TimmR error for hgu133a.db
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0
Entering edit mode
@pascalschulthess-12533
Last seen 5.2 years ago

Hello everyone,

I'd like to teach students to annotation gene expression data. For that I've written a script on my Mac that starts with

source("https://bioconductor.org/biocLite.R")
library(BiocInstaller)
biocLite("Biobase")
library(Biobase)
biocLite("GEOquery")
library(GEOquery)
biocLite("annotate")
library(annotate)
biocLite("hgu133a.db")
library(hgu133a.db)

This runs smoothly on the Mac. But when I want to run in ion a Windows machine I get the following error right after hgu113a downloads all kind of stuff:

Warning message:
package 'TinnR' is not available (for R version 3.3.2)
Error in library(TinnR) : there is no package called 'TinnR'
Execution halted

How is that possible? And more importantly, how can I resolve this?

Thanks

Pascal

Edit:

Session info for the windows machine is:

R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252   
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.1252    
attached base packages:
[1] stats4    parallel  stats     graphics  grDevices datasets  utils     methods   base     
other attached packages:
[1] BiocInstaller_1.24.0 annotate_1.52.1      XML_3.98-1.5         AnnotationDbi_1.36.2
[5] IRanges_2.8.1        S4Vectors_0.12.1     GEOquery_2.40.0      Biobase_2.34.0      
[9] BiocGenerics_0.20.0 
loaded via a namespace (and not attached):
[1] Rcpp_0.12.9    digest_0.6.12  bitops_1.0-6   R6_2.2.0       xtable_1.8-2   DBI_0.5-1     
[7] RSQLite_1.1-2  httr_1.2.1     tools_3.3.2    RCurl_1.95-4.8 memoise_1.0.0

and for the Mac:

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] hgu133a.db_3.2.3     org.Hs.eg.db_3.4.0   AnnotationDbi_1.36.2 IRanges_2.8.1        S4Vectors_0.12.1     Biobase_2.34.0       BiocGenerics_0.20.0  BiocInstaller_1.24.0
loaded via a namespace (and not attached):
[1] DBI_0.5-1     tools_3.3.2   memoise_1.0.0 Rcpp_0.12.9   RSQLite_1.1-2 digest_0.6.12
software error annotate hgu133a • 810 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 41 minutes ago
United States

TinnR isn't a Bioconductor package, so this isn't the place to ask about it. In addition, if you google TinnR, you will find that it has been removed from CRAN, which is never a good sign for a package.

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Entering edit mode

Yes, I know. TimmR is a very old package that's not on CRAN anymore since 2014. But, the question still stands. When I execute

biocLite("hgu133a.db")

I get the error. Thus, this is indeed a Bioconductor related problem in my view.

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Entering edit mode

Put another way, none of the packages that you are installing have a dependency on TinnR, so it's doubtful that the error has anything to do with biocLite. The TinnR package was designed to include scripts for running R under Tinn-R. Are you using that IDE? If so, perhaps that's the problem.

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Entering edit mode

And no, it's not Bioconductor. I can install the hgu133a.db package without problems on the same R/Bioc version on Windows.

> biocLite("hgu133a.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) 'hgu133a.db'
installing the source package 'hgu133a.db'

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 903473 bytes (882 KB)
downloaded 882 KB

* installing *source* package 'hgu133a.db' ...
** R
** inst
** preparing package for lazy loading
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
*** arch - x64
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
* DONE (hgu133a.db)

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] compiler_3.3.2 tools_3.3.2  
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