"How are you" = /haʊɑːjuː/~/haʊɑːju/: "linking r" is not used before semivowels in present-day standard Southern British English. (I don't know if any accent exists or has ever existed that does that.)
In general, semivowels in the onset of a syllable are not treated the same as nuclear vowels in English for the purposes of allophony and morpho-phonological rules. Another example is the use of "a" vs "an": the form "an" is used before nuclear vowels, but it is not used before semivowels (/j/ or /w/).
Another example of how word-intial /w/ and /j/ don't affect the pronunciation of a preceding word in the same way as word-initial nuclear vowels in English could be the treatment of t-flapping in American English. Word-final /t/ can be voiced and flapped in some circumstances when followed by a word starting with an unstressed vowel (e.g. in "eat it" the /t/ in "eat" could be flapped) but before /j/ in a following syllable, /t/ is not voiced, but instead tends to be affricated to [tʃ] and/or glottalized (as in "eat you"). Before /w/ in a following syllable, I believe I glottalize /t/, as in "eat with them".