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Let $M=SU_3$, the compact semisimple Lie group. Write the left invariant Maurer--Cartan form $g^{-1}dg$ as $(\omega_{\mu\bar\nu})$ for $\mu,\nu=1,2,3$. The coframing $\omega_{1\bar{1}}+i\omega_{2\bar{2}},\omega_{1\bar{2}},\omega_{1\bar{3}},\omega_{2\bar{3}}$ is complex linear for a unique left invariant complex structure. Take a function $f(g)=1+e^{-|g_{1\bar{2}}|^2/\varepsilon}$. This is so close to $1$, for small enough $\varepsilon$, that the coframing $\omega_{1\bar{1}}+if\omega_{2\bar{2}},\omega_{1\bar{2}},\omega_{1\bar{3}},\omega_{2\bar{3}}$ continues to have linearly independent real and imaginary parts, so is still complex linear for a unique almost complex structure. But since $f$ is not holomorphic and is not constant, there is a nonzero Nijenhuis tensor. You could also take $f$ to be instead some smooth function with support in some small compact set, and then you get complex structure on some open set turning smoothly almost complex, not complex, on some other open set, so clearly not algebraic.