Skip to content

/ rcppapt

Permalink
master

rcppapt/vignettes/binnmuAfterR340.Rmd

Go to file
 
 
Cannot retrieve contributors at this time
663 lines (575 sloc) 27.8 KB
Raw Blame
---
title: "Minimal Set of binnmu Packages"
subtitle: "Combining the R and Debian package systems"
author: "Dirk Eddelbuettel"
date: "First version 2017-Jul-16; this version 2017-Aug-05"
output:
prettydoc::html_pretty:
theme: tactile
highlight: github
vignette: >
%\VignetteIndexEntry{Minimal Set of binnmu Packages}
%\VignettePackage{RcppAPT}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
## Step 0: Problem Definition
### Upstream Change
R 3.4.0, released in April, included the following paragraph in its NEWS file:
* Packages which register native routines for .C or .Fortran need
to be re-installed for this version (unless installed with
R-devel SVN revision r72375 or later).
This transition has no fallback behavior (as is more common with R changes)
and requires a rebuild. Packages build under older R version still _load_
and function partially, but will be unable to access any native (_i.e._, compiled)
routines.
### Impact
For the Debian packages, this means that we need to consider the set of packages which
- match `r-cran-*`, `r-bioc-*` and alike
- contain compiled code (as R-only packages have no native routines)
- use at least one `.C()` or `.Fortran()` (but _not_ `.Call()`) call
- use (the hitherto optional) routine registration (so that the change in behaviour is noticible)
- have _not yet_ been recompiled with R 3.4.0 or R 3.4.1
This note computes this set and provides the input for a
[wanna-build](https://release.debian.org/wanna-build.txt) request.
This version is updated version which reflects the fourth point above which was pointed out to
me by Kurt Hornik after I shared the initial version with him. The point he raised ("does it use
`R_registerRoutines` ?") is important and further reduces the effective set.
## Step 1: Reverse Dependencies of R
### Fresh Debian unstable session
For this we drop into a clean Docker container running Debian unstable. Later, we will need
the current sources of the [`RcppAPT`](https://github.com/eddelbuettel/rcppapt) package so
we start from a local git directory:
```sh
server> cd ~/git && docker run --rm -ti -v $(pwd):/mnt debian:unstable
```
### Update Debian
Inside the Docker container, we update the package information and install what
is needed to build [`RcppAPT`](https://github.com/eddelbuettel/rcppapt) for R.
This includes Rcpp and `libapt-pkg-dev`. We also install the data.table package
used for aggregating the (R and Debian) package data computed below.
This step takes a short moment, with the exact time dependent on the network
connection and other factors.
```sh
docker> apt-get update
docker> apt-get -y dist-upgrade
docker> apt-get -y install r-cran-rcpp r-cran-data.table libapt-pkg-dev less
docker> cd /mnt
docker> R CMD INSTALL rcppapt/ # assuming we're above rcppapt
```
### Launch R
#### All Candidates
Inside the same Docker session, we now launch R and run (almost all of) the remainder from R.
```{r, eval=FALSE}
> library(RcppAPT)
> library(data.table)
> rd <- reverseDepends("r-base-core") # 516 x 2
> rd <- rd[grepl("^r-", rd[,1]), ] # 489 x 2
> rd <- rd[order(rd[,2]), ]
> setDT(rd)
```
We use `RcppAPT` to compute the reverse depends of the main R package providing the R engine: `r-base-core`.
Among those (currently) 516 packages are both other packages from the upstream source (`r-base*`, `r-doc*`) which
we exclude first as well as other, non-R-package dependencies (such as `rpy2`) which we also exclude.
This leaves 489 candidate packages out of the initial 514. The version field tells which r-base-core version
was used to build the package---information we need per the setup described above.
```{r, eval=FALSE}
> rd
> rd
package version
1: r-doc-pdf
2: r-doc-info
3: r-doc-html
4: r-base-html
5: r-other-rot
---
485: r-base-core-dbg 3.4.1-2
486: r-base 3.4.1-2
487: r-cran-mgcv 3.4.1-2
488: r-cran-boot 3.4.1-2
489: r-cran-car 3.4.1-2
>
```
Next we need to filter out two versions with unsortable (_i.e._,non-semantic) version numbers,
and apply a logical filter depending on whether the package was built with R version 3.3.3 or
earlier, indicating a possibe required rebuild.
```{r, eval=FALSE}
> rd[ version=="3.0.0~20130330-1", version := "3.0.0.20130330-1"]
> rd[ version=="3.2.4-revised-1", version := "3.2.4.1-1"]
> rd[version!="", oldVersion := version <= package_version("3.3.3-1")]
> rd[ is.na(oldVersion), oldVersion := FALSE]
> rd[ !grepl("r-(doc|base)", package), ]
package version oldVersion
1: r-other-rot FALSE
2: r-cran-epitools 3.0.0-2 TRUE
3: r-cran-combinat 3.0.0-2 TRUE
4: r-cran-gmaps 3.0.0.20130330-1 TRUE
5: r-cran-wdi 3.0.1-6 TRUE
---
478: r-recommended 3.4.1-2 FALSE
479: r-mathlib 3.4.1-2 FALSE
480: r-cran-mgcv 3.4.1-2 FALSE
481: r-cran-boot 3.4.1-2 FALSE
482: r-cran-car 3.4.1-2 FALSE
```
To cover some corner case, we derive a `skip` field:
```{r, eval=FALSE}
> rd[ version=="", skip:=TRUE ]
> rd[ is.na(skip), skip:=FALSE]
> rd[ skip==FALSE, ]
package version oldVersion skip
1: r-cran-epitools 3.0.0-2 TRUE FALSE
2: r-cran-combinat 3.0.0-2 TRUE FALSE
3: r-cran-gmaps 3.0.0.20130330-1 TRUE FALSE
4: r-cran-wdi 3.0.1-6 TRUE FALSE
5: r-cran-bitops 3.0.1-6 TRUE FALSE
---
480: r-base-core-dbg 3.4.1-2 FALSE FALSE
481: r-base 3.4.1-2 FALSE FALSE
482: r-cran-mgcv 3.4.1-2 FALSE FALSE
483: r-cran-boot 3.4.1-2 FALSE FALSE
484: r-cran-car 3.4.1-2 FALSE FALSE
>
```
#### Compiled Packages
Next, we find the actual dependencies of each of these packages by constructing
a large regular expression which we feed into `RcppAPT::getDepends()`
```{r, eval=FALSE}
> regexp <- paste(paste0("^", rd[skip==FALSE, package], "$"), collapse="|")
> dep <- getDepends(regexp)
> setDT(dep)
> dep
srcpkg deppkg cmpop version
1: r-bioc-hypergraph r-base-core 2 3.3.1.20161024-1
2: r-bioc-hypergraph r-api-3 0 (null)
3: r-bioc-hypergraph r-bioc-graph 0 (null)
4: r-bioc-hypergraph r-bioc-biocgenerics 0 (null)
5: r-bioc-hypergraph r-cran-runit 0 (null)
---
3744: r-cran-viridislite r-api-3 0 (null)
3745: r-cran-xtable r-base-core 2 3.2.5-1
3746: r-cran-xtable r-api-3 0 (null)
3747: r-cran-pkgkitten r-base-core 2 3.3.2-1
3748: r-cran-pkgkitten r-api-3 0 (null)
>
```
Next we subset to those have `libc6` as a Depends, meaning they are compiled packages.
This excludes all the R packages having only R code.
```{r, eval=FALSE}
> comp <- dep[deppkg=="libc6"] # 242
> comp
srcpkg deppkg cmpop version isCompiled
1: r-bioc-makecdfenv libc6 2 2.4 TRUE
2: r-cran-bio3d libc6 2 2.14 TRUE
3: r-bioc-rsamtools libc6 2 2.15 TRUE
4: r-cran-foreign libc6 2 2.14 TRUE
5: r-bioc-multtest libc6 2 2.14 TRUE
---
238: r-cran-nleqslv libc6 2 2.4 TRUE
239: r-other-amsmercury libc6 2 2.14 TRUE
240: r-cran-gnm libc6 2 2.4 TRUE
241: r-cran-gsl libc6 2 2.4 TRUE
242: r-cran-gss libc6 2 2.4 TRUE
>
```
We are now getting closer. We set keys on the `data.table` objects, and then do
an inner join:
```{r, eval=FALSE}
> setkey(comp, srcpkg)
> setkey(rd, package)
> all <- rd[comp[, c(1,5)]] # inner join (by default on columns with keys)
> all[order(version),]
package version oldVersion skip isCompiled
1: r-cran-bitops 3.0.1-6 TRUE FALSE TRUE
2: r-cran-mnp 3.0.2-1 TRUE FALSE TRUE
3: r-other-mott-happy.hbrem 3.0.2-1 TRUE FALSE TRUE
4: r-cran-amore 3.1.0-1 TRUE FALSE TRUE
5: r-cran-deal 3.1.0-1 TRUE FALSE TRUE
---
238: r-cran-rcpp 3.4.1-2 FALSE FALSE TRUE
239: r-cran-rmysql 3.4.1-2 FALSE FALSE TRUE
240: r-cran-rsymphony 3.4.1-2 FALSE FALSE TRUE
241: r-cran-ttr 3.4.1-2 FALSE FALSE TRUE
242: r-mathlib 3.4.1-2 FALSE FALSE TRUE
>
```
We have 242 _potential_ rebuilds, down from 514 reverse depends at the outset.
#### Version check
Next, we can concentrate on those having been built with the older versions requiring
a rebuild:
```{r, eval=FALSE}
> all[oldVersion==TRUE,][order(version),] # 167
package version oldVersion skip isCompiled
1: r-cran-bitops 3.0.1-6 TRUE FALSE TRUE
2: r-cran-mnp 3.0.2-1 TRUE FALSE TRUE
3: r-other-mott-happy.hbrem 3.0.2-1 TRUE FALSE TRUE
4: r-cran-amore 3.1.0-1 TRUE FALSE TRUE
5: r-cran-deal 3.1.0-1 TRUE FALSE TRUE
---
163: r-cran-rcppgsl 3.3.3-1 TRUE FALSE TRUE
164: r-cran-rodbc 3.3.3-1 TRUE FALSE TRUE
165: r-cran-snowballc 3.3.3-1 TRUE FALSE TRUE
166: r-cran-v8 3.3.3-1 TRUE FALSE TRUE
167: r-cran-zoo 3.3.3-1 TRUE FALSE TRUE
>
```
Now we are down to 167 packages.
```{r, eval=FALSE}
> all[, cran:=grepl("^r-cran", package) ]
> all[, bioc:=grepl("^r-bioc", package) ]
> all[bioc==TRUE & oldVersion==TRUE,] # 17 BioC
package version oldVersion skip isCompiled cran bioc
1: r-bioc-affy 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
2: r-bioc-affyio 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
3: r-bioc-biobase 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
4: r-bioc-biovizbase 3.3.2-1 TRUE FALSE TRUE FALSE TRUE
5: r-bioc-deseq2 3.3.2-1 TRUE FALSE TRUE FALSE TRUE
6: r-bioc-dnacopy 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
7: r-bioc-edger 3.3.0-2 TRUE FALSE TRUE FALSE TRUE
8: r-bioc-genefilter 3.3.2-1 TRUE FALSE TRUE FALSE TRUE
9: r-bioc-graph 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
10: r-bioc-hilbertvis 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
11: r-bioc-limma 3.3.2-1 TRUE FALSE TRUE FALSE TRUE
12: r-bioc-makecdfenv 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
13: r-bioc-multtest 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
14: r-bioc-preprocesscore 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
15: r-bioc-rbgl 3.3.2-1 TRUE FALSE TRUE FALSE TRUE
16: r-bioc-rtracklayer 3.3.2-1 TRUE FALSE TRUE FALSE TRUE
17: r-bioc-snpstats 3.3.1.20161024-1 TRUE FALSE TRUE FALSE TRUE
>
```
Among these are 17 BioConductor packages. This is a superset as we do not know which of these
use only `.Call()` meaning that no rebuild would be required.
```{r, eval=FALSE}
> all[bioc!=TRUE & cran!=TRUE & oldVersion==TRUE,] # 3 other
package version oldVersion skip isCompiled cran bioc
1: r-other-amsmercury 3.3.2-1 TRUE FALSE TRUE FALSE FALSE
2: r-other-iwrlars 3.3.2-1 TRUE FALSE TRUE FALSE FALSE
3: r-other-mott-happy.hbrem 3.0.2-1 TRUE FALSE TRUE FALSE FALSE
>
```
There are also three which are neither BioC nor CRAN.
```{r, eval=FALSE}
> cand <- all[ cran==TRUE & oldVersion==TRUE, ] # 147
> cand
package version oldVersion skip isCompiled cran bioc
1: r-cran-ade4 3.3.2-1 TRUE FALSE TRUE TRUE FALSE
2: r-cran-adegenet 3.3.1-1 TRUE FALSE TRUE TRUE FALSE
3: r-cran-adephylo 3.3.2-1 TRUE FALSE TRUE TRUE FALSE
4: r-cran-amelia 3.2.3-1 TRUE FALSE TRUE TRUE FALSE
5: r-cran-amore 3.1.0-1 TRUE FALSE TRUE TRUE FALSE
---
143: r-cran-vegan 3.3.2-1 TRUE FALSE TRUE TRUE FALSE
144: r-cran-vgam 3.3.2-1 TRUE FALSE TRUE TRUE FALSE
145: r-cran-xml2 3.3.2-1 TRUE FALSE TRUE TRUE FALSE
146: r-cran-yaml 3.3.2-1 TRUE FALSE TRUE TRUE FALSE
147: r-cran-zoo 3.3.3-1 TRUE FALSE TRUE TRUE FALSE
>
```
We have 147 possible NMUs based off CRAN.
Next, we mix this with information from CRAN.
```{r, eval=FALSE}
> db <- tools::CRAN_package_db() # CRAN pkge info: N rows x 65 cols
> setDT(db)
> db[, package:=paste0("r-cran-", tolower(Package))]
> setkey(db, package) # key on package field
> foo <- db[ cand ] # inner join
> foo[, .(package, Package, Version, NeedsCompilation, oldVersion, skip)]
package Package Version NeedsCompilation oldVersion skip
1: r-cran-ade4 ade4 1.7-6 yes TRUE FALSE
2: r-cran-adegenet adegenet 2.0.1 yes TRUE FALSE
3: r-cran-adephylo adephylo 1.1-10 yes TRUE FALSE
4: r-cran-amelia Amelia 1.7.4 yes TRUE FALSE
5: r-cran-amore AMORE 0.2-15 yes TRUE FALSE
---
143: r-cran-vegan vegan 2.4-3 yes TRUE FALSE
144: r-cran-vgam VGAM 1.0-3 yes TRUE FALSE
145: r-cran-xml2 xml2 1.1.1 yes TRUE FALSE
146: r-cran-yaml yaml 2.1.14 yes TRUE FALSE
147: r-cran-zoo zoo 1.8-0 yes TRUE FALSE
>
```
This is our set of 147 candidate packages with their CRAN name, Debian name and upstream version.
```{r, eval=FALSE}
> saveRDS(foo[, .(package, Package, Version, NeedsCompilation, oldVersion, skip)], file="debpackages.rds")
```
We save this file to be used on another machine.
## Step 2: Grep
On another machine with access to all CRAN package sources (which I happen to have access to), we use the list
of 147 candidate packages and run a recursive grep for each. We store the output from two `egrep` runs, called via `system()`,
directly in the same data structure. The first checks for `.C()` or `.Fortran()` calls in the R scripts; the second checks
for `R_registerRoutines()` in the compiled C code (with thanks again to Kurt Hornik for the suggestion)
```{r, eval=FALSE}
deb <- readRDS("~/debpackages.rds")
for (i in 1:nrow(deb)) {
deb[i, "dotCorFortran"] <- if (is.na(deb[i, "Package"])) NA
else system(paste0("egrep -r -q \"\\.(C|Fortran)\\(\" ", deb[i, "Package"], "/R/*"))==0
deb[i, "hasRegistration"] <- if (is.na(deb[i, "Package"])) NA
else system(paste0("egrep -r -q \"R_registerRoutines\\(\" ", deb[i, "Package"], "/src/*"))==0
}
saveRDS(deb, "~/debpackagesout.rds")
```
## Step 3: Finalize
We read the data back in and subset on those for which the recursive grep found actual uses of
`.C()` or `.Fortran()`. The list contains 72 packages.
```{r, eval=FALSE}
> deb <- readRDS("debpackagesout.rds")
> setDT(deb)
> deb[ is.na(dotCorFortran) |(dotCorFortran & hasRegistration), 1:3]
package Package Version
1: r-cran-ade4 ade4 1.7-6
2: r-cran-bayesm bayesm 3.1-0.1
3: r-cran-blockmodeling blockmodeling 0.1.9
4: r-cran-brglm brglm 0.6.1
5: r-cran-caret caret 6.0-76
6: r-cran-coin coin 1.2-1
7: r-cran-contfrac contfrac 1.1-11
8: r-cran-data.table data.table 1.10.4
9: r-cran-deldir deldir 0.1-14
10: r-cran-desolve deSolve 1.20
11: r-cran-eco eco 4.0-1
12: r-cran-expm expm 0.999-2
13: r-cran-fields fields 9.0
14: r-cran-gam gam 1.14-4
15: r-cran-glmnet glmnet 2.0-10
16: r-cran-goftest goftest 1.1-1
17: r-cran-hdf5 NA NA
18: r-cran-igraph igraph 1.1.2
19: r-cran-mapproj mapproj 1.2-5
20: r-cran-maps maps 3.2.0
21: r-cran-maptools maptools 0.9-2
22: r-cran-mcmc mcmc 0.9-5
23: r-cran-mcmcpack MCMCpack 1.4-0
24: r-cran-medadherence NA NA
25: r-cran-mixtools mixtools 1.1.0
26: r-cran-mnp MNP 3.0-2
27: r-cran-ncdf4 ncdf4 1.16
28: r-cran-phangorn phangorn 2.2.0
29: r-cran-phylobase phylobase 0.8.4
30: r-cran-qtl qtl 1.41-6
31: r-cran-randomfields RandomFields 3.1.50
32: r-cran-randomfieldsutils RandomFieldsUtils 0.3.25
33: r-cran-rcurl RCurl 1.95-4.8
34: r-cran-rniftilib NA NA
35: r-cran-sp sp 1.2-5
36: r-cran-spam spam 2.1-1
37: r-cran-spatstat spatstat 1.51-0
38: r-cran-spdep spdep 0.6-13
39: r-cran-surveillance surveillance 1.14.0
40: r-cran-treescape NA NA
41: r-cran-vegan vegan 2.4-3
42: r-cran-vgam VGAM 1.0-4
package Package Version
>
```
Similarly, the 17 BioC and 3 other packages can be tested via recursive greps (not shown) in a directory
filled with `apt-get source` downloads:
```{r, eval=FALSE}
pkgs <- rbind(all[bioc!=TRUE & cran!=TRUE & oldVersion==TRUE, 1],
all[bioc==TRUE & oldVersion==TRUE, 1])[[1]]
dir.create("/tmp/scratch")
setwd("/tmp/scratch")
cat("deb-src http://deb.debian.org/debian unstable main\n",
file="/etc/apt/sources.list", append=TRUE)
system("apt-get update")
for (p in pkgs) system(paste("apt-get source", p))
df <- data.frame(package=pkgs, stringsAsFactors=FALSE)
for (i in 1:nrow(df)) {
p <- df[i, 1]
df[i, "dotCorFortran"] <- system(paste0("egrep -r -q \"\\.(C|Fortran)\\(\" ", p, "*/R/*"))==0
df[i, "hasRegistration"] <- system(paste0("egrep -r -q \"R_registerRoutines\\(\" ", p, "*/src/*"))==0
}
setDT(df)
```
This leads to a further four packages:
```{r, eval=FALSE}
> df[dotCorFortran & hasRegistration, 1]
pkg
1: r-bioc-affy
2: r-bioc-edger
3: r-bioc-genefilter
4: r-bioc-preprocesscore
>
```
These 42, along with the 4 (from the initally 17 BioC and 3 'other') packages are our target set.
```{r, eval=FALSE}
> nmu <- deb[ is.na(dotCorFortran) | (dotCorFortran & hasRegistration), 1] #42
> oth <- df[dotCorFortran & hasRegistration, 1]
>
> nmu <- rbind(nmu, oth) ## 46
> nmu
package
1: r-cran-ade4
2: r-cran-bayesm
3: r-cran-blockmodeling
4: r-cran-brglm
5: r-cran-caret
6: r-cran-coin
7: r-cran-contfrac
8: r-cran-data.table
9: r-cran-deldir
10: r-cran-desolve
11: r-cran-eco
12: r-cran-expm
13: r-cran-fields
14: r-cran-gam
15: r-cran-glmnet
16: r-cran-goftest
17: r-cran-hdf5
18: r-cran-igraph
19: r-cran-mapproj
20: r-cran-maps
21: r-cran-maptools
22: r-cran-mcmc
23: r-cran-mcmcpack
24: r-cran-medadherence
25: r-cran-mixtools
26: r-cran-mnp
27: r-cran-ncdf4
28: r-cran-phangorn
29: r-cran-phylobase
30: r-cran-qtl
31: r-cran-randomfields
32: r-cran-randomfieldsutils
33: r-cran-rcurl
34: r-cran-rniftilib
35: r-cran-sp
36: r-cran-spam
37: r-cran-spatstat
38: r-cran-spdep
39: r-cran-surveillance
40: r-cran-treescape
41: r-cran-vegan
42: r-cran-vgam
43: r-bioc-affy
44: r-bioc-edger
45: r-bioc-genefilter
46: r-bioc-preprocesscore
package
>
>
```
We need to retrieve the version number in Debian unstable of these packages by once agaim
relying of a function from [`RcppAPT`](https://github.com/eddelbuettel/rcppapt)
```{r, eval=FALSE}
> regexp <- paste(paste0("^", nmu[[1]], "$"), collapse="|")
>
> res <- getPackages(regexp)
> res
Package Version
1 r-bioc-edger 3.14.0+dfsg-1
2 r-cran-coin 1.1-3-1
3 r-cran-mnp 2.6-4-1
4 r-cran-fields 8.10-1
5 r-cran-desolve 1.14-1
6 r-cran-deldir 0.1-12-1
7 r-cran-rniftilib 0.0-35.r79-2
8 r-cran-data.table 1.10.0-1
9 r-cran-qtl 1.40-8-1
10 r-bioc-preprocesscore 1.36.0-1
11 r-cran-contfrac 1.1-10-1
12 r-cran-glmnet 2.0-5-1
13 r-cran-sp 1:1.2-4-1
14 r-cran-brglm 0.5-9-1
15 r-bioc-affy 1.52.0-1
16 r-cran-ncdf4 1.15-1+b2
17 r-cran-treescape 1.10.18-6
18 r-cran-mapproj 1.2-4-1
19 r-cran-blockmodeling 0.1.8-1
20 r-cran-hdf5 1.6.10-4+b1
21 r-cran-ade4 1.7-5-1
22 r-cran-vgam 1.0-3-1
23 r-cran-mixtools 1.0.4-1
24 r-cran-phylobase 0.8.2-1
25 r-cran-spam 1.4-0-1
26 r-cran-medadherence 1.03-2
27 r-cran-surveillance 1.13.0-1
28 r-cran-randomfieldsutils 0.3.15-1
29 r-cran-rcurl 1.95-4.8-2
30 r-cran-mcmcpack 1.3-8-1
31 r-cran-spatstat 1.48-0-1
32 r-cran-vegan 2.4-2-1
33 r-cran-bayesm 3.0-2-2
34 r-cran-expm 0.999-0-1
35 r-cran-phangorn 2.1.1-1
36 r-cran-maptools 1:0.8-41+dfsg-1
37 r-cran-caret 6.0-73+dfsg1-1
38 r-cran-goftest 1.0-3-1
39 r-cran-igraph 1.0.1-1
40 r-cran-maps 3.1.1-1
41 r-cran-eco 3.1-7-1
42 r-cran-randomfields 3.1.36-1
43 r-bioc-genefilter 1.56.0-1
44 r-cran-mcmc 0.9-4-2
45 r-cran-spdep 0.6-9-1
46 r-cran-gam 1.14-1
>
```
With this, we can write out the content of the NMU request:
```{r, eval=FALSE}
>
> for (i in 1:nrow(res))
+ cat("nmu", paste(res[i,], collapse="_"), ". ANY . -m 'Rebuild against R 3.4.*, see #861333'\n")
nmu r-bioc-edger_3.14.0+dfsg-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-coin_1.1-3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-mnp_2.6-4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-fields_8.10-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-desolve_1.14-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-deldir_0.1-12-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-rniftilib_0.0-35.r79-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-data.table_1.10.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-qtl_1.40-8-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-preprocesscore_1.36.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-contfrac_1.1-10-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-glmnet_2.0-5-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-sp_1:1.2-4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-brglm_0.5-9-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-affy_1.52.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-ncdf4_1.15-1+b2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-treescape_1.10.18-6 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-mapproj_1.2-4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-blockmodeling_0.1.8-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-hdf5_1.6.10-4+b1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-ade4_1.7-5-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-vgam_1.0-3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-mixtools_1.0.4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-phylobase_0.8.2-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-spam_1.4-0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-medadherence_1.03-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-surveillance_1.13.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-randomfieldsutils_0.3.15-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-rcurl_1.95-4.8-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-mcmcpack_1.3-8-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-spatstat_1.48-0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-vegan_2.4-2-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-bayesm_3.0-2-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-expm_0.999-0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-phangorn_2.1.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-maptools_1:0.8-41+dfsg-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-caret_6.0-73+dfsg1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-goftest_1.0-3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-igraph_1.0.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-maps_3.1.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-eco_3.1-7-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-randomfields_3.1.36-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-genefilter_1.56.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-mcmc_0.9-4-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-spdep_0.6-9-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-gam_1.14-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
>
```
## Summary
The final set of 46 NMUs is the minimal change required, and reasonable relative to the
516 reverse dependencies of R itself. We are able to narrow the set of packages requiring
a rebuild down by a combining data from the R package system, the Debian package system
and (some) package sources we were able to access on a CRAN-related server.
### Acknowledgements
Thanks for Kurt Hornik for pointing out the additional check for `R_registerRoutine` in the in C code, leading
to a further reduction from 90+ packages to 46.
### History
The first published version (Julyu 2017) did not check for `R_registerRoutines`. The second version (August 2017)
does, leading to 46 suggested NMUs.
### See Also
The [source file](https://github.com/eddelbuettel/rcppapt/blob/master/vignettes/binnmuAfterR340.Rmd) is on GitHub
as is the [revision history](https://github.com/eddelbuettel/rcppapt/commits/master/vignettes/binnmuAfterR340.Rmd).
The [corresponding Debian bug report](https://bugs.debian.org/868558) is based on this analysis.
You can’t perform that action at this time.