Combining the R and Debian package systems
First version 2017-Jul-16; this version 2017-Aug-05
R 3.4.0, released in April, included the following paragraph in its NEWS file:
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.
For the Debian packages, this means that we need to consider the set of packages which
r-cran-*, r-bioc-* and alike.C() or .Fortran() (but not .Call()) callThis note computes this set and provides the input for a wanna-build 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.
For this we drop into a clean Docker container running Debian unstable. Later, we will need the current sources of the RcppAPT package so we start from a local git directory:
server> cd ~/git && docker run --rm -ti -v $(pwd):/mnt debian:unstableInside the Docker container, we update the package information and install what is needed to build 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.
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 rcppaptInside the same Docker session, we now launch R and run (almost all of) the remainder from R.
> 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.
> 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.
> 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 FALSETo cover some corner case, we derive a skip field:
> 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
>Next, we find the actual dependencies of each of these packages by constructing a large regular expression which we feed into RcppAPT::getDepends()
> 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.
> 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:
> 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.
Next, we can concentrate on those having been built with the older versions requiring a rebuild:
> 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.
> 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.
> 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.
> 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.
> 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.
> saveRDS(foo[, .(package, Package, Version, NeedsCompilation, oldVersion, skip)], file="debpackages.rds")We save this file to be used on another machine.
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)
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")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.
> 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:
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:
> 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.
> 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
> 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:
>
> 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'
>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.
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.
The first published version (Julyu 2017) did not check for R_registerRoutines. The second version (August 2017) does, leading to 46 suggested NMUs.
The source file is on GitHub as is the revision history. The corresponding Debian bug report is based on this analysis.