Fix package about outbreaks HOT 3 CLOSED

Using worker: worker-linux-docker-474c03de.prod.travis-ci.org:travis-linux-9
system_info
Build system information
Build language: r
Build group: stable
Build dist: precise
Build id: 171347950
Job id: 171347951
travis-build version: f2e5e21fe
Build image provisioning date and time
Thu Feb  5 15:09:33 UTC 2015
Operating System Details
Distributor ID: Ubuntu
Description:    Ubuntu 12.04.5 LTS
Release:    12.04
Codename:   precise
Linux Version
3.13.0-29-generic
Cookbooks Version
a68419e https://github.com/travis-ci/travis-cookbooks/tree/a68419e
GCC version
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
LLVM version
clang version 3.4 (tags/RELEASE_34/final)
Target: x86_64-unknown-linux-gnu
Thread model: posix
Pre-installed Ruby versions
ruby-1.9.3-p551
Pre-installed Node.js versions
v0.10.36
Pre-installed Go versions
1.4.1
Redis version
redis-server 2.8.19
riak version
2.0.2
MongoDB version
MongoDB 2.4.12
CouchDB version
couchdb 1.6.1
Neo4j version
1.9.4
RabbitMQ Version
3.4.3
ElasticSearch version
1.4.0
Installed Sphinx versions
2.0.10
2.1.9
2.2.6
Default Sphinx version
2.2.6
Installed Firefox version
firefox 31.0esr
PhantomJS version
1.9.8
ant -version
Apache Ant(TM) version 1.8.2 compiled on December 3 2011
mvn -version
Apache Maven 3.2.5 (12a6b3acb947671f09b81f49094c53f426d8cea1; 2014-12-14T17:29:23+00:00)
Maven home: /usr/local/maven
Java version: 1.7.0_76, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-7-oracle/jre
Default locale: en_US, platform encoding: ANSI_X3.4-1968
OS name: "linux", version: "3.13.0-29-generic", arch: "amd64", family: "unix"
fix.CVE-2015-7547
$ export DEBIAN_FRONTEND=noninteractive
W: Size of file /var/lib/apt/lists/us.archive.ubuntu.com_ubuntu_dists_precise-backports_multiverse_source_Sources.gz is not what the server reported 5886 5888
W: Size of file /var/lib/apt/lists/ppa.launchpad.net_travis-ci_zero-mq_ubuntu_dists_precise_main_binary-amd64_Packages.gz is not what the server reported 832 1195
W: Size of file /var/lib/apt/lists/ppa.launchpad.net_ubuntugis_ppa_ubuntu_dists_precise_main_binary-amd64_Packages.gz is not what the server reported 33653 36677
W: Size of file /var/lib/apt/lists/ppa.launchpad.net_ubuntugis_ppa_ubuntu_dists_precise_main_binary-i386_Packages.gz is not what the server reported 33699 36733
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  libc-bin libc-dev-bin libc6-dev
Suggested packages:
  glibc-doc
The following packages will be upgraded:
  libc-bin libc-dev-bin libc6 libc6-dev
4 upgraded, 0 newly installed, 0 to remove and 258 not upgraded.
Need to get 8,840 kB of archives.
After this operation, 14.3 kB disk space will be freed.
Get:1 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main libc6-dev amd64 2.15-0ubuntu10.15 [2,943 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main libc-dev-bin amd64 2.15-0ubuntu10.15 [84.7 kB]
Get:3 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main libc-bin amd64 2.15-0ubuntu10.15 [1,177 kB]
Get:4 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main libc6 amd64 2.15-0ubuntu10.15 [4,636 kB]
Fetched 8,840 kB in 0s (35.6 MB/s)
Preconfiguring packages ...
(Reading database ... 71420 files and directories currently installed.)
Preparing to replace libc6-dev 2.15-0ubuntu10.10 (using .../libc6-dev_2.15-0ubuntu10.15_amd64.deb) ...
Unpacking replacement libc6-dev ...
Preparing to replace libc-dev-bin 2.15-0ubuntu10.10 (using .../libc-dev-bin_2.15-0ubuntu10.15_amd64.deb) ...
Unpacking replacement libc-dev-bin ...
Preparing to replace libc-bin 2.15-0ubuntu10.10 (using .../libc-bin_2.15-0ubuntu10.15_amd64.deb) ...
Unpacking replacement libc-bin ...
Processing triggers for man-db ...
Setting up libc-bin (2.15-0ubuntu10.15) ...
(Reading database ... 71419 files and directories currently installed.)
Preparing to replace libc6 2.15-0ubuntu10.10 (using .../libc6_2.15-0ubuntu10.15_amd64.deb) ...
Unpacking replacement libc6 ...
Setting up libc6 (2.15-0ubuntu10.15) ...
Setting up libc-dev-bin (2.15-0ubuntu10.15) ...
Setting up libc6-dev (2.15-0ubuntu10.15) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
R for Travis-CI is not officially supported, but is community maintained.
Please file any issues at https://github.com/travis-ci/travis-ci/issues
and mention @craigcitro, @hadley and @jimhester in the issue
R-install
Installing R
0.43s$ sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)/"
0.28s$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --secret-keyring /tmp/tmp.CQXJsmvUoQ --trustdb-name /etc/apt/trustdb.gpg --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyring /etc/apt/trusted.gpg.d//apt.postgresql.org.gpg --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com
gpg: key E084DAB9: public key "Michael Rutter <[email protected]>" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
1.14s$ sudo add-apt-repository -y "ppa:marutter/rrutter"
gpg: keyring `/tmp/tmptmnaRo/secring.gpg' created
gpg: keyring `/tmp/tmptmnaRo/pubring.gpg' created
gpg: requesting key B04C661B from hkp server keyserver.ubuntu.com
gpg: /tmp/tmptmnaRo/trustdb.gpg: trustdb created
gpg: key B04C661B: public key "Launchpad PPA for marutter" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
OK
1.08s$ sudo add-apt-repository -y "ppa:marutter/c2d4u"
gpg: keyring `/tmp/tmpEo6C1q/secring.gpg' created
gpg: keyring `/tmp/tmpEo6C1q/pubring.gpg' created
gpg: requesting key B04C661B from hkp server keyserver.ubuntu.com
gpg: /tmp/tmpEo6C1q/trustdb.gpg: trustdb created
gpg: key B04C661B: public key "Launchpad PPA for marutter" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
OK
6.77s$ sudo apt-get update -qq
16.90s$ sudo apt-get install -y --no-install-recommends build-essential gcc g++ gfortran libblas-dev liblapack-dev libncurses5-dev libreadline-dev libjpeg-dev libpng-dev zlib1g-dev libbz2-dev liblzma-dev cdbs qpdf texinfo
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting 'libpng12-dev' instead of 'libpng-dev'
g++ is already the newest version.
g++ set to manually installed.
gcc is already the newest version.
gcc set to manually installed.
libbz2-dev is already the newest version.
libjpeg-dev is already the newest version.
libjpeg-dev set to manually installed.
libncurses5-dev is already the newest version.
libreadline-dev is already the newest version.
zlib1g-dev is already the newest version.
zlib1g-dev set to manually installed.
build-essential is already the newest version.
The following extra packages will be installed:
  dh-translations gfortran-4.6 intltool libencode-locale-perl
  libfile-listing-perl libhtml-parser-perl libhtml-tagset-perl
  libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl
  libhttp-message-perl libhttp-negotiate-perl libintl-perl
  libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl
  libnet-http-perl libnet-ssleay-perl libpng12-0 libqpdf3
  libtext-unidecode-perl liburi-perl libwww-perl libwww-robotrules-perl
  libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl
  libxml-sax-base-perl libxml-sax-perl python-scour
Suggested packages:
  devscripts gfortran-multilib gfortran-doc gfortran-4.6-multilib
  gfortran-4.6-doc libgfortran3-dbg libdata-dump-perl libintl-xs-perl
  libcrypt-ssleay-perl liblzma-doc libauthen-ntlm-perl python-rsvg
  python-cairo texlive-base texlive-latex-base texlive-generic-recommended
  texinfo-doc-nonfree
Recommended packages:
  libio-socket-inet6-perl libhtml-form-perl libhtml-format-perl
  libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl
The following NEW packages will be installed:
  cdbs dh-translations gfortran gfortran-4.6 intltool libblas-dev
  libencode-locale-perl libfile-listing-perl libhtml-parser-perl
  libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl
  libhttp-message-perl libhttp-negotiate-perl libintl-perl
  libio-socket-ssl-perl liblapack-dev liblwp-mediatypes-perl
  liblwp-protocol-https-perl liblzma-dev libnet-http-perl libnet-ssleay-perl
  libqpdf3 libtext-unidecode-perl liburi-perl libwww-perl
  libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl
  libxml-parser-perl libxml-sax-base-perl libxml-sax-perl python-scour qpdf
  texinfo
The following packages will be upgraded:
  libpng12-0 libpng12-dev
2 upgraded, 36 newly installed, 0 to remove and 256 not upgraded.
Need to get 15.8 MB of archives.
After this operation, 47.7 MB of additional disk space will be used.
Get:1 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main libpng12-dev amd64 1.2.46-3ubuntu4.2 [207 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main libpng12-0 amd64 1.2.46-3ubuntu4.2 [133 kB]
Get:3 http://us.archive.ubuntu.com/ubuntu/ precise/universe libtext-unidecode-perl all 0.04-2 [115 kB]
Get:4 http://us.archive.ubuntu.com/ubuntu/ precise/main libintl-perl all 1.20-1build2 [1,187 kB]
Get:5 http://us.archive.ubuntu.com/ubuntu/ precise/main libxml-namespacesupport-perl all 1.09-3 [15.3 kB]
Get:6 http://us.archive.ubuntu.com/ubuntu/ precise/main libxml-sax-base-perl all 1.07-1 [21.5 kB]
Get:7 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main libxml-sax-perl all 0.99+dfsg-1ubuntu0.2 [66.8 kB]
Get:8 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main libxml-libxml-perl amd64 1.89+dfsg-1ubuntu0.1 [389 kB]
Get:9 http://us.archive.ubuntu.com/ubuntu/ precise/main liburi-perl all 1.59-1 [90.3 kB]
Get:10 http://us.archive.ubuntu.com/ubuntu/ precise/main libencode-locale-perl all 1.02-2 [12.0 kB]
Get:11 http://us.archive.ubuntu.com/ubuntu/ precise/main libhttp-date-perl all 6.00-1 [10.1 kB]
Get:12 http://us.archive.ubuntu.com/ubuntu/ precise/main libfile-listing-perl all 6.03-1 [9,690 B]
Get:13 http://us.archive.ubuntu.com/ubuntu/ precise/main libhtml-tagset-perl all 3.20-2 [13.5 kB]
Get:14 http://us.archive.ubuntu.com/ubuntu/ precise/main libhtml-parser-perl amd64 3.69-1build1 [97.3 kB]
Get:15 http://us.archive.ubuntu.com/ubuntu/ precise/main libhtml-tree-perl all 4.2-1 [205 kB]
Get:16 http://us.archive.ubuntu.com/ubuntu/ precise/main liblwp-mediatypes-perl all 6.01-1 [17.5 kB]
Get:17 http://us.archive.ubuntu.com/ubuntu/ precise/main libhttp-message-perl all 6.01-1 [77.6 kB]
Get:18 http://us.archive.ubuntu.com/ubuntu/ precise/main libhttp-cookies-perl all 6.00-2 [23.3 kB]
Get:19 http://us.archive.ubuntu.com/ubuntu/ precise/main libhttp-negotiate-perl all 6.00-2 [13.4 kB]
Get:20 http://us.archive.ubuntu.com/ubuntu/ precise/main libnet-http-perl all 6.02-1 [23.5 kB]
Get:21 http://us.archive.ubuntu.com/ubuntu/ precise/main libnet-ssleay-perl amd64 1.42-1build1 [188 kB]
Get:22 http://us.archive.ubuntu.com/ubuntu/ precise/main libio-socket-ssl-perl all 1.53-1 [47.5 kB]
Get:23 http://us.archive.ubuntu.com/ubuntu/ precise/main liblwp-protocol-https-perl all 6.02-1 [6,746 B]
Get:24 http://us.archive.ubuntu.com/ubuntu/ precise/main libwww-robotrules-perl all 6.01-1 [14.1 kB]
Get:25 http://us.archive.ubuntu.com/ubuntu/ precise/main libwww-perl all 6.03-1 [156 kB]
Get:26 http://us.archive.ubuntu.com/ubuntu/ precise/main libxml-parser-perl amd64 2.41-1build1 [265 kB]
Get:27 http://us.archive.ubuntu.com/ubuntu/ precise/main intltool all 0.50.2-2 [52.0 kB]
Get:28 http://us.archive.ubuntu.com/ubuntu/ precise/main dh-translations all 116 [21.6 kB]
Get:29 http://us.archive.ubuntu.com/ubuntu/ precise/main python-scour all 0.26-3 [46.5 kB]
Get:30 http://us.archive.ubuntu.com/ubuntu/ precise/main cdbs all 0.4.100ubuntu2 [47.6 kB]
Get:31 http://us.archive.ubuntu.com/ubuntu/ precise/main gfortran-4.6 amd64 4.6.3-1ubuntu5 [5,579 kB]
Get:32 http://ppa.launchpad.net/marutter/rrutter/ubuntu/ precise/main texinfo amd64 5.1.dfsg.1-4ubuntu1~ubuntu12.04.1~ppa1 [934 kB]
Get:33 http://us.archive.ubuntu.com/ubuntu/ precise/main gfortran amd64 4:4.6.3-1ubuntu5 [1,206 B]
Get:34 http://us.archive.ubuntu.com/ubuntu/ precise/main libblas-dev amd64 1.2.20110419-2ubuntu1 [302 kB]
Get:35 http://us.archive.ubuntu.com/ubuntu/ precise/main liblapack-dev amd64 3.3.1-1 [4,873 kB]
Get:36 http://us.archive.ubuntu.com/ubuntu/ precise/universe libqpdf3 amd64 2.3.1-1 [269 kB]
Get:37 http://us.archive.ubuntu.com/ubuntu/ precise/universe qpdf amd64 2.3.1-1 [147 kB]
Get:38 http://us.archive.ubuntu.com/ubuntu/ precise/main liblzma-dev amd64 5.1.1alpha+20110809-3 [98.4 kB]
Fetched 15.8 MB in 0s (21.6 MB/s)
Extracting templates from packages: 100%
(Reading database ... 71419 files and directories currently installed.)
Preparing to replace libpng12-dev 1.2.46-3ubuntu4 (using .../libpng12-dev_1.2.46-3ubuntu4.2_amd64.deb) ...
Unpacking replacement libpng12-dev ...
Preparing to replace libpng12-0 1.2.46-3ubuntu4 (using .../libpng12-0_1.2.46-3ubuntu4.2_amd64.deb) ...
Unpacking replacement libpng12-0 ...
Selecting previously unselected package libtext-unidecode-perl.
Unpacking libtext-unidecode-perl (from .../libtext-unidecode-perl_0.04-2_all.deb) ...
Selecting previously unselected package libintl-perl.
Unpacking libintl-perl (from .../libintl-perl_1.20-1build2_all.deb) ...
Selecting previously unselected package libxml-namespacesupport-perl.
Unpacking libxml-namespacesupport-perl (from .../libxml-namespacesupport-perl_1.09-3_all.deb) ...
Selecting previously unselected package libxml-sax-base-perl.
Unpacking libxml-sax-base-perl (from .../libxml-sax-base-perl_1.07-1_all.deb) ...
Selecting previously unselected package libxml-sax-perl.
Unpacking libxml-sax-perl (from .../libxml-sax-perl_0.99+dfsg-1ubuntu0.2_all.deb) ...
Selecting previously unselected package libxml-libxml-perl.
Unpacking libxml-libxml-perl (from .../libxml-libxml-perl_1.89+dfsg-1ubuntu0.1_amd64.deb) ...
Selecting previously unselected package texinfo.
Unpacking texinfo (from .../texinfo_5.1.dfsg.1-4ubuntu1~ubuntu12.04.1~ppa1_amd64.deb) ...
Selecting previously unselected package liburi-perl.
Unpacking liburi-perl (from .../liburi-perl_1.59-1_all.deb) ...
Selecting previously unselected package libencode-locale-perl.
Unpacking libencode-locale-perl (from .../libencode-locale-perl_1.02-2_all.deb) ...
Selecting previously unselected package libhttp-date-perl.
Unpacking libhttp-date-perl (from .../libhttp-date-perl_6.00-1_all.deb) ...
Selecting previously unselected package libfile-listing-perl.
Unpacking libfile-listing-perl (from .../libfile-listing-perl_6.03-1_all.deb) ...
Selecting previously unselected package libhtml-tagset-perl.
Unpacking libhtml-tagset-perl (from .../libhtml-tagset-perl_3.20-2_all.deb) ...
Selecting previously unselected package libhtml-parser-perl.
Unpacking libhtml-parser-perl (from .../libhtml-parser-perl_3.69-1build1_amd64.deb) ...
Selecting previously unselected package libhtml-tree-perl.
Unpacking libhtml-tree-perl (from .../libhtml-tree-perl_4.2-1_all.deb) ...
Selecting previously unselected package liblwp-mediatypes-perl.
Unpacking liblwp-mediatypes-perl (from .../liblwp-mediatypes-perl_6.01-1_all.deb) ...
Selecting previously unselected package libhttp-message-perl.
Unpacking libhttp-message-perl (from .../libhttp-message-perl_6.01-1_all.deb) ...
Selecting previously unselected package libhttp-cookies-perl.
Unpacking libhttp-cookies-perl (from .../libhttp-cookies-perl_6.00-2_all.deb) ...
Selecting previously unselected package libhttp-negotiate-perl.
Unpacking libhttp-negotiate-perl (from .../libhttp-negotiate-perl_6.00-2_all.deb) ...
Selecting previously unselected package libnet-http-perl.
Unpacking libnet-http-perl (from .../libnet-http-perl_6.02-1_all.deb) ...
Selecting previously unselected package libnet-ssleay-perl.
Unpacking libnet-ssleay-perl (from .../libnet-ssleay-perl_1.42-1build1_amd64.deb) ...
Selecting previously unselected package libio-socket-ssl-perl.
Unpacking libio-socket-ssl-perl (from .../libio-socket-ssl-perl_1.53-1_all.deb) ...
Selecting previously unselected package liblwp-protocol-https-perl.
Unpacking liblwp-protocol-https-perl (from .../liblwp-protocol-https-perl_6.02-1_all.deb) ...
Selecting previously unselected package libwww-robotrules-perl.
Unpacking libwww-robotrules-perl (from .../libwww-robotrules-perl_6.01-1_all.deb) ...
Selecting previously unselected package libwww-perl.
Unpacking libwww-perl (from .../libwww-perl_6.03-1_all.deb) ...
Selecting previously unselected package libxml-parser-perl.
Unpacking libxml-parser-perl (from .../libxml-parser-perl_2.41-1build1_amd64.deb) ...
Selecting previously unselected package intltool.
Unpacking intltool (from .../intltool_0.50.2-2_all.deb) ...
Selecting previously unselected package dh-translations.
Unpacking dh-translations (from .../dh-translations_116_all.deb) ...
Selecting previously unselected package python-scour.
Unpacking python-scour (from .../python-scour_0.26-3_all.deb) ...
Selecting previously unselected package cdbs.
Unpacking cdbs (from .../cdbs_0.4.100ubuntu2_all.deb) ...
Selecting previously unselected package gfortran-4.6.
Unpacking gfortran-4.6 (from .../gfortran-4.6_4.6.3-1ubuntu5_amd64.deb) ...
Selecting previously unselected package gfortran.
Unpacking gfortran (from .../gfortran_4%3a4.6.3-1ubuntu5_amd64.deb) ...
Selecting previously unselected package libblas-dev.
Unpacking libblas-dev (from .../libblas-dev_1.2.20110419-2ubuntu1_amd64.deb) ...
Selecting previously unselected package liblapack-dev.
Unpacking liblapack-dev (from .../liblapack-dev_3.3.1-1_amd64.deb) ...
Selecting previously unselected package libqpdf3.
Unpacking libqpdf3 (from .../libqpdf3_2.3.1-1_amd64.deb) ...
Selecting previously unselected package qpdf.
Unpacking qpdf (from .../qpdf_2.3.1-1_amd64.deb) ...
Selecting previously unselected package liblzma-dev.
Unpacking liblzma-dev (from .../liblzma-dev_5.1.1alpha+20110809-3_amd64.deb) ...
Processing triggers for man-db ...
Processing triggers for ccache ...
Updating symlinks in /usr/lib/ccache ...
Setting up libpng12-0 (1.2.46-3ubuntu4.2) ...
Setting up libpng12-dev (1.2.46-3ubuntu4.2) ...
Setting up libtext-unidecode-perl (0.04-2) ...
Setting up libintl-perl (1.20-1build2) ...
Setting up libxml-namespacesupport-perl (1.09-3) ...
Setting up libxml-sax-base-perl (1.07-1) ...
Setting up libxml-sax-perl (0.99+dfsg-1ubuntu0.2) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libxml-libxml-perl (1.89+dfsg-1ubuntu0.1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up texinfo (5.1.dfsg.1-4ubuntu1~ubuntu12.04.1~ppa1) ...
Setting up liburi-perl (1.59-1) ...
Setting up libencode-locale-perl (1.02-2) ...
Setting up libhttp-date-perl (6.00-1) ...
Setting up libfile-listing-perl (6.03-1) ...
Setting up libhtml-tagset-perl (3.20-2) ...
Setting up libhtml-parser-perl (3.69-1build1) ...
Setting up libhtml-tree-perl (4.2-1) ...
Setting up liblwp-mediatypes-perl (6.01-1) ...
Setting up libhttp-message-perl (6.01-1) ...
Setting up libhttp-cookies-perl (6.00-2) ...
Setting up libhttp-negotiate-perl (6.00-2) ...
Setting up libnet-http-perl (6.02-1) ...
Setting up libnet-ssleay-perl (1.42-1build1) ...
Setting up libio-socket-ssl-perl (1.53-1) ...
Setting up libwww-robotrules-perl (6.01-1) ...
Setting up python-scour (0.26-3) ...
Setting up gfortran-4.6 (4.6.3-1ubuntu5) ...
Setting up gfortran (4:4.6.3-1ubuntu5) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode.
Setting up libblas-dev (1.2.20110419-2ubuntu1) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode.
Setting up liblapack-dev (3.3.1-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode.
Setting up libqpdf3 (2.3.1-1) ...
Setting up qpdf (2.3.1-1) ...
Setting up liblzma-dev (5.1.1alpha+20110809-3) ...
Setting up liblwp-protocol-https-perl (6.02-1) ...
Setting up libwww-perl (6.03-1) ...
Setting up libxml-parser-perl (2.41-1build1) ...
Setting up intltool (0.50.2-2) ...
Setting up dh-translations (116) ...
Setting up cdbs (0.4.100ubuntu2) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
1.62s$ curl -Lo /tmp/R-3.3.1.xz https://s3.amazonaws.com/rstudio-travis/R-3.3.1.xz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 39.1M  100 39.1M    0     0  24.4M      0  0:00:01  0:00:01 --:--:-- 24.4M
3.22s$ tar xJf /tmp/R-3.3.1.xz -C ~
$ rm /tmp/R-3.3.1.xz
0.01s$ sudo mkdir -p /usr/local/lib/R/site-library $R_LIBS_USER
0.01s$ sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library $R_LIBS_USER
0.00s$ echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' > ~/.Rprofile.site
1.18s$ curl -Lo /tmp/texlive.tar.gz https://github.com/jimhester/ubuntu-bin/releases/download/latest/texlive.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   590    0   590    0     0  12588      0 --:--:-- --:--:-- --:--:-- 13111
100 79.6M  100 79.6M    0     0  67.8M      0  0:00:01  0:00:01 --:--:-- 74.4M
2.24s$ tar xzf /tmp/texlive.tar.gz -C ~
$ export PATH=/$HOME/texlive/bin/x86_64-linux:$PATH
4.06s$ tlmgr update --self
tlmgr: package repository http://ctan.sharelatex.com/tex-archive/systems/texlive/tlnet (verified)
tlmgr: saving backups to /home/travis/texlive/tlpkg/backups
[1/1, ??:??/??:??] update: texlive.infra [190k] (41280 -> 41476) ... done
tlmgr: package log updated: /home/travis/texlive/texmf-var/web2c/tlmgr.log
running mktexlsr ...
done running mktexlsr.
0.49s$ curl -Lo /tmp/pandoc-1.15.2-1-amd64.deb https://github.com/jgm/pandoc/releases/download/1.15.2/pandoc-1.15.2-1-amd64.deb
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0  10513      0 --:--:-- --:--:-- --:--:-- 10909
100 18.8M  100 18.8M    0     0  40.2M      0 --:--:-- --:--:-- --:--:-- 40.2M
1.39s$ sudo dpkg -i /tmp/pandoc-1.15.2-1-amd64.deb
Selecting previously unselected package pandoc.
(Reading database ... 72979 files and directories currently installed.)
Unpacking pandoc (from /tmp/pandoc-1.15.2-1-amd64.deb) ...
Setting up pandoc (1.15.2-1) ...
Processing triggers for man-db ...
3.42s$ sudo apt-get install -f
Reading package lists... Done
Building dependency tree       
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 256 not upgraded.
$ rm /tmp/pandoc-1.15.2-1-amd64.deb
git.checkout
1.09s$ git clone --depth=50 --branch=master https://github.com/reconhub/incidence.git reconhub/incidence
Cloning into 'reconhub/incidence'...
remote: Counting objects: 496, done.
remote: Compressing objects: 100% (303/303), done.
remote: Total 496 (delta 189), reused 482 (delta 182), pack-reused 0
Receiving objects: 100% (496/496), 3.84 MiB | 0 bytes/s, done.
Resolving deltas: 100% (189/189), done.
Checking connectivity... done.
$ cd reconhub/incidence
$ git checkout -qf ad936876c48c3b977f49a83f1595ec75dbf9b24b
This job is running on container-based infrastructure, which does not allow use of 'sudo', setuid and setguid executables.
If you require sudo, add 'sudo: required' to your .travis.yml
See https://docs.travis-ci.com/user/workers/container-based-infrastructure/ for details.
cache.1
Setting up build cache
$ export CASHER_DIR=$HOME/.casher
0.05s$ Installing caching utilities
0.00s
1.43sattempting to download cache archive
fetching master/cache-linux-precise-e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855--R-3.3.1.tgz
found cache
package
Setting up package cache
0.00s
2.79sadding /home/travis/R/Library to cache
R-session-info
R session information
$ Rscript -e 'sessionInfo()'
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
attached base packages:
[1] stats     graphics  grDevices utils     datasets  base     
Installing package dependencies
Installing R packages: devtools
3.77s$ Rscript -e 'install.packages(c("devtools"));if (!all(c("devtools") %in% installed.packages())) { q(status = 1, save = "no")}'
Installing package into ‘/home/travis/R/Library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/devtools_1.12.0.tar.gz'
Content type 'application/x-gzip' length 467113 bytes (456 KB)
==================================================
downloaded 456 KB
* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG  -I/home/travis/R-bin/include    -fpic  -g -O2  -c devtools.c -o devtools.o
gcc -std=gnu99 -shared -L/home/travis/R-bin/lib -o devtools.so devtools.o
installing to /home/travis/R/Library/devtools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (devtools)
The downloaded source packages are in
    ‘/tmp/RtmpnhY7r3/downloaded_packages’
Installing R packages from GitHub: reconhub/outbreaks
2.13s$ Rscript -e 'devtools::install_github(c("reconhub/outbreaks"), build_vignettes = FALSE)'
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Downloading GitHub repo reconhub/outbreaks@master
from URL https://api.github.com/repos/reconhub/outbreaks/zipball/master
Installing outbreaks
'/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpiOGlOa/devtools20b7569127b7/reconhub-outbreaks-0722bb3'  \
  --library='/home/travis/R/Library' --install-tests 
* installing *source* package ‘outbreaks’ ...
Error : Invalid DESCRIPTION file
Malformed maintainer field.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ERROR: installing package DESCRIPTION failed for package ‘outbreaks’
* removing ‘/home/travis/R/Library/outbreaks’
* restoring previous ‘/home/travis/R/Library/outbreaks’
Error: Command failed (1)
Execution halted
The command "Rscript -e 'devtools::install_github(c("reconhub/outbreaks"), build_vignettes = FALSE)'" failed and exited with 1 during .
Your build has been stopped.