Update to the latest version of deeptools. It was introduced recently. Alternatively,do the following (a bit slower but who cares):

## Calculate the normalization factor
SCALE_FACTOR=$(bc <<< "scale=8;1000000/$(samtools idxstats $1 | mawk '{SUM+=$3} END {print SUM}')")

## Get the bedgraph
bedtools genomecov -bg -pc -ibam in.bam -scale ${SCALE_FACTOR} > out.bedGraph

## to bigwig
bedGraphToBigWig out.bedGraph $CHROMSIZES ${BAM%.bam}_CPM.bigwig && rm out_CPM.bigwig

Or, my personal favorit if you are on Linux (not Mac), get mosdepth. This script should give you a normalized bigwig with only one or two cores in a few minutes. Mosdepth is really awesomely fast.

#!/bin/bash

BAM=$1
CHROMSIZES=$2

## 1. Make the depth file:
mosdepth -t 2 ${1%.bam} $1

## 2. Calculate scaling factor:
SCALE_FACTOR=$(bc <<< "scale=8;1000000/$(samtools idxstats $1 | mawk '{SUM+=$3} END {print SUM}')")

## 3. Normalize:
mawk -v SF=${SCALE_FACTOR} 'OFS="\t" {print $1, $2, $3, $4*SF}' <(bgzip -c -d ${BAM%.bam}.per-base.bed.gz) | sort -k1,1 -k2,2n > ${BAM%.bam}_norm.bedGraph.tmp

## 4. to bigwig (cannot read from stdin so far:)
bedGraphToBigWig ${BAM%.bam}_norm.bedGraph.tmp $CHROMSIZES ${BAM%.bam}_CPM.bigwig && rm ${BAM%.bam}_norm.bedGraph.tmp ${BAM%.bam}.per-base* ${BAM%.bam}*mosdepth*

## Use:
./script.sh in.bam chromsizes.txt