[Bioc-devel] affycoretools in devel failed to install
Martin Morgan
mtmorgan at fhcrc.org
Tue Jul 29 13:15:46 CEST 2014
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 <kulvait at 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 <mtmorgan at 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 at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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