Hi, I see this issue on Gentoo::RAP install. I realzied I have no sys-apps/man installed and therefore, the /usr/bin/man does not look into the manpages in /scratch/mmorkejs/gentoo_rap prefix. although this is probably a samtools package issue, could this be caught in general by portage? Lets say raise QA issue if a package install *.[0-9] file into a path like "man/"? $ USE="man doc" emerge -pv samtools These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-biology/samtools-1.3-r1::gentoo USE="-examples" PYTHON_TARGETS="python2_7" 0 KiB $
Can you please better describe the issue you are reporting? > I see this issue on Gentoo::RAP install What is Gentoo::RAP? > I realzied I have no sys-apps/man installed Perhaps you have sys-apps/man-db installed instead? > therefore, the /usr/bin/man does not look into the manpages in /scratch/mmorkejs/gentoo_rap prefix What? I do not understand this conclusion.
(In reply to Mike Gilbert from comment #1) > Can you please better describe the issue you are reporting? > > > I see this issue on Gentoo::RAP install > > What is Gentoo::RAP? An alternative to Getoo:Prefix, see https://wiki.gentoo.org/wiki/Prefix/libc . In respect to this issue, one can install Gentoo Linux into "prefixed" location on another OS. I installed in on a Redhat system (providing the /usr/bin/man utility and obviously, unless the man utility installed in Gentoo:RAP is installed the RedHat'provided man binary has no way to know about the Gentoo installation and its own manpages. Gentoo:RAP uses the main Gentoo portage tree (unlike Gentoo:Prefix). > > > I realzied I have no sys-apps/man installed > > Perhaps you have sys-apps/man-db installed instead? No, not really: $ emerge -pv sys-apps/man-db These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] app-text/manpager-1::gentoo 0 KiB [ebuild N ] sys-apps/groff-1.22.3::gentoo USE="X -examples" 0 KiB [ebuild N ] dev-perl/SGMLSpm-1.1-r1::gentoo 0 KiB [ebuild N ] app-text/opensp-1.5.2-r4::gentoo USE="nls -doc -static-libs {-test}" 0 KiB [ebuild N ] dev-perl/Text-CharWidth-0.40.0-r1::gentoo 0 KiB [ebuild N ] dev-libs/libpipeline-1.4.1::gentoo USE="-static-libs {-test}" 0 KiB [ebuild N ] dev-perl/Text-WrapI18N-0.60.0-r1::gentoo 0 KiB [ebuild N ] app-text/openjade-1.3.2-r6::gentoo USE="-static-libs" 0 KiB [ebuild N ] app-text/po4a-0.45-r3::gentoo USE="{-test}" LINGUAS="cs -af -ca -da -de -eo -es -et -eu -fr -hr -id -it -ja -kn -ko -nb -nl -pl -pt -pt_BR -ru -sl -sv -uk -vi -zh_CN -zh_HK" 0 KiB [ebuild N ] sys-apps/man-db-2.7.5::gentoo USE="berkdb gdbm manpager nls zlib (-selinux) -static-libs" 0 KiB Total: 10 packages (10 new), Size of downloads: 0 KiB $ > > > therefore, the /usr/bin/man does not look into the manpages in /scratch/mmokrejs/gentoo_rap prefix > > What? I do not understand this conclusion. $ echo $PATH /scratch/mmokrejs/gentoo_rap/usr/local/bin:/scratch/mmokrejs/gentoo_rap/usr/bin:/scratch/mmokrejs/gentoo_rap/bin:/scratch/mmokrejs/gentoo_rap/opt/bin:/scratch/mmokrejs/gentoo_rap/usr/sbin:/scratch/mmokrejs/gentoo_rap/sbin:/scratch/mmokrejs/gentoo_rap/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0:/usr/bin:/bin:/home/mmokrejs/bin $ As you can see, the Gentoo Linux-provided binaries have precedence over the tools and libs (although now LD_LIBRARY_PATH is not shown here) provided by the host RedHat Linux(with 2.12 glibc, too old to compile apps against). So, I could say sci-biology/samtools package needs to respect IUSE flag before "doman *.1" would be allowed and that something should ensure that there is a utility to actually read the manpages. However, I think emerge could ensure this by default - that there is sys-apps/man installed before any USE=man is accepted. Therefore, I don't think is actually a samtools package issue but a general DEPENDency issue. I assume sys-apps/man is needed because I want the package with a man executable to be included in the DEPENDencies: other_Gentoo_host # equery belongs /usr/bin/man * Searching for /usr/bin/man ... sys-apps/man-1.6g (/usr/bin/man) other_Gentoo_host# Surely, one could argue whether we want to require a manpage reader to be installed prior to any manpage file being qmerged, especially because some manpages are pre-formatted and do not need mandoc/troff/groff or whatever are the formatting utilities.
I still don't understand what problem you are experiencing.
Hi Martin, I thi
Hi Martin, I don't think this
Hi Martin, I don't think this a valid issue. Because: 1. doman guarantees the manpages are installed into the correct directory. 2. How you read the manpages is another story, it could be sys-apps/man-db, sys-apps/man, or emacs woman. 3. sys-apps/man-db is in @system for Gentoo in general. But I chose to remove man-db from @system because it is not essential for a RAP system to function. 4. You can still use host /usr/bin/man to access Gentoo manpages. Please env-update and inspect if MANPATH is set correctly. Therefore I intend to close this bug as invalid. What do you think? (In reply to Martin Mokrejš from comment #0) > the /usr/bin/man does not look into the manpages in > /scratch/mmorkejs/gentoo_rap prefix. I does look into gentoo if you have MANPATH environment variable set (in EPREFIX/etc/env.d). > although this is probably a samtools > package issue, could this be caught in general by portage? Lets say raise QA > issue if a package install *.[0-9] file into a path like "man/"? That unnecessarily complicates things, which I don't want. > $ USE="man doc" emerge -pv samtools > > These are the packages that would be merged, in order: > > Calculating dependencies... done! > [ebuild R ] sci-biology/samtools-1.3-r1::gentoo USE="-examples" > PYTHON_TARGETS="python2_7" 0 KiB > $ USE flags are not for this purpose. USE=man does not guarantee you have a man reader. (In reply to Martin Mokrejš from comment #2) > So, I could say sci-biology/samtools package needs to respect IUSE flag > before "doman *.1" would be allowed and that something should ensure that > there is a utility to actually read the manpages. No it should not do that. > However, I think emerge > could ensure this by default - that there is sys-apps/man installed before > any USE=man is accepted. This cannot be done globally. > Therefore, I don't think is actually a samtools > package issue but a general DEPENDency issue. > > Surely, one could argue whether we want to require a manpage reader to be > installed prior to any manpage file being qmerged, especially because some > manpages are pre-formatted and do not need mandoc/troff/groff or whatever > are the formatting utilities. And come on. It just a package. emerge sys-apps/man and everyone is happy.
(In reply to Benda Xu from comment #6) > Hi Martin, > > I don't think this a valid issue. Because: > > 1. doman guarantees the manpages are installed into the correct directory. > 2. How you read the manpages is another story, it could be > sys-apps/man-db, sys-apps/man, or emacs woman. > 3. sys-apps/man-db is in @system for Gentoo in general. But I chose to > remove man-db from @system because it is not essential for a RAP system to > function. > 4. You can still use host /usr/bin/man to access Gentoo manpages. Please > env-update and inspect if MANPATH is set correctly. $ printenv | grep MANPATH MANPATH=/usr/man:/usr/share/man:/usr/local/man:/usr/local/share/man:/usr/X11R6/man:/opt/modules/default/Modules/share/man $ $ env-update $ printenv | grep MANPATH MANPATH=/usr/man:/usr/share/man:/usr/local/man:/usr/local/share/man:/usr/X11R6/man:/opt/modules/default/Modules/share/man $ Something is wrong. $ grep MANPATH /scratch/mmokrejs/gentoo_rap/etc/env.d/* /scratch/mmokrejs/gentoo_rap/etc/env.d/00basic:MANPATH="/scratch/mmokrejs/gentoo_rap/usr/local/share/man:/scratch/mmokrejs/gentoo_rap/usr/share/man" /scratch/mmokrejs/gentoo_rap/etc/env.d/04gcc-x86_64-pc-linux-gnu:MANPATH="/scratch/mmokrejs/gentoo_rap/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/man" /scratch/mmokrejs/gentoo_rap/etc/env.d/05binutils:MANPATH=/scratch/mmokrejs/gentoo_rap/usr/share/binutils-data/x86_64-pc-linux-gnu/2.26/man /scratch/mmokrejs/gentoo_rap/etc/env.d/20java-config:MANPATH="/scratch/mmokrejs/gentoo_rap/etc/java-config-2/current-system-vm/man/" ... $ So is none of the files sourced? > > Therefore I intend to close this bug as invalid. What do you think? If Gentoo:RAP setups MANPATH properly, I assume /usr/bin/man from Redhat will start to find manpages installed through Gentoo:RAP, and that will be OK for me. > > > (In reply to Martin Mokrejš from comment #0) > > the /usr/bin/man does not look into the manpages in > > /scratch/mmorkejs/gentoo_rap prefix. > > I does look into gentoo if you have MANPATH environment variable set (in > EPREFIX/etc/env.d). > > > although this is probably a samtools > > package issue, could this be caught in general by portage? Lets say raise QA > > issue if a package install *.[0-9] file into a path like "man/"? > > That unnecessarily complicates things, which I don't want. Well it is the surprise. I installed apps with USE=man and "man samtools" just does not find the manpage. ;-) > > Surely, one could argue whether we want to require a manpage reader to be > > installed prior to any manpage file being qmerged, especially because some > > manpages are pre-formatted and do not need mandoc/troff/groff or whatever > > are the formatting utilities. > > And come on. It just a package. emerge sys-apps/man and everyone is happy. Well, you know, I wanted to report the issue at first. I do not know why sys-apps/man-db should be preferred over sys-apps/man, as you see much less is needed to be installed for the latter: $ emerge -pv sys-apps/man ... Calculating dependencies... done! [ebuild N ] sys-apps/groff-1.22.3::gentoo USE="X -examples" 0 KiB [ebuild N ] sys-apps/man-1.6g-r1::gentoo USE="lzma nls (-selinux)" 251 KiB $
I just opened bug #589738 happening on this Gentoo:RAP host.
Any chance MANPATH is setup automatically to include my ${EPREFIX} at the very front?
(In reply to Martin Mokrejš from comment #9) > Any chance MANPATH is setup automatically to include my ${EPREFIX} at the > very front? Hi Martin, this issue is of low priority to me. If you would like to work out a patch, I am happy to incorporate it.
What's the status of this bug?
Is this still an issue? man/man-db should be in @system, and presumably fixed for the Prefix MANPATHs.
