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.
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") # 514 x 2
> rd <- rd[!grepl("r-(doc|base)", rd[,1]), ] # 506 x 2
> rd <- rd[grepl("^r-", rd[,1]), ] # 480 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) 514 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 480 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
package version
1: r-cran-phylobase 3.2.4.20160406-1
2: r-cran-zelig 3.0.2-1
3: r-cran-urca 3.4.0-1
4: r-cran-tseries 3.3.3.20170413-1
5: r-cran-tkrplot 3.3.0.20160615-1
---
476: r-cran-bitops 3.0.1-6
477: r-cran-cairodevice 3.4.0-1
478: r-cran-boot 3.4.0-1
479: r-cran-acepack 3.4.0-1
480: r-cran-abind 3.3.1-1
> 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
package version oldVersion
1: r-cran-phylobase 3.2.4.20160406-1 TRUE
2: r-cran-zelig 3.0.2-1 TRUE
3: r-cran-urca 3.4.0-1 FALSE
4: r-cran-tseries 3.3.3.20170413-1 FALSE
5: r-cran-tkrplot 3.3.0.20160615-1 TRUE
---
476: r-cran-bitops 3.0.1-6 TRUE
477: r-cran-cairodevice 3.4.0-1 FALSE
478: r-cran-boot 3.4.0-1 FALSE
479: r-cran-acepack 3.4.0-1 FALSE
480: r-cran-abind 3.3.1-1 TRUE
> To cover some corner case, we derive a skip field:
> rd[ version=="", skip:=TRUE ]
> rd[ is.na(skip), skip:=FALSE]
> rd
package version oldVersion skip
1: r-cran-phylobase 3.2.4.20160406-1 TRUE FALSE
2: r-cran-zelig 3.0.2-1 TRUE FALSE
3: r-cran-urca 3.4.0-1 FALSE FALSE
4: r-cran-tseries 3.3.3.20170413-1 FALSE FALSE
5: r-cran-tkrplot 3.3.0.20160615-1 TRUE FALSE
---
476: r-cran-bitops 3.0.1-6 TRUE FALSE
477: r-cran-cairodevice 3.4.0-1 FALSE FALSE
478: r-cran-boot 3.4.0-1 FALSE FALSE
479: r-cran-acepack 3.4.0-1 FALSE FALSE
480: r-cran-abind 3.3.1-1 TRUE 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)
---
3690: r-cran-viridislite r-api-3 0 (null)
3691: r-cran-xtable r-base-core 2 3.2.5-1
3692: r-cran-xtable r-api-3 0 (null)
3693: r-cran-pkgkitten r-base-core 2 3.3.2-1
3694: 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"] # about 241
> comp[, isCompiled:=TRUE]
> 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
---
237: r-cran-nleqslv libc6 2 2.4 TRUE
238: r-other-amsmercury libc6 2 2.14 TRUE
239: r-cran-gnm libc6 2 2.4 TRUE
240: r-cran-gsl libc6 2 2.4 TRUE
241: 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
---
237: r-cran-statmod 3.4.1-1 FALSE FALSE TRUE
238: r-cran-ape 3.4.1-2 FALSE FALSE TRUE
239: r-cran-nleqslv 3.4.1-2 FALSE FALSE TRUE
240: r-cran-rmysql 3.4.1-2 FALSE FALSE TRUE
241: r-mathlib 3.4.1-2 FALSE FALSE TRUE
> We have 241 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 egrep, called via system(), directly in the same data structure:
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
}
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(deb[, dotCorFortran]) | deb[, dotCorFortran]==TRUE, 1:3] ## 72
package Package Version
1: r-cran-ade4 ade4 1.7-6
2: r-cran-adegenet adegenet 2.0.1
3: r-cran-adephylo adephylo 1.1-10
4: r-cran-amelia Amelia 1.7.4
5: r-cran-bayesm bayesm 3.1-0
6: r-cran-bitops bitops 1.0-6
7: r-cran-blockmodeling blockmodeling 0.1.9
8: r-cran-boolnet BoolNet 2.1.3
9: r-cran-brglm brglm 0.6.1
10: r-cran-caret caret 6.0-76
11: r-cran-catools caTools 1.17.1
12: r-cran-cmprsk cmprsk 2.2-7
13: r-cran-coin coin 1.2-0
14: r-cran-contfrac contfrac 1.1-11
15: r-cran-data.table data.table 1.10.4
16: r-cran-deal deal 1.2-37
17: r-cran-deldir deldir 0.1-14
18: r-cran-desolve deSolve 1.20
19: r-cran-dosefinding DoseFinding 0.9-15
20: r-cran-eco eco 3.1-7
21: r-cran-erm eRm 0.15-7
22: r-cran-etm etm 0.6-2
23: r-cran-evd evd 2.3-2
24: r-cran-expm expm 0.999-2
25: r-cran-fields fields 9.0
26: r-cran-gam gam 1.14-4
27: r-cran-genabel GenABEL 1.8-0
28: r-cran-glmnet glmnet 2.0-10
29: r-cran-goftest goftest 1.1-1
30: r-cran-gsl gsl 1.9-10.3
31: r-cran-haplo.stats haplo.stats 1.7.7
32: r-cran-hdf5 NA NA
33: r-cran-hexbin hexbin 1.27.1
34: r-cran-igraph igraph 1.0.1
35: r-cran-lhs lhs 0.14
36: r-cran-logspline logspline 2.1.9
37: r-cran-mapproj mapproj 1.2-5
38: r-cran-maps maps 3.2.0
39: r-cran-maptools maptools 0.9-2
40: r-cran-mcmc mcmc 0.9-5
41: r-cran-mcmcpack MCMCpack 1.4-0
42: r-cran-medadherence NA NA
43: r-cran-mixtools mixtools 1.1.0
44: r-cran-mlbench mlbench 2.1-1
45: r-cran-mnp MNP 3.0-2
46: r-cran-msm msm 1.6.4
47: r-cran-ncdf4 ncdf4 1.16
48: r-cran-nnls nnls 1.4
49: r-cran-pbivnorm pbivnorm 0.6.0
50: r-cran-phangorn phangorn 2.2.0
51: r-cran-phylobase phylobase 0.8.4
52: r-cran-polycub polyCub 0.6.0
53: r-cran-princurve princurve 1.1-12
54: r-cran-pscl pscl 1.4.9
55: r-cran-qtl qtl 1.41-6
56: r-cran-randomfields RandomFields 3.1.50
57: r-cran-randomfieldsutils RandomFieldsUtils 0.3.25
58: r-cran-randomforest randomForest 4.6-12
59: r-cran-raschsampler RaschSampler 0.8-8
60: r-cran-rcurl RCurl 1.95-4.8
61: r-cran-rniftilib NA NA
62: r-cran-sp sp 1.2-5
63: r-cran-spam spam 2.1-1
64: r-cran-spatstat spatstat 1.51-0
65: r-cran-spc spc 0.5.3
66: r-cran-spdep spdep 0.6-13
67: r-cran-surveillance surveillance 1.14.0
68: r-cran-tgp tgp 2.4-14
69: r-cran-tikzdevice tikzDevice 0.10-1
70: r-cran-treescape NA NA
71: r-cran-vegan vegan 2.4-3
72: r-cran-vgam VGAM 1.0-3
package Package Version
> These 72, along with the 17 BioC and 3 ‘other’ packages are our target set.
> nmu <- deb[ is.na(deb[, dotCorFortran]) | deb[, dotCorFortran]==TRUE, 1]
> nmu <- rbind(nmu, all[bioc!=TRUE & cran!=TRUE & oldVersion==TRUE, 1]) # 'other'
> nmu <- rbind(nmu, all[bioc==TRUE & oldVersion==TRUE, 1]) # BioC
>
> options("width"=80)
> nmu[[1]]
[1] "r-cran-ade4" "r-cran-adegenet"
[3] "r-cran-adephylo" "r-cran-amelia"
[5] "r-cran-bayesm" "r-cran-bitops"
[7] "r-cran-blockmodeling" "r-cran-boolnet"
[9] "r-cran-brglm" "r-cran-caret"
[11] "r-cran-catools" "r-cran-cmprsk"
[13] "r-cran-coin" "r-cran-contfrac"
[15] "r-cran-data.table" "r-cran-deal"
[17] "r-cran-deldir" "r-cran-desolve"
[19] "r-cran-dosefinding" "r-cran-eco"
[21] "r-cran-erm" "r-cran-etm"
[23] "r-cran-evd" "r-cran-expm"
[25] "r-cran-fields" "r-cran-gam"
[27] "r-cran-genabel" "r-cran-glmnet"
[29] "r-cran-goftest" "r-cran-gsl"
[31] "r-cran-haplo.stats" "r-cran-hdf5"
[33] "r-cran-hexbin" "r-cran-igraph"
[35] "r-cran-lhs" "r-cran-logspline"
[37] "r-cran-mapproj" "r-cran-maps"
[39] "r-cran-maptools" "r-cran-mcmc"
[41] "r-cran-mcmcpack" "r-cran-medadherence"
[43] "r-cran-mixtools" "r-cran-mlbench"
[45] "r-cran-mnp" "r-cran-msm"
[47] "r-cran-ncdf4" "r-cran-nnls"
[49] "r-cran-pbivnorm" "r-cran-phangorn"
[51] "r-cran-phylobase" "r-cran-polycub"
[53] "r-cran-princurve" "r-cran-pscl"
[55] "r-cran-qtl" "r-cran-randomfields"
[57] "r-cran-randomfieldsutils" "r-cran-randomforest"
[59] "r-cran-raschsampler" "r-cran-rcurl"
[61] "r-cran-rniftilib" "r-cran-sp"
[63] "r-cran-spam" "r-cran-spatstat"
[65] "r-cran-spc" "r-cran-spdep"
[67] "r-cran-surveillance" "r-cran-tgp"
[69] "r-cran-tikzdevice" "r-cran-treescape"
[71] "r-cran-vegan" "r-cran-vgam"
[73] "r-other-amsmercury" "r-other-iwrlars"
[75] "r-other-mott-happy.hbrem" "r-bioc-affy"
[77] "r-bioc-affyio" "r-bioc-biobase"
[79] "r-bioc-biovizbase" "r-bioc-deseq2"
[81] "r-bioc-dnacopy" "r-bioc-edger"
[83] "r-bioc-genefilter" "r-bioc-graph"
[85] "r-bioc-hilbertvis" "r-bioc-limma"
[87] "r-bioc-makecdfenv" "r-bioc-multtest"
[89] "r-bioc-preprocesscore" "r-bioc-rbgl"
[91] "r-bioc-rtracklayer" "r-bioc-snpstats"
> 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
> res
Package Version
1 r-bioc-makecdfenv 1.50.0-1
2 r-bioc-multtest 2.30.0-1
3 r-bioc-edger 3.14.0+dfsg-1
4 r-cran-boolnet 2.1.3-1
5 r-cran-tikzdevice 0.10-1-1
6 r-cran-logspline 2.1.9-1
7 r-cran-genabel 1.8-0-1+b1
8 r-cran-lhs 0.14-1
9 r-bioc-limma 3.30.8+dfsg-1
10 r-cran-coin 1.1-3-1
11 r-other-iwrlars 0.9-5-2
12 r-cran-mnp 2.6-4-1
13 r-cran-msm 1.6.4-1
14 r-cran-fields 8.10-1
15 r-cran-desolve 1.14-1
16 r-cran-adephylo 1.1-10-2
17 r-cran-dosefinding 0.9-15-1
18 r-cran-deldir 0.1-12-1
19 r-cran-rniftilib 0.0-35.r79-2
20 r-cran-data.table 1.10.0-1
21 r-cran-qtl 1.40-8-1
22 r-bioc-preprocesscore 1.36.0-1
23 r-cran-contfrac 1.1-10-1
24 r-cran-glmnet 2.0-5-1
25 r-cran-bitops 1.0-6-1
26 r-cran-sp 1:1.2-4-1
27 r-cran-spc 1:0.5.3-1
28 r-bioc-snpstats 1.24.0+dfsg-1
29 r-cran-tgp 2.4-14-2
30 r-cran-brglm 0.5-9-1
31 r-cran-cmprsk 2.2-7-2
32 r-bioc-affy 1.52.0-1
33 r-cran-ncdf4 1.15-1+b2
34 r-cran-treescape 1.10.18-6
35 r-bioc-rbgl 1.50.0+dfsg1-1
36 r-bioc-rtracklayer 1.34.1-1
37 r-cran-hexbin 1.27.1-1
38 r-cran-princurve 1.1-12-1
39 r-cran-mapproj 1.2-4-1
40 r-cran-blockmodeling 0.1.8-1
41 r-cran-hdf5 1.6.10-4+b1
42 r-cran-pscl 1.4.9-1
43 r-cran-ade4 1.7-5-1
44 r-cran-vgam 1.0-3-1
45 r-cran-adegenet 2.0.1-1
46 r-cran-mixtools 1.0.4-1
47 r-cran-phylobase 0.8.2-1
48 r-cran-amelia 1.7.4-1
49 r-cran-spam 1.4-0-1
50 r-cran-medadherence 1.03-2
51 r-bioc-biobase 2.34.0-1
52 r-cran-surveillance 1.13.0-1
53 r-cran-randomfieldsutils 0.3.15-1
54 r-cran-deal 1:1.2-37-2
55 r-bioc-hilbertvis 1.32.0-1
56 r-cran-rcurl 1.95-4.8-2
57 r-other-mott-happy.hbrem 2.4-1
58 r-cran-mcmcpack 1.3-8-1
59 r-cran-spatstat 1.48-0-1
60 r-cran-vegan 2.4-2-1
61 r-cran-haplo.stats 1.7.7-1
62 r-cran-bayesm 3.0-2-2
63 r-cran-expm 0.999-0-1
64 r-bioc-dnacopy 1.48.0-1
65 r-cran-phangorn 2.1.1-1
66 r-cran-maptools 1:0.8-41+dfsg-1
67 r-cran-mlbench 2.1-1-1
68 r-bioc-affyio 1.44.0-1
69 r-bioc-graph 1.52.0-1
70 r-cran-polycub 0.5-2-1
71 r-bioc-deseq2 1.14.1-1
72 r-cran-pbivnorm 0.6.0-1
73 r-cran-caret 6.0-73+dfsg1-1
74 r-bioc-biovizbase 1.22.0-2
75 r-cran-nnls 1.4-1
76 r-cran-goftest 1.0-3-1
77 r-cran-igraph 1.0.1-1
78 r-cran-maps 3.1.1-1
79 r-cran-eco 3.1-7-1
80 r-cran-catools 1.17.1-1+b1
81 r-cran-randomfields 3.1.36-1
82 r-cran-erm 0.15-7-1
83 r-cran-etm 0.6-2-3
84 r-cran-randomforest 4.6-12-1
85 r-cran-evd 2.3-2-1
86 r-cran-raschsampler 0.8-8-1
87 r-bioc-genefilter 1.56.0-1
88 r-cran-mcmc 0.9-4-2
89 r-cran-spdep 0.6-9-1
90 r-cran-gam 1.14-1
91 r-other-amsmercury 1.3.0-2
92 r-cran-gsl 1.9-10.3-1
> 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-makecdfenv_1.50.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-multtest_2.30.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-edger_3.14.0+dfsg-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-boolnet_2.1.3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-tikzdevice_0.10-1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-logspline_2.1.9-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-genabel_1.8-0-1+b1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-lhs_0.14-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-limma_3.30.8+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-other-iwrlars_0.9-5-2 . 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-msm_1.6.4-1 . 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-adephylo_1.1-10-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-dosefinding_0.9-15-1 . 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-bitops_1.0-6-1 . 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-spc_1:0.5.3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-snpstats_1.24.0+dfsg-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-tgp_2.4-14-2 . 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-cran-cmprsk_2.2-7-2 . 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-bioc-rbgl_1.50.0+dfsg1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-rtracklayer_1.34.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-hexbin_1.27.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-princurve_1.1-12-1 . 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-pscl_1.4.9-1 . 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-adegenet_2.0.1-1 . 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-amelia_1.7.4-1 . 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-bioc-biobase_2.34.0-1 . 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-deal_1:1.2-37-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-hilbertvis_1.32.0-1 . 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-other-mott-happy.hbrem_2.4-1 . 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-haplo.stats_1.7.7-1 . 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-bioc-dnacopy_1.48.0-1 . 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-mlbench_2.1-1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-affyio_1.44.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-graph_1.52.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-polycub_0.5-2-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-bioc-deseq2_1.14.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-pbivnorm_0.6.0-1 . 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-bioc-biovizbase_1.22.0-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-nnls_1.4-1 . 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-catools_1.17.1-1+b1 . 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-cran-erm_0.15-7-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-etm_0.6-2-3 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-randomforest_4.6-12-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-evd_2.3-2-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-raschsampler_0.8-8-1 . 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'
nmu r-other-amsmercury_1.3.0-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
nmu r-cran-gsl_1.9-10.3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
> The finalu set of 92 NMUs is the minimal change required, and reasonable relative to the over 500 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.