It shows > install.packages("synapser") Installing package into ?/usr/local/lib/R/4.0/site-library? (as ?lib? is unspecified) Warning in install.packages : package ?synapser? is not available (for R version 4.0.2)

Created by Xuye Luo luoxuye
Great! Happy to hear that your issue is resolved. Thanks, Jineta
Thank you for your reply, I finally fix it today. I tried many methods that are not working. It is a homebrew issue, I installed r by homebrew. After I uninstall r and reinstall r by https://www.r-project.org/. It is working. Thank you very much!
@luoxuye : please try the following for the installation of synapser : ```plaintext install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"), type="mac.binary") ``` Please see this response from our platform team for the explanation: "This indicates that on their Mac their R installation is attempting to compile packages from source rather than using the pre-built binary packages. On a Mac, a version of R that was installed from brew or that was itself compiled from source rather than installed from a binary pkg installer as available from e.g. https://cloud.r-project.org/bin/macosx/ will by default compile all CRAN packages from source even when compiled binary packages are available (all packages not just synapser). The dependencies necessary to compile synapser (due to PythonEmbedInR) requires a development toolchain that may not be installed on all Macs. On such a version of R you can force it to use binary packages using the extra type="mac.binary" parameter to install.packages, e.g. `install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"), type="mac.binary")` "
The sessionInfo() looks fine and should be able to support `synapser`. So it seems that the problem is related to `openssl`. Did any of the suggestions in the link or reinstalling `openssl` work for you?
> sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin19.5.0 (64-bit) Running under: macOS Catalina 10.15.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /usr/local/Cellar/openblas/0.3.10_1/lib/libopenblasp-r0.3.10.dylib 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] stats graphics grDevices utils datasets [6] methods base loaded via a namespace (and not attached): [1] BiocManager_1.30.10 compiler_4.0.2 [3] tools_4.0.2
Some other options to try: check out this link: https://gist.github.com/aklap/e885721ef15c8668ed0a1dd64d2ea1a7#gistcomment-2814899
Hi @luoxuye, sorry to hear that you are having trouble with Synapser. I could not reproduce the error you are seeing. From the preliminary look it seems like you are missing this file : `/usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib`. Can you confirm that you have openssl installed? You can run `brew install openssl` from your terminal to install it. Also, can you please paste in the output you get when you run `sessionInfo()`in Rstudio ? Thanks, Jineta
But I still can not install synapser, I tried many times and I did not find the solution.
> install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")) Installing package into ?/usr/local/lib/R/4.0/site-library? (as ?lib? is unspecified) also installing the dependency ?PythonEmbedInR? trying URL 'https://sage-bionetworks.github.io/ran/src/contrib/PythonEmbedInR_0.3.25.tar.gz' Content type 'application/gzip' length 93845 bytes (91 KB) ================================================== downloaded 91 KB trying URL 'https://sage-bionetworks.github.io/ran/src/contrib/synapser_0.6.54.tar.gz' Content type 'application/gzip' length 132790 bytes (129 KB) ================================================== downloaded 129 KB * installing *source* package ?PythonEmbedInR? ... ** using staged installation ./configure: line 32: wget: command not found % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 1 19.6M 1 206k100 19.6M 100 19.6M 0 0 16.1M 0 0:00:01 0:00:01 --:--:-- 16.1M Mac specific configuration cp: /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib: No such file or directory ERROR: configuration failed for package ?PythonEmbedInR? * removing ?/usr/local/lib/R/4.0/site-library/PythonEmbedInR? Warning in install.packages : installation of package ?PythonEmbedInR? had non-zero exit status ERROR: dependency ?PythonEmbedInR? is not available for package ?synapser? * removing ?/usr/local/lib/R/4.0/site-library/synapser? Warning in install.packages : installation of package ?synapser? had non-zero exit status The downloaded source packages are in ?/private/var/folders/4q/45syd7xn5sv9szdjg542vcym0000gn/T/Rtmpc4zExH/downloaded_packages?
Hi @luoxuye : Please use the following to install synapser: ``` install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")) ``` Please see the documentation here: https://r-docs.synapse.org/

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