Use of minfi using (maverick3.2 and Developer) on Yosemite OS
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0
Entering edit mode
morrisht • 0
@morrisht-7605
Last seen 9.6 years ago
United States

Not certain if this is an issue regarding the version of R or my minimal
 experience of using it.   I am at an epigenetics NIH workshop that has a
short computer based R section for analyzing epigenetic data.  As someone
mostly interested in understanding what tools are available for routine
analysis of illumina methylation arrays, I thought it was strange that I could not load "minfi" library on
the R version 3.2 or from the R developer version for the Mac (Maverick) using
the Yosemite operating system.  My understanding is that Yosemite is the
 newer operating system for Mac. It is not certain why the minfi library was
not downloaded from the site when I updated R to 3.2  for the Mac OS or for the Developer site(maverick). 

We are not currently working on these methylation arrays, however for future studies
 it may be critical to know whether this is simply just an issue I am having
regarding my inexperience in using R or if it is has more to do with the
differences in R versions in using the Yosemite vs Maverick Operating
systems.  Mostly asking since the class was using R version 3.1.13 on a Dell?
version compatibility minfi • 2.5k views
ADD COMMENT •
0
Entering edit mode

It would help if you included the command you used to try to install minfi, and its complete output.

Try installing it this way:

source("http://bioconductor.org/biocLite.R")
biocLite("minfi")

minfi is available for Mavericks (and thus for Yosemite) for the version of R/Bioconductor you are using. See its landing page.

ADD REPLY •
0
Entering edit mode

I am only copying the last bit of command information.  If needed I can post the entire information associated with the download, however there is still an issue in the download since the library is not opening and there are warning messages. 

The downloaded source packages are in
    ‘/private/var/folders/r3/bm48884x2l13vrb9fp41pzbm0000gn/T/Rtmp28ccVf/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘plyr’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘matrixStats’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘mclust’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RSQLite’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘reshape’ had non-zero exit status

 

> library(‘minfi’)
Error: unexpected input in "library(‚"
>
> library (‘minfi’)
Error: unexpected input in "library (‚"
>
> library (‘minfi’)
Error: unexpected input in "library (‚"
>

 

ADD REPLY •
0
Entering edit mode

Perhaps this is the issue when I initially run the command it asks:

 

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.17.7), R version 3.2.0.
Installing package(s) ‘minfi’
also installing the dependencies ‘plyr’, ‘matrixStats’, ‘mclust’, ‘reshape’


  There is a binary version available but the source version is later:
       binary source needs_compilation
mclust    4.4  5.0.0              TRUE

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

I said yes, but maybe I should have said no? 

ADD REPLY •
0
Entering edit mode

If I say no, this is the message:

Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘plyr’ ‘matrixStats’
Do you want to attempt to install these from sources?
y/n:

ADD REPLY •
0
Entering edit mode

Please post the whole message, INCLUDING the actual command. I have no idea what command you typed to try and install minfi. Also, try starting R with "R --vanilla". And you should say "no" to the question unless you have Xcode and gfortran installed.

 

 

ADD REPLY •
0
Entering edit mode
morrisht • 0
@morrisht-7605
Last seen 9.6 years ago
United States

R version 3.2.0 RC (2015-04-09 r68171) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.

[R.app GUI 1.65 (6931) x86_64-apple-darwin13.4.0]

[History restored from /Users/tammymorrish/.Rapp.history]

> "hi"
[1] "hi"
> #source("http://bioconductor.org/biocLite.R")
>
> #biocLite(“minfi")
>
> source("http://bioconductor.org/biocLite.R")
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/BiocInstaller_1.17.7.tgz'
Content type 'application/x-gzip' length 51613 bytes (50 KB)
==================================================
downloaded 50 KB


The downloaded binary packages are in
    /var/folders/r3/bm48884x2l13vrb9fp41pzbm0000gn/T//Rtmp28ccVf/downloaded_packages
Bioconductor version 3.1 (BiocInstaller 1.17.7), ?biocLite for help
> library(‘minfi’)
Error: unexpected input in "library(‚"
>
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.17.7), ?biocLite for help
> biocLite("minfi")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.17.7), R version 3.2.0.
Installing package(s) ‘minfi’
also installing the dependencies ‘lambda.r’, ‘futile.options’, ‘futile.logger’, ‘snow’, ‘BiocParallel’, ‘stringr’, ‘digest’, ‘registry’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rngtools’, ‘pkgmaker’, ‘DBI’, ‘RSQLite’, ‘rtracklayer’, ‘biomaRt’, ‘xtable’, ‘Rcpp’, ‘bitops’, ‘XVector’, ‘zlibbioc’, ‘foreach’, ‘iterators’, ‘locfit’, ‘doRNG’, ‘GenomicFeatures’, ‘AnnotationDbi’, ‘multtest’, ‘base64’, ‘annotate’, ‘plyr’, ‘XML’, ‘RCurl’, ‘BiocGenerics’, ‘Biobase’, ‘GenomicRanges’, ‘Biostrings’, ‘bumphunter’, ‘S4Vectors’, ‘GenomeInfoDb’, ‘IRanges’, ‘beanplot’, ‘RColorBrewer’, ‘nor1mix’, ‘siggenes’, ‘limma’, ‘preprocessCore’, ‘illuminaio’, ‘matrixStats’, ‘mclust’, ‘genefilter’, ‘reshape’, ‘quadprog’, ‘GEOquery’


  There is a binary version available but the source version is later:
       binary source needs_compilation
mclust    4.4  5.0.0              TRUE

Do you want to install from sources the package which needs compilation?
y/n: y
Packages which are only available in source form, and may need compilation of
  C/C++/Fortran: ‘RSQLite’ ‘plyr’ ‘matrixStats’
Do you want to attempt to install these from sources?
y/n: y
trying URL 'http://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.2/lambda.r_1.1.7.tgz'
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The downloaded binary packages are in
    /var/folders/r3/bm48884x2l13vrb9fp41pzbm0000gn/T//Rtmp28ccVf/downloaded_packages
installing the source packages ‘futile.logger’, ‘stringr’, ‘rngtools’, ‘pkgmaker’, ‘DBI’, ‘RSQLite’, ‘doRNG’, ‘plyr’, ‘matrixStats’, ‘mclust’, ‘reshape’

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* installing *source* package ‘futile.logger’ ...
** package ‘futile.logger’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (futile.logger)
* installing *source* package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (stringr)
* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (DBI)
* installing *source* package ‘plyr’ ...
** package ‘plyr’ successfully unpacked and MD5 sums checked
** libs
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
ERROR: compilation failed for package ‘plyr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/plyr’
* installing *source* package ‘matrixStats’ ...
** package ‘matrixStats’ successfully unpacked and MD5 sums checked
** libs
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
ERROR: compilation failed for package ‘matrixStats’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/matrixStats’
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** libs
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
ERROR: compilation failed for package ‘mclust’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/mclust’
* installing *source* package ‘pkgmaker’ ...
** package ‘pkgmaker’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Creating meta registry in package 'pkgmaker' ... OK
Creating registry 'extra_handler' in package 'pkgmaker' ... OK
Creating registry 'extra_action' in package 'pkgmaker' ... OK
Registering extra handler 'install.packages' [function] ... OK
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pkgmaker)
* installing *source* package ‘RSQLite’ ...
** package ‘RSQLite’ successfully unpacked and MD5 sums checked
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
checking for gcc... gcc
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.
checking whether the C compiler works... no
configure: error: in `/private/var/folders/r3/bm48884x2l13vrb9fp41pzbm0000gn/T/Rtmpnwya7M/R.INSTALL2e7d4806858e/RSQLite':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘RSQLite’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite’
ERROR: dependency ‘plyr’ is not available for package ‘reshape’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/reshape’
* installing *source* package ‘rngtools’ ...
** package ‘rngtools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rngtools)
* installing *source* package ‘doRNG’ ...
** package ‘doRNG’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (doRNG)

The downloaded source packages are in
    ‘/private/var/folders/r3/bm48884x2l13vrb9fp41pzbm0000gn/T/Rtmp28ccVf/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘plyr’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘matrixStats’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘mclust’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RSQLite’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘reshape’ had non-zero exit status
> #biocLite ("wateRmelon")
> )
Error: unexpected ')' in ")"
> #biocLite ('wateRmelon')
>
> #source("http://bioconductor.org/biocLite.R")
>
> #biocLite(“watermelon")
>
> #biocLite(“wateRmelon")
>
> library(‘minfi’)
Error: unexpected input in "library(‚"
>
> library (‘minfi’)
Error: unexpected input in "library (‚"
>
> library (‘minfi’)
Error: unexpected input in "library (‚"
2015-04-15 19:19:12.308 R[11282:326342] Layout still needs update after calling -[NSScrollView layout].  NSScrollView or one of its superclasses may have overridden -layout without calling super. Or, something may have dirtied layout in the middle of updating it.  Both are programming errors in Cocoa Autolayout.  The former is pretty likely to arise if some pre-Cocoa Autolayout class had a method called layout, but it should be fixed.
> exit
Error: object 'exit' not found
> quit
function (save = "default", status = 0, runLast = TRUE)
.Call("RappQuit", save, status, runLast)
<environment: 0x7fac6a1df2b0>
> "hi"
[1] "hi"
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.17.7), ?biocLite for help
> biocLite("minfi")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.17.7), R version 3.2.0.
Installing package(s) ‘minfi’
also installing the dependencies ‘plyr’, ‘matrixStats’, ‘mclust’, ‘reshape’


  There is a binary version available but the source version is later:
       binary source needs_compilation
mclust    4.4  5.0.0              TRUE

Do you want to install from sources the package which needs compilation?
y/n: n
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘plyr’ ‘matrixStats’
Do you want to attempt to install these from sources?
y/n:
trying URL 'http://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.2/mclust_4.4.tgz'
Content type 'application/x-gzip' length 2553399 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/minfi_1.13.13.tgz'
Content type 'application/x-gzip' length 659841 bytes (644 KB)
==================================================
downloaded 644 KB


The downloaded binary packages are in
    /var/folders/r3/bm48884x2l13vrb9fp41pzbm0000gn/T//Rtmp28ccVf/downloaded_packages
installing the source package ‘reshape’

trying URL 'http://cran.fhcrc.org/src/contrib/reshape_0.8.5.tar.gz'
Content type 'application/x-gzip' length 42350 bytes (41 KB)
==================================================
downloaded 41 KB

ERROR: dependency ‘plyr’ is not available for package ‘reshape’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/reshape’

The downloaded source packages are in
    ‘/private/var/folders/r3/bm48884x2l13vrb9fp41pzbm0000gn/T/Rtmp28ccVf/downloaded_packages’
Old packages: 'mclust'
Update all/some/none? [a/s/n]:

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

  There is a binary version available but the source version is later:
       binary source needs_compilation
mclust    4.4  5.0.0              TRUE

Do you want to install from sources the package which needs compilation?
y/n:
ADD COMMENT •
0
Entering edit mode

OK, let's start over again.

Start R from the terminal (/Applications/Utiltities/Terminal.app). In the terminal window, type:

R --vanilla

At the R prompt, type:

source("http://bioconductor.org/biocLite.R")
biocLite("minfi")

 

If you are asked to install anything from source, say NO.

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