I have built a working system with the Apalis TK1 LT4 3.10.40 sources with a Debian jessie root file system.
The PCIe bus is functional with TK1 LT4 image but not with the mainline build of 4.9 kernel. With the mainline Linux kernel the system boots but the PCIe bus is not connecting, no link.
Are there any changes required to the kernel sources or DTS files for the TK1?
Apalis TK1 LT4 3.10.40
[ 0.600210] PCIE.C: tegra_pcie_enable_regulators : regulator hvdd_pex
[ 0.600311] PCIE.C: tegra_pcie_enable_regulators : regulator pexio
[ 0.600403] PCIE.C: tegra_pcie_enable_regulators : regulator avdd_plle
[ 1.306007] PCIE: port 0: link down, retrying
[ 1.708212] PCIE: port 0: link down, retrying
[ 2.110412] PCIE: port 0: link down, retrying
[ 2.312488] PCIE: port 0: link down, ignoring
[ 2.326670] PCI host bridge to bus 0000:00
[ 2.326699] pci_bus 0000:00: root bus resource [mem 0x32100000-0x3fffffff]
[ 2.326729] pci_bus 0000:00: root bus resource [mem 0x12100000-0x320fffff pref]
[ 2.326760] pci_bus 0000:00: root bus resource [io 0x1000-0xffff]
[ 2.326808] pci_bus 0000:00: No busn resource found for root bus, will use [bus 00-ff]
[ 2.327209] PCI: bus0: Fast back to back transfers disabled
[ 2.327238] pci 0000:00:00.0: bridge configuration invalid ([bus 00-00]), reconfiguring
[ 2.329853] PCI: bus1: Fast back to back transfers disabled
[ 2.330197] pcieport 0000:00:00.0: Signaling PME through PCIe PME interrupt
[ 2.330227] pci 0000:01:00.0: Signaling PME through PCIe PME interrupt
[ 2.330474] pcieport 0000:00:00.0: BAR 8: assigned [mem 0x32100000-0x321fffff]
[ 2.330508] pcieport 0000:00:00.0: BAR 7: assigned [io 0x1000-0x1fff]
[ 2.330540] pci 0000:01:00.0: BAR 0: assigned [mem 0x32100000-0x3211ffff]
[ 2.330575] pci 0000:01:00.0: BAR 3: assigned [mem 0x32120000-0x32123fff]
[ 2.330608] pci 0000:01:00.0: BAR 2: assigned [io 0x1000-0x101f]
[ 2.330639] pcieport 0000:00:00.0: PCI bridge to [bus 01]
[ 2.330666] pcieport 0000:00:00.0: bridge window [io 0x1000-0x1fff]
[ 2.330695] pcieport 0000:00:00.0: bridge window [mem 0x32100000-0x321fffff]
[ 2.330737] PCIE: No Link speed change happened
Linux mainline 4.9.79
[ 3.188768] tegra-pcie 1003000.pcie-controller: link 0 down, retrying
[ 3.617905] tegra-pcie 1003000.pcie-controller: link 0 down, retrying
[ 4.046984] tegra-pcie 1003000.pcie-controller: link 0 down, retrying
[ 4.055596] tegra-pcie 1003000.pcie-controller: link 0 down, ignoring
[ 4.062075] tegra-pcie 1003000.pcie-controller: probing port 1, using 1 lanes
[ 4.071413] tegra-pcie 1003000.pcie-controller: Slot present pin change, signature: 00000000
[ 4.491905] tegra-pcie 1003000.pcie-controller: link 1 down, retrying
[ 4.921031] tegra-pcie 1003000.pcie-controller: link 1 down, retrying
[ 5.350114] tegra-pcie 1003000.pcie-controller: link 1 down, retrying
[ 5.358721] tegra-pcie 1003000.pcie-controller: link 1 down, ignoring
[ 5.365760] tegra-pcie 1003000.pcie-controller: PCI host bridge to bus 0000:00
[ 5.373020] pci_bus 0000:00: root bus resource [io 0x0000-0xffff]
[ 5.379210] pci_bus 0000:00: root bus resource [mem 0x13000000-0x1fffffff]
[ 5.386108] pci_bus 0000:00: root bus resource [mem 0x20000000-0x3fffffff pref]
[ 5.393449] pci_bus 0000:00: root bus resource [bus 00-ff]
[ 5.398966] PCI: bus0: Fast back to back transfers enabled