can't install the packages 'backports','nlme'

[HL2007]

When I install the JunctionSeq by using "BiocManager::install("JunctionSeq")" in R current version 3.5.3, and it gave me as the following error messages. Can the "JunctionSeq" not be run on the R 3.5.3? Thanks,

installing the source packages ‘backports’, ‘nlme’

trying URL 'https://cran.rstudio.com/src/contrib/backports_1.1.4.tar.gz' Content type 'application/x-gzip' length 13859 bytes (13 KB)

downloaded 13 KB

trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-139.tar.gz' Content type 'application/x-gzip' length 793473 bytes (774 KB)

downloaded 774 KB

• installing source package ‘backports’ ... package ‘backports’ successfully unpacked and MD5 sums checked libs Users/.R/Makevars:4: *** missing separator. Stop. ERROR: compilation failed for package ‘backports’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/backports’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/backports’
• installing source package ‘nlme’ ... package ‘nlme’ successfully unpacked and MD5 sums checked libs /Users/.R/Makevars:4: *** missing separator. Stop. ERROR: compilation failed for package ‘nlme’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/nlme’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/nlme’

[hartleys]

Are you on windows or linux or mac?

For whatever reason these packages have source versions that are newer than the binary versions, so it's trying to compile from source and failing. Probably because you don't have a compiler hooked up (many people don't, and unless you develop R packages you don't really need to).

Easiest fix is to install them manually:

install.packages("nlme") install.packages("backports")

And each time when it asks you "Do you want to install from sources the package which needs compilation?" type "N" to install the most recent binary version instead.