search

MikeJSeo / SAM

SAM (Significance Analysis of Microarrays) shiny app
https://cran.r-project.org/web/packages/samr/index.html
37 stars 20 forks source link

SAMR installation has non-zero exit status #30

Open Sebbeluriusbelurius opened 6 years ago

Sebbeluriusbelurius commented 6 years ago

Hello.

After years of using, I am now having trouble running SAM on MAC OSX 10.13.3 (High Sierra) and R version 3.4.3. I get the following error message:

Listening on http://127.0.0.1:3388 Warning: Error in library: there is no package called ‘samr’ Stack trace (innermost first): 42: library 3: runApp 2: runUrl 1: runGitHub Error in library(samr) : there is no package called ‘samr’ ERROR: [on_request_read] connection reset by peer

This error seems to be connected to the changes in version number of my MAC OS rather than errors in SAM. Can you please help me?

MikeJSeo commented 6 years ago

I need you need to install the samr package again.. Sorry for terribly late response. install.packages("samr")

Sebbeluriusbelurius commented 6 years ago

Hello Mike.

Thank you for the reply, however late. I am sorry to bother you about this again, as the solution presented does not seem to work.

Here is the text i get in reply from R when writing the install command:

install.packages("samr") Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘samr’ Do you want to attempt to install these from sources? y/n: y installing the source package ‘samr’

trying URL 'http://cran.uib.no/src/contrib/samr_2.0.tar.gz' Content type 'application/x-gzip' length 36702 bytes (35 KB)

downloaded 35 KB

The downloaded source packages are in ‘/private/var/folders/1p/b54tdshx0_l_y_vl_6v8mkl40000gn/T/Rtmp1CS3dh/downloaded_packages’ Warning message: In install.packages("samr") : installation of package ‘samr’ had non-zero exit status

Do you have a suggestion on how to overcome this? I am grateful for your reply.

Best regards,

Sebastian Meltzer

  1. mar. 2018 kl. 17:14 skrev Michael Seo notifications@github.com:

install.packages("samr")

generaldzyroot commented 6 years ago

Hi, i got the same problem as you do, if you have any suggestions? Best wishes,

Sebbeluriusbelurius commented 6 years ago

Hello. I actually found a solution. I am not sure if it is the best, but it worked. I followed the solution on this link: https://apple.stackexchange.com/questions/254380/macos-sierra-invalid-active-developer-path Essentially, I installed Xcode, and wrote xcode-select --install in the terminal. After that I restarted the computer, and was finally allowed to install the SAMR package, so that everything worked again.

Hope this works for more than me.

Sebastian Meltzer