sage-bionetworks / rsynapseclient Goto Github PK

I recently found out about MSL through a conference on free and open source software. I'm a current student at Seneca College about to complete my degree in bioinformatics. The size and diversity of the online community within this field is remarkable, and I would like to try my best to contribute back to all the developers that have enabled me to do the work I do now!

This issue was created by @nishanthmerwin via Mozilla Science Lab Collaborate

Thinking this might be browser specific, I tried safari also:

https://github.com/Sage-Bionetworks/rSynapseClient/blob/master/docs.synapse.org/articles/getting_started.html

_Hi,

I'm trying to install Synapse Client for R 3.3.1 and getting the following error._

> source('http://depot.sagebase.org/CRAN.R')
> pkgInstall("synapseClient")

.....Multiple packages got installed nicely until rjson....

Loading required package: rjson
** libs
gcc -std=gnu99 -I/opt/local/stow/R-3.3.1/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_init_Synapse.c -o R_init_Synapse.o
gcc -std=gnu99 -I/opt/local/stow/R-3.3.1/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c synapse_curl.c -o synapse_curl.o
gcc -std=gnu99 -shared -L/opt/local/stow/R-3.3.1/lib64/R/lib -Wl,-rpath=/opt/local/stow/R-3.3.1/lib64/R/lib:/opt/local/stow/R-3.3.1/lib/R/lib -o synapseClient.so R_init_Synapse.o synapse_curl.o -L/opt/local/stow/R-3.3.1/lib64/R/lib -lR
installing to /cbcbhomes/sanju/R/x86_64-pc-linux-gnu-library/3.3/synapseClient/libs
** R
** inst
** preparing package for lazy loading
Error in read.table(system.file("resources/s4ClassesToGenerate.txt", package = "synapseClient"), :
no lines available in input
Error : unable to load R code in package 'synapseClient'
ERROR: lazy loading failed for package 'synapseClient'

• removing '/cbcbhomes/sanju/R/x86_64-pc-linux-gnu-library/3.3/synapseClient'

The downloaded source packages are in
'/tmp/Rtmp9DWxCm/downloaded_packages'
Warning message:
In install.packages(package, repos = c(sageRepo, "http://cran.r-project.org"), :
installation of package 'synapseClient' had non-zero exit status

The file resources/s4ClassesToGenerate.txt has some problem. Also, tried downloading the developing phase one.

> library(devtools)
> install_github('Sage-Bionetworks/rSynapseClient', ref='develop')

Again similar problem in rjson package.

** preparing package for lazy loading
Error in read.table(system.file("resources/s4ClassesToGenerate.txt", package = "synapseClient"), :
no lines available in input
Error : unable to load R code in package 'synapseClient'
ERROR: lazy loading failed for package 'synapseClient'

• removing '/cbcbhomes/sanju/R/x86_64-pc-linux-gnu-library/3.3/synapseClient'
  Installation failed: Command failed (1)

Thanks.

Hello,
I'm a statistics undergrad from Sylhet, Bangladesh. Currently I'm studying statistics at Shahjalal University of Science and Technology, Sylhet. So, as a statistics student I'm very much interested in this project.

Basically I'm a hardcore PHP developer. But I had some courses on "R Programming Language" (As I mentioned earlier I'm a statistics undergrad) as a part of my undergrad courses. So I think I can contribute to this project.

Thank You.

This issue was created by @rnaby via Mozilla Science Lab Collaborate

This issue was created by @BinaryScripter via Mozilla Science Lab Collaborate

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

Dear Sage-Bionetworks team,

I am having trouble installing the rSynapseClient on Mac OS X with R 3.4. I get the following error:

install.packages("rSynapseClient",
    repos= c("http://depot.sagebase.org/CRAN/prod/3.4", "http://cran.r-project.org"))
Warning in install.packages :
  package ‘synapseClient’ is not available (for R version 3.4.0)

Next, I tried to install the development version using devtools, but without success:

> 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
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/rq/q19k6q511wqglz6kt7jl_t_r0000gp/T/RtmpNvD51o/devtoolsd3d91be26ac3/Sage-Bionetworks-rSynapseClient-2be9324'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests 

* installing *source* package ‘synapseClient’ ...
--2017-07-05 11:27:51--  http://sagebionetworks.artifactoryonline.com/sagebionetworks/libs-releases-local/org/sagebionetworks/lib-auto-generated/174.0/lib-auto-generated-174.0.jar
Resolving sagebionetworks.artifactoryonline.com... 107.23.217.190, 34.207.22.79
Connecting to sagebionetworks.artifactoryonline.com|107.23.217.190|:80... connected.
HTTP request sent, awaiting response... 403 Forbidden
2017-07-05 11:27:52 ERROR 403: Forbidden.

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100  6387  100  6387    0     0  37608      0 --:--:-- --:--:-- --:--:-- 37792
[temp.jar]
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of temp.jar or
        temp.jar.zip, and cannot find temp.jar.ZIP, period.
Loading required package: rjson
Error in readSchema(schemaName, schemaPath) : 
  Could not find file: ./inst/resources/schema/org/sagebionetworks/repo/model/message/Settings.json for entity: org.sagebionetworks.repo.model.message.Settings
Calls: autoGenerateRdFiles ... createRdFromSchema -> getEffectivePropertySchemas -> readSchema
Execution halted
ERROR: configuration failed for package ‘synapseClient’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/synapseClient’
Installation failed: Command failed (1)

Any hints on how to install the package?
Many thanks,
Thomas

> synapseLogin()
To upload files to a private AWS S3 bucket, you must use version 1.8 (or later).

Welcome tschaffter!

I tried using sink() and capture.output() to suppress the message but it doesn't work. This is particularly problematic when used in a R Notebook.

Thanks!

Hello, Sage,

Say we have a project folder with a bunch of tables in it. I'm wondering if there is a way to fetch all the table names and IDs in that project folder?

I tried to use something like synGet(project_id, downloadFile = F) but it seems like I cannot find the information I need in the result.

Thanks!