limma changelog say:
- symbols2indices() renamed to ids2indices().
2014-07-29 12:35 GMT+02:00 Vojtech Kulvait <kulv...@gmail.com>:
> 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
>>>
>>
>>
>
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