Determining deep holes is an important topic in decoding Reed-Solomon codes. Let $l\ge 1$ be an integer and $a_1,\ldots,a_l$ be arbitrarily given $l$ distinct elements of the finite field ${\bf F}_q$ of $q$ elements with the odd prime number $p$ as its characteristic. Let $D={\bf F}_q\backslash\{a_1,\ldots,a_l\}$ and $k$ be an integer such that $2\le k\le q-l-1$. In this paper, we study the deep holes of generalized projective Reed-Solomon code ${\rm GPRS}_q(D, k)$ of length $q-l+1$ and dimension $k$ over ${\bf F}_q$. For any $f(x)\in {\bf F}_q[x]$, we let $f(D)=(f(y_1),\ldots,f(y_{q-l}))$ if $D=\{y_1, ..., y_{q-l}\}$ and $c_{k-1}(f(x))$ be the coefficient of $x^{k-1}$ of $f(x)$. By using Dür's theorem on the relation between the covering radius and minimum distance of ${\rm GPRS}_q(D, k)$, we show that if $u(x)\in {\bf F}_q[x]$ with $°(u(x))=k$, then the received codeword $(u(D), c_{k-1}(u(x)))$ is a deep hole of ${\rm GPRS}_q(D, k)$ if and only if the sum $\sum\limits_{y\in I}y$ is nonzero for any subset $I\subseteq D$ with $\#(I)=k$. We show also that if $j$ is an integer with $1\leq j\leq l$ and $u_j(x):= λ_j(x-a_j)^{q-2}+ν_j x^{k-1}+f_{\leq k-2}^{(j)}(x)$ with $λ_j\in {\bf F}_q^*$, $ν_j\in {\bf F}_q$ and $f_{\leq{k-2}}^{(j)}(x)\in{\bf F}_q[x]$ being a polynomial of degree at most $k-2$, then $(u_j(D), c_{k-1}(u_j(x)))$ is a deep hole of ${\rm GPRS}_q(D, k)$ if and only if the sum $\binom{q-2}{k-1}(-a_j)^{q-1-k}\prod\limits_{y\in I}(a_j-y)+e$ is nonzero for any subset $I\subseteq D$ with $\#(I)=k$, where $e$ is the identity of the group ${\bf F}_q^*$. This implies that $(u_j(D), c_{k-1}(u_j(x)))$ is a deep hole of ${\rm GPRS}_q(D, k)$ if $p|k$.