RSEM-v1.3.1: "make pRSEM" fails while loading GenomicRanges

Prior to running make pRSEM, I ran make and make ebseq, both of which completed successfully.

$ make pRSEM
cd pRSEM && make all
make[1]: Entering directory `/home/groups/test/Apps/RSEM-1.3.1/pRSEM'
if [ ! -e "bigWigSummary" ]; then \
  curl -O http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64.v287/bigWigSummary; \
  chmod +x bigWigSummary; \
  fi
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   239  100   239    0     0  34142      0 --:--:-- --:--:-- --:--:-- 34142
if [ ! -d "RLib" ]; then mkdir RLib/; fi; \
  cd RLib/; Rscript ../installRLib.R 
Hi test, welcome to R...
trying URL 'http://cran.us.r-project.org/src/contrib/devtools_2.0.1.tar.gz'
...
...
...
Downloading package from url: http://bioconductor.org/packages/3.3/bioc/src/contrib/GenomicRanges_1.24.3.tar.gz

Skipping 4 packages ahead of CRAN: GenomeInfoDb, IRanges, XVector, zlibbioc
...
...
...
Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : 
  methods can add arguments to the generic ‘seqinfo<-’ only if '...' is an argument to the generic
Error : unable to load R code in package ‘GenomicRanges’
ERROR: lazy loading failed for package ‘GenomicRanges’
* removing ‘/home/groups/test/Apps/RSEM-1.3.1/pRSEM/RLib/GenomicRanges’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/tmp/RtmpWi4io9/remotes2d001150ec772/GenomicRanges’ had non-zero exit status
Calls: main ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
make[1]: *** [RLib] Error 1
make[1]: Leaving directory `/home/groups/test/Apps/RSEM-1.3.1/pRSEM'
make: *** [pRSEM] Error 2

GenomicRanges loads fine on its own!

$ R

R version 3.5.2 Patched (2019-01-24 r76013) -- "Eggshell Igloo"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

Hi test, welcome to R...
> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> packageVersion("GenomicRanges")
[1] ‘1.34.0’
>

I can also remove and reinstall GenomicRanges independently! I do not think I really understand what is causing this issue, however, one possibility is that make pRSEM is trying to install a very old http://bioconductor.org/packages/3.3/bioc/src/contrib/GenomicRanges_1.24.3.tar.gz version of GenomicRanges.

If after the error in R the first time while running make pRSEM, if I just rerun make pRSEM again it shows no error:

$ make pRSEM
cd pRSEM && make all
make[1]: Entering directory `/home/groups/test/Apps/RSEM-1.3.1/pRSEM'
g++ filterSam2Bed.c ../samtools-1.3/libbam.a ../samtools-1.3/htslib-1.3/libhts.a -lz -lpthread -I../samtools-1.3 -I../samtools-1.3/htslib-1.3 -o filterSam2Bed
make[1]: Leaving directory `/home/groups/test/Apps/RSEM-1.3.1/pRSEM'
$

deweylab / RSEM

RSEM-v1.3.1: "make pRSEM" fails while loading GenomicRanges #114