I tried all your advice: reinstall R, change mirror, still biocLite("affycoretools") does not install the package bit automatically
and downloading the tgz from bit, the package bit does not compile

Mayte Suarez-Farinas
Research Assistant Professor
Laboratory of Investigative Dermatology
Biostatistician, Center for Clinical and Translational Science
The Rockefeller University
1230 York Ave, Box 178
New York, NY 10065
Phone:  +1(212) 327-8213
Fax:       +1(212) 327-8232



On Sep 16, 2013, at 1:55 PM, Dan Tenenbaum wrote:



----- Original Message -----
From: "Mayte Suarez-Farinas" <farinam@mail.rockefeller.edu<mailto:farinam@mail.rockefeller.edu>>
To: "Dan Tenenbaum" <dtenenba@fhcrc.org<mailto:dtenenba@fhcrc.org>>
Cc: "Mayte Suarez-Farinas" <farinam@mail.rockefeller.edu<mailto:farinam@mail.rockefeller.edu>>, "Steve Lianoglou" <lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>>,
"<bioconductor@r-project.org<mailto:bioconductor@r-project.org>>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>, "James W. MacDonald" <jmacdon@uw.edu<mailto:jmacdon@uw.edu>>
Sent: Monday, September 16, 2013 10:50:08 AM
Subject: Re: [BioC] problem while loading affycoretools



Hi James and Dan


I installed R from scratch and then run the following two lines:


biocLite() (success)
biocLite("affycoretools")

which, after installing several packages gave me the "error: package
‘AnnotationDbi’ could not be loaded" (see ALL outputs below)'


Dan, here is the output of biocinstallRepos.
librarybiocInstall()
biocinstallRepos()

BioCsoft
" http://bioconductor.org/packages/2.12/bioc "
BioCann
" http://bioconductor.org/packages/2.12/data/annotation "
BioCexp
" http://bioconductor.org/packages/2.12/data/experiment "
BioCextra
" http://bioconductor.org/packages/2.12/extra "
CRAN
" http://cran.opensourceresources.org "


It appears that the CRAN mirror you are using is not working properly.
Try picking a mirror from this list:
http://cran.r-project.org/mirrors.html

You can change mirrors with the chooseCRANmirror() function.
Dan







ALL OUTPUTS:




source(" http://bioconductor.org/biocLite.R ")
Installing package into ‘/Users/mayte/Library/R/3.0/library’
(as ‘lib’ is unspecified)
trying URL '
http://www.bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BiocInstaller_1.10.3.tgz'
Content type 'application/x-gzip' length 46533 bytes (45 Kb)
opened URL
==================================================
downloaded 45 Kb




The downloaded binary packages are in
/var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloaded_packages
Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help
biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version
3.0.1.
Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
Warning: unable to access index for repository
http://cran.opensourceresources.org/bin/macosx/contrib/3.0
Warning: dependencies ‘DBI’, ‘RSQLite’ are not available
also installing the dependency ‘BiocGenerics’


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BiocGenerics_0.6.0.tgz'
Content type 'application/x-gzip' length 333465 bytes (325 Kb)
opened URL
==================================================
downloaded 325 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Biobase_2.20.1.tgz'
Content type 'application/x-gzip' length 2354463 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/IRanges_1.18.3.tgz'
Content type 'application/x-gzip' length 1978262 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/AnnotationDbi_1.22.6.tgz'
Content type 'application/x-gzip' length 4066815 bytes (3.9 Mb)
opened URL
==================================================
downloaded 3.9 Mb




The downloaded binary packages are in
/var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloaded_packages
Warning: unable to access index for repository
http://cran.opensourceresources.org/bin/macosx/contrib/3.0
biocLite("affycoretools")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version
3.0.1.
Installing package(s) 'affycoretools'
Warning: unable to access index for repository
http://cran.opensourceresources.org/bin/macosx/contrib/3.0
Warning: dependencies ‘xtable’, ‘gplots’, ‘R2HTML’, ‘hwriter’, ‘XML’,
‘RCurl’, ‘DBI’, ‘foreach’, ‘R.utils’, ‘RSQLite’, ‘reshape2’,
‘gtable’, ‘gridExtra’, ‘scales’, ‘Hmisc’, ‘RColorBrewer’,
‘dichromat’, ‘bitops’ are not available
also installing the dependencies ‘org.Hs.eg.db’, ‘biovizBase’,
‘GenomicFeatures’, ‘Rsamtools’, ‘BSgenome’, ‘VariantAnnotation’,
‘rtracklayer’, ‘affyio’, ‘preprocessCore’, ‘zlibbioc’, ‘Category’,
‘graph’, ‘RBGL’, ‘AnnotationForge’, ‘Biostrings’, ‘GenomicRanges’,
‘edgeR’, ‘PFAM.db’, ‘GSEABase’, ‘ggbio’, ‘affy’, ‘GO.db’, ‘KEGG.db’,
‘biomaRt’, ‘limma’, ‘GOstats’, ‘annotate’, ‘annaffy’, ‘gcrma’,
‘oligoClasses’, ‘ReportingTools’


trying URL '
http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contrib/3.0/org.Hs.eg.db_2.9.0.tgz'
Content type 'application/x-gzip' length 53095874 bytes (50.6 Mb)
opened URL
==================================================
downloaded 50.6 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/biovizBase_1.8.1.tgz'
Content type 'application/x-gzip' length 1136533 bytes (1.1 Mb)
opened URL
==================================================
downloaded 1.1 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GenomicFeatures_1.12.3.tgz'
Content type 'application/x-gzip' length 971035 bytes (948 Kb)
opened URL
==================================================
downloaded 948 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Rsamtools_1.12.4.tgz'
Content type 'application/x-gzip' length 3768247 bytes (3.6 Mb)
opened URL
==================================================
downloaded 3.6 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BSgenome_1.28.0.tgz'
Content type 'application/x-gzip' length 746888 bytes (729 Kb)
opened URL
==================================================
downloaded 729 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/VariantAnnotation_1.6.7.tgz'
Content type 'application/x-gzip' length 1689203 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/rtracklayer_1.20.4.tgz'
Content type 'application/x-gzip' length 1861493 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affyio_1.28.0.tgz'
Content type 'application/x-gzip' length 94024 bytes (91 Kb)
opened URL
==================================================
downloaded 91 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/preprocessCore_1.22.0.tgz'
Content type 'application/x-gzip' length 128027 bytes (125 Kb)
opened URL
==================================================
downloaded 125 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/zlibbioc_1.6.0.tgz'
Content type 'application/x-gzip' length 124184 bytes (121 Kb)
opened URL
==================================================
downloaded 121 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Category_2.26.0.tgz'
Content type 'application/x-gzip' length 933299 bytes (911 Kb)
opened URL
==================================================
downloaded 911 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/graph_1.38.3.tgz'
Content type 'application/x-gzip' length 1327243 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/RBGL_1.36.2.tgz'
Content type 'application/x-gzip' length 911905 bytes (890 Kb)
opened URL
==================================================
downloaded 890 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/AnnotationForge_1.2.2.tgz'
Content type 'application/x-gzip' length 4149568 bytes (4.0 Mb)
opened URL
==================================================
downloaded 4.0 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Biostrings_2.28.0.tgz'
Content type 'application/x-gzip' length 2215378 bytes (2.1 Mb)
opened URL
==================================================
downloaded 2.1 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GenomicRanges_1.12.5.tgz'
Content type 'application/x-gzip' length 3293184 bytes (3.1 Mb)
opened URL
==================================================
downloaded 3.1 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/edgeR_3.2.4.tgz'
Content type 'application/x-gzip' length 1470863 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb


trying URL '
http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contrib/3.0/PFAM.db_2.9.0.tgz'
Content type 'application/x-gzip' length 2325707 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GSEABase_1.22.0.tgz'
Content type 'application/x-gzip' length 606089 bytes (591 Kb)
opened URL
==================================================
downloaded 591 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ggbio_1.8.5.tgz'
Content type 'application/x-gzip' length 2272353 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affy_1.38.1.tgz'
Content type 'application/x-gzip' length 1458286 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb


trying URL '
http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contrib/3.0/GO.db_2.9.0.tgz'
Content type 'application/x-gzip' length 25061115 bytes (23.9 Mb)
opened URL
==================================================
downloaded 23.9 Mb


trying URL '
http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contrib/3.0/KEGG.db_2.9.1.tgz'
Content type 'application/x-gzip' length 2032486 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/biomaRt_2.16.0.tgz'
Content type 'application/x-gzip' length 365452 bytes (356 Kb)
opened URL
==================================================
downloaded 356 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/limma_3.16.7.tgz'
Content type 'application/x-gzip' length 1568068 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GOstats_2.26.0.tgz'
Content type 'application/x-gzip' length 1725303 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/annotate_1.38.0.tgz'
Content type 'application/x-gzip' length 1971349 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/annaffy_1.32.0.tgz'
Content type 'application/x-gzip' length 380113 bytes (371 Kb)
opened URL
==================================================
downloaded 371 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gcrma_2.32.0.tgz'
Content type 'application/x-gzip' length 240351 bytes (234 Kb)
opened URL
==================================================
downloaded 234 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/oligoClasses_1.22.0.tgz'
Content type 'application/x-gzip' length 872393 bytes (851 Kb)
opened URL
==================================================
downloaded 851 Kb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ReportingTools_2.0.1.tgz'
Content type 'application/x-gzip' length 2063622 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb


trying URL '
http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affycoretools_1.32.1.tgz'
Content type 'application/x-gzip' length 7077475 bytes (6.7 Mb)
opened URL
==================================================
downloaded 6.7 Mb




The downloaded binary packages are in
/var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloaded_packages
Warning: unable to access index for repository
http://cran.opensourceresources.org/bin/macosx/contrib/3.0











Mayte Suarez-Farinas
Research Assistant Professor
Laboratory of Investigative Dermatology
Biostatistician, Center for Clinical and Translational Science
The Rockefeller University
1230 York Ave, Box 178
New York, NY 10065
Phone: +1(212) 327-8213
Fax: +1(212) 327-8232





On Sep 16, 2013, at 1:36 PM, Dan Tenenbaum wrote:





----- Original Message -----


From: "Mayte Suarez-Farinas" < farinam@mail.rockefeller.edu >


To: "James W. MacDonald" < jmacdon@uw.edu >


Cc: "Steve Lianoglou" < lianoglou.steve@gene.com >,
bioconductor@r-project.org


Sent: Monday, September 16, 2013 9:14:00 AM


Subject: Re: [BioC] problem while loading affycoretools








Dear James, Henrik and Steve





I tried biocLite("ff") and got the msg: package ‘ff’ is not available


(for R version 3.0.1)


(see below). Then I went ahead and download the tar package form


( http://cran.r-project.org/web/packages/ff/index.html ) and used R


CMD install to install it. However,


while loading ff (library(ff)) it complains that the package bit was


missing, biocLite gave me


same error (package ‘bit’ is not available (for R version 3.0.1) )


and I could not instll via CMD install


gave me the following error





dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar


* installing to library ‘/Users/mayte/Library/R/3.0/library’


* installing *source* package ‘bit’ ...


** package ‘bit’ successfully unpacked and MD5 sums checked


** libs


sh: make: command not found


You downloaded the source tarball for bit (.tar.gz); you wanted the
Mac binary (.tgz).

As for the problem with biocLite("bit") I'm not sure--are you behind
a proxy or firewall?
What is the output of the following:

library(BiocInstaller)
biocinstallRepos()

?

Dan




ERROR: compilation failed for package ‘bit’


* removing ‘/Users/mayte/Library/R/3.0/library/bit’


dhcp-129-85-243-253:Desktop mayte$





Please help out, life without affycoretools is very difficult ;-)








From: James W. MacDonald [ jmacdon@uw.edu ]


Sent: Monday, September 16, 2013 11:03 AM


To: Mayte Suarez-Farinas


Cc: bioconductor@r-project.org


Subject: Re: [BioC] problem while loading affycoretools





Hi Mayte,





I have not seen this error in the past. Have you tried simply


installing


ff first?





biocLite("ff")


biocLite("affycoretools")





Best,





Jim








On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote:




I updated to the most recent R version. After this brand new




installation, I get the following error while loading library




affycoretools:









library(affycoretools)




Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),




versionCheck = vI[[j]]) :




there is no package called ‘ff’




Error: package or namespace load failed for ‘affycoretools’









After checking mailing list, I followed James advice




(
https://stat.ethz.ch/pipermail/bioconductor/2012-December/049895.html
)




and updated all packages




library(BiocInstaller)




biocLite(character(0))









Additionally, I updated all R packages as well









Still, the same problem arise. My R session info is bellow














R version 3.0.1 (2013-05-16)




Platform: x86_64-apple-darwin10.8.0 (64-bit)









locale:




[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8









attached base packages:




[1] parallel stats graphics grDevices utils datasets




methods base









other attached packages:




[1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4




DBI_0.2-7




[5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1




BiocGenerics_0.6.0




[9] BiocInstaller_1.10.3









loaded via a namespace (and not attached):




[1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0




[4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0




[7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2




[10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0




[13] gplots_2.11.3 graph_1.38.3 grid_3.0.1




[16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3




[19] lattice_0.20-23 limma_3.16.7




preprocessCore_1.22.0




[22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1




[25] splines_3.0.1 stats4_3.0.1 survival_2.37-4




[28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1




[31] zlibbioc_1.6.0














[[alternative HTML version deleted]]



















_______________________________________________




Bioconductor mailing list




Bioconductor@r-project.org




https://stat.ethz.ch/mailman/listinfo/bioconductor




Search the archives:




http://news.gmane.org/gmane.science.biology.informatics.conductor





--


James W. MacDonald, M.S.


Biostatistician


University of Washington


Environmental and Occupational Health Sciences


4225 Roosevelt Way NE, # 100


Seattle WA 98105-6099








_______________________________________________


Bioconductor mailing list


Bioconductor@r-project.org


https://stat.ethz.ch/mailman/listinfo/bioconductor


Search the archives:


http://news.gmane.org/gmane.science.biology.informatics.conductor







	[[alternative HTML version deleted]]

