing package for lazy loading
Error : object âsymbols2indicesâ is not exported by 'namespace:limma'
ERROR: lazy loading failed for package âaffycoretoolsâ
* removing â/usr/local/lib/R-3.1.1/library/affycoretoolsâ
The downloaded source packages are in
â/tmp/RtmpjACGfx/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package âaffycoretoolsâ had non-zero exit status
2014-07-29 12:32 GMT+02:00 Vojtech Kulvait <kulv...@gmail.com>:
> Hi,
> thank you for your replies. I am sending full output of my R session
> started few minutes ago.
> The problem is still remaining.
> Best,
> Vojtech.
>
> R version 3.1.1 (2014-07-10) -- "Sock it to Me"
> Copyright (C) 2014 The R Foundation for Statistical Computing
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > library(BiocInstaller)
> Bioconductor version 3.0 (BiocInstaller 1.15.5), ?biocLite for help
> > BiocInstaller::biocValid()
> [1] TRUE
> > BiocInstaller::biocLite()
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
> > BiocInstaller::biocLite("affycoretools")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
> Installing package(s) 'affycoretools'
> trying URL '
> http://bioconductor.org/packages/3.0/bioc/src/contrib/affycoretools_1.37.1.tar.gz
> '
> Content type 'application/x-gzip' length 6909574 bytes (6.6 Mb)
> opened URL
> ==================================================
> downloaded 6.6 Mb
>
> * installing *source* package âaffycoretoolsâ ...
>
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : object âsymbols2indicesâ is not exported by 'namespace:limma'
> ERROR: lazy loading failed for package âaffycoretoolsâ
> * removing â/usr/local/lib/R-3.1.1/library/affycoretoolsâ
>
> The downloaded source packages are in
> â/tmp/RtmpjACGfx/downloaded_packagesâ
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package âaffycoretoolsâ had non-zero exit status
> > sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.15.5
>
> loaded via a namespace (and not attached):
> [1] tools_3.1.1
> >
>
>
>
> 2014-07-25 17:28 GMT+02:00 Martin Morgan <mtmor...@fhcrc.org>:
>
> On 07/25/2014 04:32 AM, Vojtech Kulvait wrote:
>>
>>> Hello,
>>> when I try to install affycoretools in devel i get an error:
>>>
>>> * installing *source* package ââ¬Ëaffycoretoolsââ¬â¢ ...
>>>
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> Error : object ââ¬Ësymbols2indicesââ¬â¢ is not exported by
>>> 'namespace:limma'
>>> ERROR: lazy loading failed for package ââ¬Ëaffycoretoolsââ¬â¢
>>>
>>>
>>> I think I have up to date instalation of all packages.
>>>
>>
>> Hi Vojtech -- just to add to the advice, you can use
>>
>> BiocInstaller::biocValid()
>>
>> to check your installation,
>>
>> BiocInstaller::biocLite()
>>
>> to update your current packages.
>>
>> Martin
>>
>>
>> Vojtech.
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>
>
[[alternative HTML version deleted]]
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