synapser_check build fails on ubuntu

Description

From: http://jenkins.sagebase.org:8080/user/sagebio/my-views/view/synapser/job/synapser_check/RVERS=3.5,label=ubuntu-remote/74/consoleFull

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (PythonEmbedInR) * installing *source* package ‘synapser’ ... WARNING: ignoring environment value of R_HOME Error: package ‘PythonEmbedInR’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version In addition: Warning message: package ‘PythonEmbedInR’ was built under R version 3.5.0 Execution halted WARNING: ignoring environment value of R_HOME Error: package ‘PythonEmbedInR’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version In addition: Warning message: package ‘PythonEmbedInR’ was built under R version 3.5.0 Execution halted ERROR: configuration failed for package ‘synapser’ * removing ‘/usr/local/R/R-3.5.0/library/synapser’ The downloaded source packages are in ‘/tmp/RtmpENabtc/downloaded_packages’ Updating HTML index of packages in '.Library' Warning messages: 1: In install.packages("synapser", repos = c("http://cran.fhcrc.org", : installation of package ‘synapser’ had non-zero exit status 2: In file.create(f.tg) : cannot create file '/usr/local/R/R-3.5.0/doc/html/packages.html', reason 'Permission denied' 3: In make.packages.html(.Library) : cannot update HTML package index > library('synapser') Error in library("synapser") : there is no package called ‘synapser’ Execution halted Build step 'Execute shell' marked build as failure Sending e-mails to: platform@sagebase.org Notifying upstream projects of job completion Finished: FAILURE

Environment

Ubuntu, R 3.4/ 3.5

Status

Assignee

Unassigned

Reporter

Kimyen Truong

Labels

None

Validator

Ziming Dong

Release Version History

None

Components

Priority

Major
Configure