Answering myself...
It turns out the reason the deps are not included in the APEX is the 
presence of cfi sanitizer in their Android.bp. When this is set, 
HideFromMake for the module is set to true, and the module is then not 
included when generating out/soong/Android-${TARGET_PRODUCT}.mk

On Thursday, October 3, 2019 at 3:53:13 PM UTC-4, Michael Goffioul wrote:
>
> Hi,
>
> I'm trying to build Android Q (for android-x86, 32-bits) and I'm having a 
> problem in the generated apex for com.android.media.swcodec, where there 
> are a bunch of libraries missing in 
> $TARGET_OUT/system/apex/com.android.media.swcodec/lib/.
>
> The directory does contain various deps like libcodec2_h...@1.0.so, 
> libmedia_codecserviceregistrant.so or libstagefright_amrnb_common.so. 
> However it is missing some, most 
> notably libstagefright_bufferqueue_helper.so or all libcodec2_soft_*.so 
> modules. This then results in runtime errors when running mediaswcodec 
> service.
>
> What can be the reasons for deps to be missing from the apex?
>
> Note that I tried to find my way in build/soong/, but didn't get anywhere 
> in trying to debug this issue.
>
> Michael.
>
>

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