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.
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Phone: (206) 667-2793
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_______________________________________________
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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