Ubuntu on R Ubuntu Blog

Ubuntu CRAN reposirory: Replacing apt-key

Thu, 22 Jul 2021 00:00:00 +0000

Replacing apt-key on Ubuntu CRAN

If you have used apt-key on Ubuntu (or Debian) recently, you may mave noticed a message along the lines of Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). The final Ubuntu release with apt-key will be Ubuntu 22.04.

As the warning suggests, keyring files should be located in the /etc/apt/trusted.gpg.d/ directory. The first step is to download my .asc key file, which is an armored, ASCII version of my public key file.

wget https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc

It should be noted that the .asc public key file is no longer stored on a keyserver, but in the Ubuntu directory on CRAN. To verify that this is indeed my public key file, run

gpg --show-keys ./marutter_pubkey.asc

The resulting output should contain my fingerprint E298A3A825C0D65DFD57CBB651716619E084DAB9 with an expiration date of 2027-09-30.

Once you have verified the key, you can copy the .asc file to /etc/apt/trusted.gpg.d/. It is also possible to download the file and copy it to the proper directory with the following command:

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

This information has been added to the readme files on the CRAN Ubuntu site.

R 4.0 Now Available

Mon, 27 Apr 2020 00:00:00 +0000

Ubuntu binaries for R 4.0, the newest release, are now available in the usual locations, with some caveats. As with previous transitions to major releases, 4.0 binaries are have their own PPA or in their own directory on CRAN.

Launchpad PPA

If you like to use Launchpad PPAs, the R 4.0 binaries can be found at RRutter 4.0. The recommended packages built against 4.0 can also be found here.

CRAN

Binaries can also be found at the CRAN website in the Ubuntu folder. This website is synced with the PPA every 12 hours, so please be patient as the files and readme are updated. To use the R 4.0 binaries, the apt entry would be “deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/”. This would add the 4.0 binaries of Bionic. Full details are available on CRAN.

Adding a new major release to CRAN Ubuntu website has many steps, so if you are using the CRAN repository any you have any issues, please let me know.

Using 4.0 with existing binaries and c2d4u

As with every recent major R release, packages built against the R 3.5/3.6 series are not compatible with R 4.0. That means packages will need to be rebuilt is you install R 4.0.

If you are using packages installed from source, Dirk Eddelbuettel has an excellent blog post on moving to 4.0.

If you use some of binary packages available in Universe or my cran2deb4ubuntu project, you will need to patient as the binaries are built. First, you should be aware that there is a new 4.0 c2d4u PPA - https://launchpad.net/~c2d4u.team/+archive/ubuntu/c2d4u4.0+. Notice the change from “marutter” to “c2d4u.team” as the PPA location. Also, the PPA is called “c2d4u4.0+”, an indication that this will be the repository that contains packages for R 4.0 and beyond until the next major release.

As of this blog post, the status of the last three long term service (LTS) releases of Ubuntu varies. For Focal (20.04), I have rebuilt all the binaries available in Universe, but not the additional packages usually found in c2d4u. For Bionic (18.04), there are around 2,800 packages available with more coming every day. After the Focal and Bionic packages are built, I will start with the Xenial (16.04) backport. I will not be supporting R 4.0 for Trusty (14.04).

Future of c2d4u for R 3.5 and R 4.0 releases

For the foreseeable future, I will be building new and updated packages from the CRAN Task Views against both R 3.5 and R 4.0. At some point, building against R 3.5 will become problematic as packages will slowly begin to require 4.0. At that point I will freeze the c2d4u for 3.5 and only support R 4.0. Please be patient with packages in c2d4u, as I am trying to build against 4.0 and update the 3.5 PPA at the same time.

Cosmic Cuttlefish (18.10) on CRAN

Mon, 19 Nov 2018 00:00:00 +0000

R packages for Cosmic Cuttlefish (18.10) have been added to the RRutter3.5 PPA and therefore have been mirrored to CRAN. These are the base packages for R, plus the recommended packages as well as a couple of others (jags, ess, rpy2, and littler). Most of these are already available in the standard 18.10 repositories, but as packages are updated, I will update them for CRAN.

Since the lifespan of Cosmic Cuttlefish is so short (support ends July 2019), I will not be creating a version of c2d4u for Cosmic. If you want access to all of those packages, I suggest sticking to an LTS. And with Ubuntu’s announcement that support for Bionic (18.04) has been extended to 10 years, it will be around for a while.

November 18th c2d4u Update

Sun, 18 Nov 2018 00:00:00 +0000

86 new or updated packages added to c2d4u this weekend. The new CRAN Task View Missing Data, which was added last month.

A number of packages require R 3.5, so the number of packages updated on the R 3.5 version of c2d4u is less. Also, the rstan package, and anything related are not available for Trusty. This is due to the need of the C++14 standard for rstan. If there are any suggestions on how to get this to build on Launchpad, let me know.

PPA for packages built against R 3.4.*: c2d4u

PPA for packages built against R 3.5.*: c2d4u3.5

package	r_version
BDgraph	2.53
BiocManager	1.30.4
ChainLadder	0.2.8
DBItest	1.5-2
DescTools	0.99.26
GJRM	0.1-5
GenomeInfoDb	1.18.1
LNIRT	0.3.5
MALDIrppa	1.0.1-2
MetaStan	0.0.2
MonetDBLite	0.6.0
R4CouchDB	0.7.5
RApiSerialize	0.1.0
RBesT	1.3-6
RCassandra	0.1-3
REndo	2.0.0
RGreenplum	0.1.2
RH2	0.2.4
RJDBC	0.2-7.1
RJSONIO	1.3-1.1
RMariaDB	1.0.6
ROracle	1.3-1
RPostgres	1.1.1
RPresto	1.3.2
RSAGA	1.3.0
RcppArmadillo	0.9.200.4.0
RcppRedis	0.1.9
Rcrawler	0.1.9-1
Rmpi	0.6-9
S4Vectors	0.20.1
SmallCountRounding	0.2
TScompare	2015.4-1
anytime	0.3.3
bReeze	0.4-3
bife	0.5
cNORM	1.0.1
census	0.2.0
censusGeography	0.1.0
countrycode	1.1.0
dbfaker	0.1.0
dbscan	1.1-3
dimRed	0.2.2
divest	0.7.2
dplyr.teradata	0.3.0
elastic	0.8.4
fastLink	0.5.0
filehashSQLite	0.2-4
ggpubr	0.2
giphyr	0.1.3
googleAuthR	0.7.0
googleVis	0.6.3
hipread	0.1.1
idbr	0.3
implyr	0.2.4
ipumsr	0.3.0
liteq	1.0.1
lme4	1.1-19
mclust	5.4.2
metamedian	0.1.0
model4you	0.9-3
mongolite	2.0
noncensus	0.1
odbc	1.1.6
openssl	1.1
packrat	0.5.0
pivot	18.4.17
pointblank	0.2.0
pool	0.1.4.1
rcmdcheck	1.3.2
redux	1.1.0
reqres	0.2.2
rpostgis	1.4.2
rrcov	1.4-7
rsconnect	0.8.11
rstanarm	2.18.2
sdcTable	0.25
shinyFiles	0.7.2
showimage	1.0.0
skpr	0.57.0
svars	1.2.2
sys	2.1
tables	0.8.7
textcat	1.0-6
tidycensus	0.8.1
uptasticsearch	0.3.0
webdriver	1.0.5

August 25th c2d4u Update

Wed, 29 Aug 2018 00:00:00 +0000

64 new or updated packages on c2d4u were uploaded on August 25th. Packages are listed below.

Currently on the version 3.5 c2d4u PPA, there are 4059 packages for Bionic, 3674 for Xenial, and 3673 for Trusty. As always, if something fails to install or does not play well with other packages, please let me know.

PPA for packages built against R 3.4.*: c2d4u

PPA for packages built against R 3.5.*: c2d4u3.5

package	r_version
BLR	1.5
DoE.base	1.1-1
ELYP	0.7-5
Epi	2.32
GWmodel	2.0-6
MoEClust	1.2.0
RLT	3.2.2
RRreg	0.6.9
RSEIS	3.8-3
Rcmdr	2.5-0
RcmdrMisc	2.5-0
SSBtools	0.3.0
TraMineR	2.0-9
VGAM	1.0-6
XML	3.98-1.16
adiv	1.2
arrangements	1.1.2
bamdit	3.2.0
bridgesampling	0.5-2
brnn	0.7
callr	3.0.0
car	3.0-2
censusapi	0.4.1
chebpol	1.7
convevol	1.2
crawl	2.2.0
cvar	0.2-0
depmixS4	1.3-5
dexter	0.8.1
digest	0.6.16
effects	4.0-3
epiR	0.9-97
fs	1.2.6
ftsa	4.9
ggthemes	4.0.1
keras	2.2.0
latticeDensity	1.1.0
lfe	2.8-2
mar1s	2.1.1
markovchain	0.6.9.12
mboost	2.9-1
narray	0.4.1
phaseR	2.0
pinbasic	1.2.1
planor	1.4-1
plotmo	3.5.0
pls	2.7-0
plsgenomics	1.5-2
psychmeta	2.1.9
rdpower	0.3
roahd	1.4.1
robeth	2.7-4
rstantools	1.5.1
shapes	1.2.4
shp2graph	0-5
sparseinv	0.1.3
sweep	0.2.1.1
tergm	3.5.2
tfruns	1.4
timetk	0.1.1.1
tinytex	0.7
tsibble	0.5.1
udapi	0.1.3
wordcloud	2.6

Changes to CRAN Ubuntu webpage regarding apt-secure key

Wed, 29 Aug 2018 00:00:00 +0000

Thanks to a couple of users of the Ubuntu page on the CRAN, I was recently alerted to a duplicate key on the keyserver.ubuntu.com website. If you search for my key using the short ID string, you will find two keys listed.

One of the keys is mine, uid “Michael Rutter”. The other key, even though the date suggests otherwise, appears to be new. The uid is “Totally Legit Signing Key”. I am fairly certain that this key was placed there to demonstrate that using the short key ID is flawed, as it is easy to create a key using brute force that matches my key. This is called an key id collision. If you do a google search, you can find a similar key on another Ubuntu related project. I don’t think there was any malicious intent, but I think it is something to be aware of.

If you recently added my key using the methods describe on CRAN, it may have downloaded two keys. You can check this by running gpg --list-keys. If the other key has been added to your machine, you should see “Totally Legit Signing Key” listed as rsa1024 with a long id of CF805866AEBD82665423554F4359ED62E084DAB9.

You can delete this key by running gpg -delete-key "Totally Legit Signing Key". sudo may be needed, depending on your individual setup.

To prevent this from happening in the future, I have changed the directions on CRAN to install my public key using a longer key id. This will only download my key.

There is no reason to believe that any of the packages on CRAN have been compromised using this key. Comprimised pacakges signed with this bogus key would have to have been placed on my server located behind a firewall at a large research university. I think this is highly unlikely, as only files on that server are synced to CRAN.

If you have any questions or concerns, please contact me.

c2d4u August 18th Update

Sun, 19 Aug 2018 22:55:00 -0500

On c2d4u, 58 packages were updated or added on August 18th. The list is below. As with many recent updates, a couple of packages require R 3.5. These packages are not being updated on the 3.4 c2d4u. I also updated ess on CRAN to the most recent version, which does not install. Dirk Eddelbuettel is uploading a new version that will hopefully fix things.

PPA for packages built against R 3.4.*: c2d4u

PPA for packages built against R 3.5.*: c2d4u3.5

package	r_version
BART	1.9
BalancedSampling	1.5.3
Brobdingnag	1.2-6
CDM	6.5-12
JuliaCall	0.16.0
KScorrect	1.2.4
LDheatmap	0.99-5
Quandl	2.9.1
RNeXML	2.1.2
RQGIS	1.0.4
RcppArmadillo	0.9.100.5.0
arrangements	1.1.0
batchtools	0.9.11
bcp	4.0.3
chebpol	1.6
choroplethr	3.6.3
cmvnorm	1.0-5
emplik	1.0-4.3
emplik2	1.21
energy	1.7-5
ergm	3.9.4
fansi	0.3.0
freegroup	1.0-2
funHDDC	2.1.0
gbutils	0.3-0
grplasso	0.4-6
ipred	0.9-7
jmvcore	0.9.2.0
kohonen	3.0.6
lme4	1.1-18-1
mapview	2.5.0
metacom	1.5.1
mets	1.2.4
mirt	1.29
nilde	1.1-2
openEBGM	0.7.0
phonics	1.1.0
pkgconfig	2.0.2
pmmlTransformations	1.3.2
processx	3.2.0
ps	1.1.0
psidR	1.6
pubmed.mineR	1.0.13
randomForestSRC	2.7.0
rattle	5.2.0
rlang	0.2.2
roll	1.1.1
rpart.plot	3.0.4
rplos	0.8.4
rpostgis	1.4.1
sandwich	2.5-0
snakecase	0.9.2
spdep	0.7-8
stars	0.1-1
synthpop	1.5-0
texPreview	1.1.5
tm.plugin.mail	0.2-1
truncreg	0.2-5

June 24th, 2018 c2d4u update

Sun, 24 Jun 2018 22:00:00 -0500

Weekly c2d4u update. 66 packages either updated or new. One more package, lfe, requiring R 3.5, therefore not available on c2d4u for R 3.4. Don’t forget to install an additional PPA in order to support the spatial packages: ubuntugis-stable.

PPA for packages built against R 3.4.*: c2d4u

PPA for packages built against R 3.5.*: c2d4u3.5

package	r_version
BDgraph	2.51
CodeDepends	0.6.0
CopulaREMADA	1.1
Delaporte	6.2.0
Mcomp	2.8
NonCompart	0.4.3
RItools	0.1-16
RcmdrPlugin.temis	0.7.10
Rmixmod	2.1.2
VarSelLCM	2.1.2
VineCopula	2.1.6
acebayes	1.5
arfima	1.6-7
bisoreg	1.5
cbinom	1.2
choiceDes	0.9-3
choroplethr	3.6.2
convey	0.2.1
data.tree	0.7.6
derivmkts	0.2.3
designmatch	0.3.1
doRNG	1.7.1
docopulae	0.3.5
drake	5.2.1
ecm	3.1.0
edgeR	3.22.3
effects	4.0-2
filelock	1.0.1
forecast	8.4
future.apply	1.0.0
ggpubr	0.1.7
gnm	1.1-0
googleAuthR	0.6.3
httpuv	1.4.4.1
hypervolume	2.0.10
imputeTS	2.7
iplots	1.1-7.1
lcmm	1.7.9
lfe	2.7-2383
limma	3.36.2
mgcv	1.8-24
mice	3.1.0
mlrMBO	1.1.2
mlt	1.0-2
mombf	2.1.2
ncar	0.4.0
qrng	0.0-5
rdryad	0.4.0
recipes	0.1.3
reprex	0.2.0
rgdal	1.3-3
rnn	0.8.1
robustbase	0.93-1
rtweet	0.6.7
s20x	3.1-27
sdcTable	0.23
sigmoid	0.3.0
sjmisc	2.7.3
spData	0.2.9.0
spam	2.2-0
statnet.common	4.1.4
tm	0.7-4
tsbox	0.0.3
txtq	0.0.4
validate	0.2.5
walrus	1.0.3

June 17th, 2018 c2d4u update

Mon, 18 Jun 2018 08:00:00 -0500

Weekly c2d4u update. 101 packages either updated or new. The transition to R 3.5 is starting to be seen on CRAN, as some packages are now requiring the latest version. Of the packages listed below, piecewisesem and dae are not available on c2d4u, which is based on R 3.4. At some point, updates to that version of c2d4u will stop if too many pacakges are R 3.5 dependent.

PPA for packages built against R 3.4.*: c2d4u

PPA for packages built against R 3.5.*: c2d4u3.5

package	r_version
Bchron	4.3.0
Bivariate.Pareto	1.0.2
CMLS	1.0-0
Cyclops	1.3.4
DHS.rates	0.3.1
Deriv	3.8.5
DoE.base	1.0
LogicReg	1.5.10
MCMCvis	0.11.0
MSwM	1.3
MultiRNG	1.1
PReMiuM	3.2.0
PracTools	0.9
RAdwords	0.1.17
RGtk2	2.20.35
RcppAlgos	2.0.2
RcppDE	0.1.6
RcppGSL	0.3.6
RcppZiggurat	0.1.5
UnivRNG	1.1
WRS2	0.10-0
aplpack	1.3.2
biclust	2.0.1
blavaan	0.3-2
blocksdesign	2.9
bpca	1.3-0
bsamGP	1.2.1
bshazard	1.1
cairoDevice	2.25
catR	3.15
compositions	1.40-2
cplm	0.7-7
ctsem	2.6.4
cubature	1.4
dae	3.0-16
dexter	0.8.0
dlm	1.1-5
dng	0.2.0
dqrng	0.0.4
dtwclust	5.4.1
etm	0.6-2.1
extRemes	2.0-9
fuzzyreg	0.3
gamboostLSS	2.0-1
gamlss.cens	5.0-1
globals	0.12.0
grpreg	3.1-4
hddplot	0.59
highr	0.7
hydroPSO	0.4-1
jmvcore	0.9.1
kdist	0.2
ks	1.11.2
logspline	2.1.11
manipulateWidget	0.10.0
mboost	2.9-0
model4you	0.9-2
multiway	1.0-5
munsell	0.5.0
nimble	0.6-11
officer	0.3.1
ompr	0.8.0
overlapping	1.5.0
piecewiseSEM	2.0.0
pmultinom	1.0.0
polspline	1.1.13
polyclip	1.9-0
princurve	2.0.2
progress	1.2.0
prophet	0.3.0.1
psychmeta	2.1.1
quickpsy	0.1.5
ratematrix	1.0
rgam	0.6.6
rmarkdown	1.10
robeth	2.7-2
rstiefel	0.20
rvg	0.1.9
semds	0.9-4
smacof	1.10-8
spatstat	1.56-0
spatstat.data	1.3-1
spatstat.utils	1.8-2
splines2	0.2.8
spsurvey	3.4
stringi	1.2.3
tensorflow	1.8
testit	0.8
tidytree	0.1.9
tinytex	0.5
units	0.6-0
useful	1.2.5
visNetwork	2.0.4
visualize	4.3.0
windex	1.0
xfun	0.2
xlsx	0.6.1
zipfextR	1.0.0
zoo	1.8-2

June 11th, 2018 R 3.5.0 on Debian and Ubuntu: An Update

Sun, 10 Jun 2018 11:20:33 -0500

Overview

R 3.5.0 was released a few weeks ago. As it changes some (important) internals, packages installed with a previous version of R have to be rebuilt. This was known and expected, and we took several measured steps to get R binaries to everybody without breakage.

The question of but how do I upgrade without breaking my system was asked a few times, e.g., on the r-sig-debian list as well as in this StackOverflow question.

Debian

Core Distribution As usual, we packaged R 3.5.0 as soon as it was released – but only for the experimental distribution, awaiting a green light from the release masters to start the transition. A one-off repository [drr35](https://github.com/eddelbuettel/drr35) was created to provide R 3.5.0 binaries more immediately; this was used, e.g., by the r-base Rocker Project container / the official R Docker container which we also update after each release.

The actual transition was started last Friday, June 1, and concluded this Friday, June 8. Well over 600 packages have been rebuilt under R 3.5.0, and are now ready in the unstable distribution from which they should migrate to testing soon. The Rocker container r-base was also updated.

So if you use Debian unstable or testing, these are ready now (or will be soon once migrated to testing). This should include most Rocker containers built from Debian images.

Contributed CRAN Binaries Johannes also provided backports with a -cran35 suffix in his CRAN-mirrored Debian backport repositories, see the README.

Ubuntu

Core (Upcoming) Distribution Ubuntu, for the upcoming 18.10, has undertaken a similar transition. Few users access this release yet, so the next section may be more important.

Contributed CRAN and PPA Binaries Two new Launchpad PPA repositories were created as well. Given the rather large scope of thousands of packages, multiplied by several Ubuntu releases, this too took a moment but is now fully usable and should get mirrored to CRAN ‘soon’. It covers the most recent and still supported LTS releases as well as the current release 18.04.

One PPA contains base R and the recommended packages, RRutter3.5. This is source of the packages that will soon be available on CRAN. The second PPA (c2d4u3.5) contains over 3,500 packages mainly derived from CRAN Task Views. Details on updates can be found at Michael’s R Ubuntu Blog.

This can used for, e.g., Travis if you managed your own sources as Dirk’s r-travis does. We expect to use this relatively soon, possibly as an opt-in via a variable upon which run.sh selects the appropriate repository set. It will also be used for Rocker releases built based off Ubuntu.

In both cases, you may need to adjust the sources list for apt accordingly.

Others

There may also be ongoing efforts within Arch and other Debian-derived distributions, but we are not really aware of what is happening there. If you use those, and coordination is needed, please feel free to reach out via the the r-sig-debian list.

Closing

In case of questions or concerns, please consider posting to the r-sig-debian list.

Dirk, Michael and Johannes, June 2018

June 9th, 2018 c2d4u Update: 81 updated/new packages

Sun, 10 Jun 2018 11:20:33 -0500

Weekly c2d4u update. 81 packages either updated or new. Package of note this week is sp, a workhorse package for spatial data in R. The issue for Ubuntu is that the binary package has an epoch number of 1 (1:1:1.3-1 to be exact). These epoch numbers are often used in Debian/Ubuntu when the version numbering scheme changes, and the new version is lower than the old version. By adding the “1:”, Ubuntu can deal with the change in numbering correctly.

PPA for pacakges built against R 3.4.*: c2d4u

PPA for pacakges built against R 3.5.*: c2d4u3.5

package	r_version
BART	1.7
BAS	1.5.1
BoSSA	3.3
CompRandFld	1.0.3-5
Compositional	3.1
DepthProc	2.0.3
FixedPoint	0.5
GDINA	2.1.15
HH	3.1-35
MOCCA	1.3
PBSmapping	2.70.5
PairedData	1.1.1
ROI.plugin.qpoases	0.3-1
RSAGA	1.1.1
RcppRoll	0.3.0
RgoogleMaps	1.4.2
S4Vectors	0.18.3
SpatialNP	1.1-3
Tcomp	1.0.1
adegraphics	1.0-10
adiv	1.1
autovarCore	1.0-4
bayesImageS	0.5-2
bayou	2.1
bcp	4.0.2
brms	2.3.1
dispRity	1.0.3
dlsem	2.3
eigenmodel	1.10
equateIRT	2.0-5
evmix	2.11
extraDistr	1.8.9
fastcluster	1.1.25
fs	1.2.3
gamlss	5.1-0
gamlss.dist	5.0-6
gap	1.1-22
ggmuller	0.5.1
ibmdbR	1.50.0
later	0.7.3
leaflet	2.0.1
markovchain	0.6.9.10
meta	4.9-2
miceadds	2.12-24
mixdist	0.5-5
mokken	2.8.11
moveHMM	1.6
np	0.60-8
nsprcomp	0.5.1-2
partykit	1.2-2
pcalg	2.6-0
pcse	1.9.1.1
phylogram	2.0.1
phyreg	1.0.2
pkr	0.1.2
plotmo	3.4.1
plumber	0.4.6
quanteda	1.3.0
quickmapr	0.3.0
ranger	0.10.1
rasterVis	0.45
reticulate	1.8
rgdal	1.3-2
rgeos	0.3-28
rjson	0.2.20
simecol	0.8-12
simsem	0.5-14
sjlabelled	1.0.11
smooth	2.4.4
sp	1.3-1
statnet.common	4.1.2
stplanr	0.2.5
stringdist	0.9.5.1
svars	1.2.0
tidytree	0.1.8
tm.plugin.lexisnexis	1.4.0
treedater	0.2.0
treeplyr	0.1.4
tsDyn	0.9-48
tseries	0.10-45
xgboost	0.71.2

June 2nd, 2018 c2d4u Update: 21 updated/new packages

Sun, 03 Jun 2018 11:05:00 -0500

Small weekly update to c2d4u. 21 packages in total either updated or new.

PPA for pacakges built against R 3.4.*: c2d4u

PPA for pacakges built against R 3.5.*: c2d4u3.5

package	r_version
BART	1.7
BAS	1.5.1
BoSSA	3.3
CompRandFld	1.0.3-5
Compositional	3.1
DepthProc	2.0.3
FixedPoint	0.5
GDINA	2.1.15
HH	3.1-35
MOCCA	1.3
OBsMD	3.0
PBSmapping	2.70.5
PairedData	1.1.1
ROI.plugin.qpoases	0.3-1
RSAGA	1.1.1
RcppRoll	0.3.0
RgoogleMaps	1.4.2
RobAStBase	1.0.2
S4Vectors	0.18.3
SpatialEpi	1.2.3
SpatialNP	1.1-3
TSrepr	1.0.1
Tcomp	1.0.1
adegraphics	1.0-10
adiv	1.1
autovarCore	1.0-4
bayesImageS	0.5-2
bayou	2.1
bcp	4.0.2
brms	2.3.1
clusterSEs	2.5
dispRity	1.0.3
dlsem	2.3
eigenmodel	1.10
equateIRT	2.0-5
evmix	2.11
extraDistr	1.8.9
fastcluster	1.1.25
fs	1.2.3
fso	2.1-1
gamlss	5.1-0
gamlss.dist	5.0-6
gap	1.1-22
ggmuller	0.5.1
ibmdbR	1.50.0
later	0.7.3
leaflet	2.0.1
logspline	2.1.10
markovchain	0.6.9.10
meta	4.9-2
metaforest	0.1.2
miceadds	2.12-24
mixdist	0.5-5
mixsmsn	1.1-5
mokken	2.8.11
moveHMM	1.6
mvtnorm	1.0-8
np	0.60-8
nsprcomp	0.5.1-2
packrat	0.4.9-3
partykit	1.2-2
pcalg	2.6-0
pcse	1.9.1.1
phylogram	2.0.1
phylolm	2.6
phyreg	1.0.2
pkr	0.1.2
plotmo	3.4.1
plumber	0.4.6
prophet	0.3
quanteda	1.3.0
quickmapr	0.3.0
ranger	0.10.1
rasterVis	0.45
rbcb	0.1.4
reticulate	1.8
rgdal	1.3-2
rgeos	0.3-28
rjson	0.2.20
seacarb	3.2.7
seas	0.5-2
simecol	0.8-12
simsem	0.5-14
sjlabelled	1.0.11
skpr	0.49.1
smooth	2.4.4
sp	1.3-1
splusTimeDate	2.5.0-141
statnet.common	4.1.2
storr	1.2.0
stplanr	0.2.5
stringdist	0.9.5.1
svars	1.2.0
tidytree	0.1.8
tm.plugin.lexisnexis	1.4.0
treedater	0.2.0
treeplyr	0.1.4
tsDyn	0.9-48
tseries	0.10-45
xgboost	0.71.2

c2d4u Update: Adding New Bioconductor Release

Thu, 31 May 2018 15:12:00 -0500

When R 3.5 was released, the good folks at the Bioconductor project also released a new version, 3.7. Since I was rebuilding for R 3.5, I didn’t immediately include the updates to Bioconductor in my builds. I have now taken the time to include the update, so there are an additional 83 updated/new packages on c2d4u. (3.4 or 3.5 versions)

My PPAs do not provide all the Bioconductor packages. Some are included in a CRAN Task View, therefore they are included in c2d4u. Others are included in Ubuntu Universe, and with the move to R 3.5, I have made an attempt to rebuild those for compatibility.

Some of the packages (BiocInstaller for example) require R 3.5. Obviously, these do not build against R 3.4, but older versions of the packages are available on the PPAs. If you want to use Bioconductor 3.7, I highly suggest upgrading to R 3.5.

package	version
quantreg	5.36
data.table	1.11.4
purrr	0.2.5
bit	1.1-14
BiocGenerics	0.26.0
graph	1.58.0
RBGL	1.56.0
rJava	0.9-10
plotrix	3.7-2
sbgcop	0.980
energy	1.7-4
impute	1.54.0
MassSpecWavelet	1.46.0
metaLik	0.43.0
apcluster	1.4.7
mritc	0.5-1
Rgraphviz	2.24.0
surveillance	1.16.1
CellNOptR	1.26.0
CNORode	1.22.0
MEIGOR	1.14.0
limma	3.36.1
qvalue	2.12.0
edgeR	3.22.2
Biobase	2.40.0
ChainLadder	0.2.6
HardyWeinberg	1.6.1
zlibbioc	1.26.0
snpStats	1.30.0
ranger	0.10.0
RWeka	0.4-38
stargazer	5.2.2
joint.Cox	2.15
EBImage	4.22.0
GEOquery	2.48.0
GEOmetadb	1.42.0
preprocessCore	1.42.0
multtest	2.36.0
S4Vectors	0.18.2
IRanges	2.14.10
AnnotationDbi	1.42.1
annotate	1.58.0
genefilter	1.62.0
GSEABase	1.42.0
robCompositions	2.0.8
pdftools	1.8
tidytext	0.1.9
CDM	6.3-45
mipfp	3.2
simPop	1.1.1
hypervolume	2.0.9
XVector	0.20.0
Biostrings	2.48.0
Rhdf5lib	1.2.1
rhdf5	2.24.0
biomformat	1.8.0
phyloseq	1.24.0
catR	3.14
rlang	0.2.1
soiltexture	1.4.6
rsurface	1.1.0
occ	1.1
GenomeInfoDbData	1.1.0
GenomeInfoDb	1.16.0
illuminaio	0.22.0
GenomicRanges	1.32.3
BeadDataPackR	1.32.0
BiocInstaller	1.30.0
affyio	1.50.0
beadarray	2.30.0
affy	1.58.0
Icens	1.52.0
joineRML	0.4.2
rstpm2	1.4.2
SemiMarkov	1.4.4
survcomp	1.30.0
ramcmc	0.1.0-1
bestglm	0.37
splusTimeSeries	1.5.0-75
tsibble	0.3.0
abbyyR	0.5.4
rdatacite	0.4.0
servr	0.10

c2d4u Update: 230 New and Updated Pacakges

Sun, 27 May 2018 19:01:26 -0400

On the c2d4u PPAs, my goal is to update and add new packages (from CRAN Task Views) on a weekly basis, usually on the weekend. While I was building c2d4u3.5, I put this on hold, as I didn’t want to build new (to the PPA) packages at the same time as checking old ones.

For this update, 230 R packages were either updated or added as new. At this time, I don’t provide information that distinguishes between updated or new, but that feature may be added in the future. The list of all packages is given in the table below.

Of all the packages updated today, only one failed to build a source package without intervention: m2r. This package is an interface to Macaulay2, a software system supporting research in algebraic geometry and commutative algebra. This type of interface package is fairly common, and the reason it fails to build a source package is that Macaulay2 is a system requirement (according to CRAN). While packages are available on the website and they have repository (similar the the CRAN Ubuntu repository), it is not a PPA and therefore not available in Launchpad.

In these types of cases, where a package is just an interface to a non-R package that is assumed to be on the system, I ignore that system requirement. The downside is that a user can install r-cran-m2r and it will not work, because they still need to install Macaulay2. There really is now way around this limitation (unless the Macaulay2 maintainers start a PPA), but in most cases the users of these specialized packages already have the needed software on their system. I am just providing an easy install/update path.

package	version
Rcpp	0.12.17
utf8	1.1.4
pillar	1.2.3
htmlTable	1.12
emulator	1.2-17
dplyr	0.7.5
jomo	2.6-2
tidyr	0.8.1
mitml	0.3-5
mice	3.0.0
contfrac	1.1-12
BayesFactor	0.9.12-4.2
bit	1.1-13
ff	2.2-14
BayesX	0.3-0
rrcov	1.4-4
inline	0.3.15
shiny	1.1.0
miniUI	0.1.1.1
nleqslv	3.3.2
brms	2.3.0
GGally	1.4.0
MCMCpack	1.4-3
openEBGM	0.6.0
plotrix	3.7-1
polyclip	1.8-7
rust	1.3.5
AnalyzeFMRI	1.1-17
astrochron	0.8
kohonen	3.0.5
openxlsx	4.1.0
enpls	6.0
homals	1.0-8
amap	0.8-16
numbers	0.7-1
pkgmaker	0.27
rngtools	1.3.1
additivityTests	1.1-4
biclust	2.0.0
BDgraph	2.50
bmixture	1.1
dbscan	1.1-2
edci	1.1-3
CVST	0.2-2
caret	6.0-80
flexCWM	1.8
RSpectra	0.13-1
RcppGSL	0.3.5
Rfast	1.9.0
vegan	2.5-2
mixAK	5.1
pbdMPI	0.3-6
psychotools	0.4-3
rebmix	2.10.2
labelled	1.1.0
Compositional	3.0
RUnit	0.4.32
emdbook	1.3.10
emg	1.0.7
GeneralizedHyperbolic	0.8-4
hermite	1.1.2
logitnorm	0.8.36
MM	1.6-5
poibin	1.3
VineCopula	2.1.5
clubSandwich	0.3.2
lavaan	0.6-1
prediction	0.3.6
margins	0.3.23
useful	1.2.4
locpol	0.7-0
sf	0.6-3
rjson	0.2.19
readstata13	0.9.2
plotmo	3.3.7
openair	2.4-2
quantregGrowth	0.4-2
secr	3.1.6
crmPack	0.2.7
dfcomb	2.5-0
dfmta	1.7-0
DiceView	1.3-2
Rdpack	0.8-0
planor	1.3-9
sFFLHD	0.1.2
kableExtra	0.9.0
skpr	0.49.0
VNM	7.1
MarkowitzR	1.0.1
MSGARCH	2.3
lambda.r	1.2.3
TAQMNGR	2018.5-1
processx	3.1.0
callr	2.0.4
timetk	0.1.1
dtw	1.20-1
refund	0.1-17
aprof	0.4.1
base64url	1.4
batchtools	0.9.10
randomForestSRC	2.6.1
ssgraph	1.3
xgboost	0.71.1
Cubist	0.2.2
C50	0.1.2
evtree	1.0-7
MXM	1.3.4
rpart.plot	2.2.0
ica	1.0-2
bigsplines	1.1-1
eegkit	1.0-3
ore	1.6.1
joineR	1.2.4
shinyAce	0.3.1
RMySQL	0.10.15
ggsci	2.9
rtf	0.4-13
sparklyr	0.8.4
mleap	0.1.2
rsparkling	0.2.4
eRm	0.16-1
mvnmle	0.1-11.1
cowsay	0.6.0
qdap	2.3.0
pdftools	1.7
gamlr	1.13-5
udpipe	0.6
geigen	2.2
m2r	1.0.0
PolynomF	1.0-2
dcurver	0.9.1
TAM	2.12-18
mirt	1.28
miceadds	2.11-87
BIFIEsurvey	2.5-44
eurostat	3.2.1
repr	0.15.0
directlabels	2018.05.22
sdcMicro	5.3.0
srvyr	0.3.3
vardpoor	0.10.0
adagio	0.7.1
CVXR	0.99
mcga	3.0.3
optmatch	0.9-9
quadprogXT	0.0.3
GPfit	1.0-0
rBayesianOptimization	1.1.0
ROI.plugin.clp	0.4
NonCompart	0.4.2
PreciseSums	0.3
RxODE	0.7.2-1
picante	1.7
hitandrun	0.5-4
MPSEM	0.3-4
PCPS	1.0.6
phyloclim	0.9.5
pmc	1.0.3
worrms	0.2.8
ritis	0.7.2
aspect	1.0-5
asymmetry	1.2.5
Epi	2.30
dexter	0.7.0
difR	5.0
EFAutilities	1.2.2
latdiag	0.2-4
semds	0.9-3
rockchalk	1.8.111
tables	0.8.4
complmrob	0.6.1
Gmedian	1.2.4
otrimle	1.1
qclust	1.0
robfilter	4.1.1
RobustAFT	1.4-2
mrfDepth	1.0.6
rospca	1.0.4
rpca	0.2.3
snipEM	1.0
jmvcore	0.8.5
walrus	1.0.1
SpatialTools	1.0.4
ncf	1.2-5
RSAGA	1.1.0
rangeMapper	0.3-3
smacpod	2.0.4
spaMM	2.4.35
spatsurv	1.2
pbmcapply	1.2.5
stplanr	0.2.4
ctmm	0.5.0
lgcp	1.5
compound.Cox	3.11
Cprob	1.4.1
frailtyEM	0.8.8
hdnom	5.0
intccr	1.0.2
kmi	0.5.4
popEpi	0.4.5
simsurv	0.2.2
survsim	1.1.5
vitality	1.3
anomalize	0.1.1
ASSA	1.0
BETS	0.4.2
ramcmc	0.1.0
diagis	0.1.3-1
bssm	0.1.5
KFAS	1.3.2
ForecastComb	1.2
greybox	0.2.2
NlinTS	1.3.2
onlineVAR	0.1-0
ptw	1.9-13
season	0.3.6
stR	0.4
timechange	0.0.1
tsbox	0.0.2
yuima	1.8.1
dataverse	0.2.0
brotli	1.2
osmdata	0.0.7
scholar	0.1.6
dtplyr	0.0.2
ndjson	0.6.0
streamR	0.4.2
FSelector	0.31
PMCMR	4.3
covr	3.1.0

Announcing cran2deb4ubuntu3.5

Sat, 26 May 2018 14:48:00 -0500

After building 10,742 packages on Launchpad, I would like announce that cran2deb4ubuntu3.5 (c2d4u3.5 for short) is now available for testing and maybe even actually use. It wasn’t difficult to find if you know your way around launchpad, but you can find the PPA here: https://launchpad.net/~marutter/+archive/ubuntu/c2d4u3.5

Many things to consider before you add this PPA to your Ubuntu machine.

The PPA supplies binaries for Trusty (14.04), Xenial (16.04), and Bionic (18.04).
They binaries are built against based on R 3.5.0, which is why a new PPA was required. If you are looking for packages for R 3.4.*, you can use c2d4u.
If you are looking for R 3.5.0 binaries for all current flavors of Ubuntu, I have another PPA. c2d4u3.5 requires this PPA to work correctly.
The packages available on c2d4u3.5 are all the packages I can get to build based on what is available from all CRAN Task Views, and a couple of extra packages. It is over 3,400 r-cran packages, and they are updated about once a week. Expect a big update tomorrow (May 27th).
Some packages require other PPAs to install. They include FFmpeg next, jq, and ubuntugis-stable. Only a small number of packages require these additional PPAs, but if you install fails, these might be the solution.
If you decide to utilize this PPA, please let me know if something is not working. There is no way I can test all 3,400+ packages and there are always little things that I miss. If there are issues, please contact me via email at marutter[at]gmail.com.
You may have a favorite package that is not on c2d4u3.5 or c2d4u. To ensure some sanity in my life, I have limited the packages to those on the CRAN Task Views. So the best way to get the package on c2d4u is to have added to a Task View. Requests to add individual packages may be ignored until I find time to respond.

Update on the Move to R 3.5.0

Sun, 20 May 2018 12:50:00 -0500

I am slowly rebuilding the set of packages in c2d4u for use with R 3.5.0. Since packages built under version 3.4.* are not compatible with 3.5.0, they all need to be rebuilt. This includes the packages that came with the new Ubuntu Bionic (18.04) release. It is taking some time.

One of the challenges with using Launchpad is that once a package is built, it needs to be published. This takes some time (around 20 minutes). Therefore, you can’t just push a series of packages to Launchpad and walk away. In order to ensure the dependencies are built, you need to wait until they have been published in the PPA. This is on top of determining the build order based on dependencies.

So part of the process has been writing an R script that takes a set of packages from a Task View, creates the dependency tree, and then determines which of the packages (could be 300+ with dependencies) are already available on the PPA. I also check to see if the most recent version is on the PPA. Then from the packages that need to be built, I determine which need to be built first, second, etc. Each set is sent to Launchpad, then I watch to see when the last package is published using the Launchpad API. I wait another four minutes (the API is a little premature), then send the next batch.

Now that the bugs have been worked out, things are running smoothly. As I post this, the new repository has 1583 packages published for Xenial. In the current c2d4u PPA, there are 3783 packages for Xenial.

As all the packages are not built yet, updating to R 3.5.0 via my PPAs will still break your system, which is why I have not officially announced the new PPA yet. As soon as the project is completed, I will let you know.