With apt-utils 1.2.4, the behavior has changed: 5 packages are not even listed in Packages anymore, including nemo_2.8.6-11_amd64.deb package:
Here, 24 packages are located in the folder: Ubuntu/dists/wily/system-tools/binary-amd64# ll *.deb -rw-r--r-- 1 root root 1116256 Mar 5 12:19 apt_1.2.4_amd64.deb -rw-r--r-- 1 root root 342418 Mar 5 12:19 apt-doc_1.2.4_all.deb -rw-r--r-- 1 root root 151352 Mar 5 12:19 apt-transport-https_1.2.4_amd64.deb -rw-r--r-- 1 root root 387240 Mar 5 12:19 apt-utils_1.2.4_amd64.deb -rw-r--r-- 1 actionmystique actionmystique 12244162 Feb 28 16:02 gimp_2.9.2-11_amd64.deb -rw-rw-r-- 1 actionmystique actionmystique 3663042 Feb 23 11:21 git_2.6.0-11_amd64.deb -rw-rw-r-- 1 actionmystique actionmystique 3647806 Feb 23 11:21 git_2.6.3-11_amd64.deb -rw-r--r-- 1 actionmystique actionmystique 3684722 Feb 28 12:03 git_2.7.2-11_amd64.deb -rw-rw-r-- 1 actionmystique actionmystique 1646294 Feb 23 11:21 gparted_0.24.0-11_amd64.deb -rw-rw-r-- 1 actionmystique actionmystique 1653508 Feb 28 15:32 gparted_0.25.0-11_amd64.deb -rw-r--r-- 1 root root 180902 Mar 5 12:19 libapt-inst2.0_1.2.4_amd64.deb -rw-r--r-- 1 root root 813750 Mar 5 12:19 libapt-pkg5.0_1.2.4_amd64.deb -rw-r--r-- 1 root root 221594 Mar 5 12:19 libapt-pkg-dev_1.2.4_amd64.deb -rw-r--r-- 1 root root 994680 Mar 5 12:20 libapt-pkg-doc_1.2.4_all.deb -rw-r--r-- 1 actionmystique actionmystique 408538 Feb 28 14:21 libbabl-0.1-0_0.1.16-11_amd64.deb -rw-r--r-- 1 actionmystique actionmystique 21538808 Feb 28 14:00 libgegl-0.3-0_0.3.4-11_amd64.deb -rw-r--r-- 1 actionmystique actionmystique 1072388 Mar 5 12:46 nemo_2.8.6-11_amd64.deb -rw-rw-r-- 1 actionmystique actionmystique 25388 Feb 23 11:21 nemo-fileroller_2.8.1-11_amd64.deb -rw-r--r-- 1 actionmystique actionmystique 129268 Feb 23 11:21 nemo-gtkhash_0.7.0-11_amd64.deb -rw-r--r-- 1 actionmystique actionmystique 779684 Mar 2 11:45 realtek-wifi-drivers_4.2.6-10_amd64.deb -rw-rw-r-- 1 actionmystique actionmystique 781530 Feb 23 11:21 realtek-wifi-drivers_4.2-rc1-10_amd64.deb -rw-rw-r-- 1 actionmystique actionmystique 533770 Feb 23 11:21 redis-server_3.0.4-10_amd64.deb -rw-r--r-- 1 actionmystique actionmystique 538628 Feb 23 11:21 redis-server_3.0.7-10_amd64.deb -rw-rw-r-- 1 actionmystique actionmystique 1071418 Feb 23 11:21 xca_1.3.2-10_amd64.deb Only 19 packages are described in Packages (cf. attached file). I have also uploaded the config file I use for apt-ftparchive. I can't find what the 5 missing packages have in common to explain this issue. ** Attachment added: "Packages file" https://bugs.launchpad.net/ubuntu/+source/apt/+bug/1550726/+attachment/4589424/+files/Packages -- You received this bug notification because you are a member of Ubuntu Touch seeded packages, which is subscribed to apt in Ubuntu. https://bugs.launchpad.net/bugs/1550726 Title: [apt-utils] Some packages are missing in Packages built by apt- ftparchive Status in apt package in Ubuntu: New Bug description: On Linux 4.2.0-30-generic #36-Ubuntu SMP Fri Feb 26 00:58:07 UTC 2016 x86_64 GNU/Linux with apt-utils 1.0.10.2 Generating Packages with (apt-ftparchive.conf is attached below.): apt-ftparchive generate --contents=off ./apt-ftparchive.conf Generated Packages contains: ################################################################# Package: nemo ... Installed-Size: 9508 ... Version: 2.8.6-11 ... Filename: dists/wily/system-tools/binary-amd64/nemo_2.8.6-11_amd64.deb Size: 1392338 MD5sum: de162d539df28402f54761f671259278 SHA1: fb5ebacfc032071d3715dce18640deb649732048 SHA256: d0c52eb9bd8224e3d876dc6426ccc1ed49f975038152c53faacd5e71e0a19a33 SHA512: e1cc7eb9865c9f3f5a8d4a8f4406862617e285a080bf6c894b3295088a4406a149b53e27ae379c43335a4231e60966f7068412e93173a6e9bfaa8c48b43ac616 ################################################################# However, on disk, we have very different file size & checksums: ll nemo* -rw-r--r-- 1 actionmystique actionmystique 1082324 Feb 27 15:01 nemo_2.8.6-11_amd64.deb md5sum nemo_2.8.6-11_amd64.deb 68d5c945d9ccd9d3d2807ba46e33cc42 nemo_2.8.6-11_amd64.deb If we generate Packages differently with: apt-ftparchive packages . > Packages Generated Packages contains this time correct file size & checksums: ################################################################# Package: nemo ... Installed-Size: 5284 ... Version: 2.8.6-11 ... Filename: ./nemo_2.8.6-11_amd64.deb Size: 1082324 MD5sum: 68d5c945d9ccd9d3d2807ba46e33cc42 SHA1: eecee7a24c20843c15997adcddcd3dad38c9c831 SHA256: 83451ab9c9975dc7e18d43f2a7d223000c4ee84c9383e82a6461bffef641760a SHA512: ce715c1d480607e347511562f6d29d10eddb900d2ced3a82d1db08e2bc1a9c24974d3c59cc1e1e83b19ba5dac90d0cc80c7288606e6e3ac06d3551df3550ad09 ################################################################# What is very strange is that all other packages in the same folder are correctly described by Packages when using the first method for generating Packages. I have the same issue with another package in another folder. I have also uploaded the deb. Any suggestion? N.B: I can upload the second package if necessary. 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