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Installation failure on R 3.5 #336

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Rongfang-Shen opened this issue Jun 24, 2018 · 2 comments
Open

Installation failure on R 3.5 #336

Rongfang-Shen opened this issue Jun 24, 2018 · 2 comments

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@Rongfang-Shen
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Rongfang-Shen commented Jun 24, 2018

Dear Sage-Bionetworks team,
I am having trouble installing the rSynapseClient on Windows with R 3.5

source("http://depot.sagebase.org/CRAN.R")
 pkgInstall(c("synapseClient"))
Warning in install.packages :
  unable to access index for repository http://depot.sagebase.org/CRAN/prod/3.5/src/contrib:
  cannot open URL 'http://depot.sagebase.org/CRAN/prod/3.5/src/contrib/PACKAGES'

Then I try to install packages through github devtools

library(devtools)
install_github('Sage-Bionetworks/rSynapseClient', ref='develop')
Downloading GitHub repo Sage-Bionetworks/rSynapseClient@develop
from URL https://api.github.com/repos/Sage-Bionetworks/rSynapseClient/zipball/develop
Installing synapseClient
"C:/PROGRA~1/R/R-35~1.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  "C:/Users/yohahah/AppData/Local/Temp/RtmpCq91C8/devtools2dc8511e3139/Sage-Bionetworks-rSynapseClient-94d5730"  \
  --library="C:/Users/yohahah/Documents/R/win-library/3.5" --install-tests 

* installing *source* package 'synapseClient' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/Rtools/mingw_64/bin/"gcc  -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_Synapse.c -o R_init_Synapse.o
"C:/Rtools/mingw_64/bin/"gcc  -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mtune=generic -c synapse_curl.c -o synapse_curl.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o synapseClient.dll tmp.def R_init_Synapse.o synapse_curl.o -LC:/PROGRA~1/R/R-35~1.0/bin/x64 -lR
installing to C:/Users/yohahah/Documents/R/win-library/3.5/synapseClient/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Error in readSchema(name, path) : 
  Could not find file: /org/sagebionetworks/repo/model/provenance/Activity.json for entity: org.sagebionetworks.repo.model.provenance.Activity
Error : unable to load R code in package 'synapseClient'
ERROR: lazy loading failed for package 'synapseClient'
* removing 'C:/Users/yohahah/Documents/R/win-library/3.5/synapseClient'
In R CMD INSTALL


I can't find a way to install it correctly.
Any hints on how to install the package?
Thanks!
Rongfang Shen

@Rongfang-Shen Rongfang-Shen changed the title Installation failure on R 3.4 Installation failure on R 3.5 Jun 24, 2018
@kimyen
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kimyen commented Jun 25, 2018

Hi @yohahah ,
We have been developing a new R package for Synapse R client, called synapser. Please see download instruction here: https://github.com/Sage-Bionetworks/synapser#installation
Some functions in synapser may behave differently than in our legacy rSynapseClient. Please see our documentation for more details: http://sage-bionetworks.github.io/synapser/articles/synapser.html

@Rongfang-Shen
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Many thanks!

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