Re: [Bioc-devel] affycoretools in devel failed to install

Tue, 29 Jul 2014 04:41:41 -0700 

Looks like I was right :)


2014-07-29 13:15 GMT+02:00 Martin Morgan <mtmor...@fhcrc.org>:

> Looks like Dan corrected symbols2indices then Jim made an additional change
>
> ------------------------------------------------------------------------
> r91908 | jmacdon | 2014-06-26 13:16:03 -0700 (Thu, 26 Jun 2014) | 1 line
>
> Converted to use roxygen2, so all Rd files changed. Also generalized
> vennSelect2 so it will work with non-Affy data. Added functions to create
> tables from GO analyses using ReportingTools.
> ------------------------------------------------------------------------
> r91900 | d.tenenbaum | 2014-06-26 10:47:24 -0700 (Thu, 26 Jun 2014) | 3
> lines
>
> replace symbols2indices throughout with ids2indices as limma
> has renamed this function.
>
>
> ... but Jim bumped the version in the wrong direction so Dan's commit
> never made it to the build system, and the 'latest' version is the version
> before Dan's.
>
> $ svn diff -c91908 DESCRIPTION
> Index: DESCRIPTION
> ===================================================================
> --- DESCRIPTION (revision 91907)
> +++ DESCRIPTION (revision 91908)
> @@ -2,7 +2,7 @@
>  Date: 2008-12-15
>  Title: Functions useful for those doing repetitive analyses
>      with Affymetrix GeneChips.
> -Version: 1.37.2
> +Version: 1.35.10
>
>
>
> On 07/29/2014 03:35 AM, Vojtech Kulvait wrote:
>
>> 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 ‘limma’ ...
>>
>> ** 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
>>      ‘/tmp/RtmpjACGfx/downloaded_packages’
>>
>> 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 ‘affycoretools’ ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Error : object ‘symbols2indices’ is not exported by 
>> 'namespace:limma'
>> ERROR: lazy loading failed for package ‘affycoretools’
>> * removing ‘/usr/local/lib/R-3.1.1/library/affycoretools’
>>
>
> I don't think the complaint is about affycoretools
>
>>
>> The downloaded source packages are in
>>      ‘/tmp/RtmpjACGfx/downloaded_packages’
>>
>> 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 ‘affycoretools’ 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 ‘affycoretools’ ...
>>>
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> Error : object ‘symbols2indices’ is not exported by 
>>> 'namespace:limma'
>>> ERROR: lazy loading failed for package ‘affycoretools’
>>> * removing ‘/usr/local/lib/R-3.1.1/library/affycoretools’
>>>
>>>
>>> The downloaded source packages are in
>>>      ‘/tmp/RtmpjACGfx/downloaded_packages’
>>>
>>> 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 ‘affycoretools’ 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 
>>>>> ‘affycoretools’ ...
>>>>>
>>>>>
>>>>> ** R
>>>>> ** inst
>>>>> ** preparing package for lazy loading
>>>>> Error : object ‘symbols2indices’ is not 
>>>>> exported by
>>>>> 'namespace:limma'
>>>>> ERROR: lazy loading failed for package 
>>>>> ‘affycoretools’
>>>>>
>>>>>
>>>>>
>>>>> 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]]
>>
>>
>>
>> _______________________________________________
>> 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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