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Question: Message asking to update and download from source functions when downloading packages
0
gravatar for larisa.espinoza
20 months ago by
larisa.espinoza0 wrote:

I would like to know why I am always asked to update and choose to dowload from source the function "lattice"? Everytime I download a package I get this question and I keep answering update "all" and "do not" install from source, am I doing the correct thing?

> source("https://bioconductor.org/biocLite.R")
Installing package into ‘C:/Users/espinla2/AppData/Local/R/win64-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/BiocInstaller_1.20.3.zip'
Content type 'application/zip' length 57033 bytes (55 KB)
downloaded 55 KB

The downloaded binary packages are in
C:\Users\espinla2\AppData\Local\Temp\Rtmpc1BouX\downloaded_packages
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite
  for help
A new version of Bioconductor is available after installing
  the most recent version of R; see
  http://bioconductor.org/install
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3
  (2015-12-10).
Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘digest’, ‘memoise’, ‘Rcpp’, ‘BH’, ‘plogr’, ‘BiocGenerics’, ‘S4Vectors’, ‘DBI’, ‘RSQLite’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/digest_0.6.12.zip'
Content type 'application/zip' length 172450 bytes (168 KB)
downloaded 168 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/memoise_1.0.0.zip'
Content type 'application/zip' length 23330 bytes (22 KB)
downloaded 22 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/Rcpp_0.12.10.zip'
Content type 'application/zip' length 3261724 bytes (3.1 MB)
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/BH_1.62.0-1.zip'
Content type 'application/zip' length 16150077 bytes (15.4 MB)
downloaded 15.4 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/plogr_0.1-1.zip'
Content type 'application/zip' length 17654 bytes (17 KB)
downloaded 17 KB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/BiocGenerics_0.16.1.zip'
Content type 'application/zip' length 962958 bytes (940 KB)
downloaded 940 KB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/S4Vectors_0.8.11.zip'
Content type 'application/zip' length 1755464 bytes (1.7 MB)
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/DBI_0.6.zip'
Content type 'application/zip' length 743128 bytes (725 KB)
downloaded 725 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/RSQLite_1.1-2.zip'
Content type 'application/zip' length 1857696 bytes (1.8 MB)
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/Biobase_2.30.0.zip'
Content type 'application/zip' length 4227858 bytes (4.0 MB)
downloaded 4.0 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/IRanges_2.4.8.zip'
Content type 'application/zip' length 3087641 bytes (2.9 MB)
downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/AnnotationDbi_1.32.3.zip'
Content type 'application/zip' length 9460389 bytes (9.0 MB)
downloaded 9.0 MB

package ‘digest’ successfully unpacked and MD5 sums checked
package ‘memoise’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘BH’ successfully unpacked and MD5 sums checked
package ‘plogr’ successfully unpacked and MD5 sums checked
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘S4Vectors’ successfully unpacked and MD5 sums checked
package ‘DBI’ successfully unpacked and MD5 sums checked
package ‘RSQLite’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\espinla2\AppData\Local\Temp\Rtmpc1BouX\downloaded_packages
Old packages: 'boot', 'cluster', 'codetools', 'foreign',
  'lattice', 'Matrix', 'mgcv', 'nlme', 'nnet', 'survival'
Update all/some/none? [a/s/n]: 

Update all/some/none? [a/s/n]:
a

  There is a binary version available but the source
  version is later:
         binary  source needs_compilation
lattice 0.20-34 0.20-35              TRUE

Do you want to install from sources the package which needs compilation?
y/n: n
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/boot_1.3-18.zip'
Content type 'application/zip' length 591979 bytes (578 KB)
downloaded 578 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/cluster_2.0.6.zip'
Content type 'application/zip' length 536894 bytes (524 KB)
downloaded 524 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/codetools_0.2-15.zip'
Content type 'application/zip' length 46174 bytes (45 KB)
downloaded 45 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/foreign_0.8-67.zip'
Content type 'application/zip' length 288578 bytes (281 KB)
downloaded 281 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/lattice_0.20-34.zip'
Content type 'application/zip' length 729637 bytes (712 KB)
downloaded 712 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/Matrix_1.2-8.zip'
Content type 'application/zip' length 2779115 bytes (2.7 MB)
downloaded 2.7 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/mgcv_1.8-17.zip'
Content type 'application/zip' length 2322937 bytes (2.2 MB)
downloaded 2.2 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/nlme_3.1-131.zip'
Content type 'application/zip' length 2160919 bytes (2.1 MB)
downloaded 2.1 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/nnet_7.3-12.zip'
Content type 'application/zip' length 121043 bytes (118 KB)
downloaded 118 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/survival_2.41-2.zip'
Content type 'application/zip' length 5242571 bytes (5.0 MB)
downloaded 5.0 MB

package ‘boot’ successfully unpacked and MD5 sums checked
package ‘cluster’ successfully unpacked and MD5 sums checked
package ‘codetools’ successfully unpacked and MD5 sums checked
package ‘foreign’ successfully unpacked and MD5 sums checked
package ‘lattice’ successfully unpacked and MD5 sums checked
package ‘Matrix’ successfully unpacked and MD5 sums checked
package ‘mgcv’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘nnet’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\espinla2\AppData\Local\Temp\Rtmpc1BouX\downloaded_packages

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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
[6] methods   base     

other attached packages:
[1] BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] tools_3.2.3

ADD COMMENTlink modified 20 months ago by Mike Smith3.1k • written 20 months ago by larisa.espinoza0
2
gravatar for James W. MacDonald
20 months ago by
United States
James W. MacDonald48k wrote:

It's pretty straightforward, and your question is answered in the question that R asks you:

There is a binary version available but the source
  version is later:
         binary  source needs_compilation
lattice 0.20-34 0.20-35              TRUE

Do you want to install from sources the package which needs compilation?

There are two versions of lattice available, and the latest version is a source package that will need to be compiled. If you aren't set up to compile C code, then you have to say 'no' because, well, you aren't set up to compile C code.

You will always be asked if you want the latest version, because that's what biocLite does - it looks for the latest version of your packages. This is sort of annoying when the source version is newer than the binary, but it IS the latest version, so you are asked if that is what you want.

ADD COMMENTlink written 20 months ago by James W. MacDonald48k
0
gravatar for Mike Smith
20 months ago by
Mike Smith3.1k
EMBL Heidelberg / de.NBI
Mike Smith3.1k wrote:

This isn't strictly a Bioconductor question, but I think the important part in the output is this:

There is a binary version available but the source
version is later:
         binary  source needs_compilation
lattice 0.20-34 0.20-35              TRUE

Do you want to install from sources the package which needs compilation?
y/n: n

This is telling you that there are two slightly different versions of the lattice package, and that the 'source' version is newer.  However, you chose to install the older 'binary' version.  Then the next time you install a package, it will again notice that there is a newer source version and will again ask if you would like to install it.  You can try answering 'y' to the question about installing the source version.  You may find that you need to install some additional tools on your computer, but that is hard to assess without seeing the outcome from trying it.

I would also recommend that you use the most recent version of R, as some packages (particularly in Bioconductor) are tied to specific versions of R and you can miss out on new features.  R is currently on version 3.3.3, and version 3.4 is due to be released next month.

ADD COMMENTlink written 20 months ago by Mike Smith3.1k
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