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kj184050
Apprentice
Joined: 29 Sep 2021
Posts: 164
Location: Devon
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 Posted: Sat Dec 04, 2021 9:00 am Post subject: [SOLVED] rstudio failed (compile phase) |
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Hi,
I have trouble with emerging rstudio.
I tried to find anything similar on the Internet...
Can someone help, please? I need it for work...
| Code: | * ERROR: sci-mathematics/rstudio-1.3.1093-r1::gentoo failed (compile phase):
* ninja -v -j16 -l0 failed
*
* Call stack:
* ebuild.sh, line 127: Called src_compile
* environment, line 4333: Called cmake_src_compile
* environment, line 952: Called cmake_build
* environment, line 921: Called eninja
* environment, line 1595: Called die
* The specific snippet of code:
* "$@" || die "${nonfatal_args[@]}" "${*} failed"
*
* If you need support, post the output of `emerge --info '=sci-mathematics/rstudio-1.3.1093-r1::gentoo'`,
* the complete build log and the output of `emerge -pqv '=sci-mathematics/rstudio-1.3.1093-r1::gentoo'`.
* The complete build log is located at '/var/tmp/portage/sci-mathematics/rstudio-1.3.1093-r1/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/rstudio-1.3.1093-r1/temp/environment'.
* Working directory: '/var/tmp/portage/sci-mathematics/rstudio-1.3.1093-r1/work/rstudio-1.3.1093_build'
* S: '/var/tmp/portage/sci-mathematics/rstudio-1.3.1093-r1/work/rstudio-1.3.1093'
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| Code: |
$: emerge --info '=sci-mathematics/rstudio-1.3.1093-r1::gentoo'
Portage 3.0.28 (python 3.9.9-final-0, default/linux/amd64/17.1/desktop/gnome, gcc-11.2.0, glibc-2.34-r2, 5.14.15-gentoo-x86_64 x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-5.14.15-gentoo-x86_64-x86_64-AMD_Ryzen_9_5950X_16-Core_Processor-with-glibc2.34
KiB Mem: 65766724 total, 53453380 free
KiB Swap: 0 total, 0 free
Timestamp of repository gentoo: Sat, 04 Dec 2021 07:30:01 +0000
Head commit of repository gentoo: 759b6894092a6eb3260f283e8e299347319f0363
Timestamp of repository steam-overlay: Tue, 09 Nov 2021 10:53:07 +0000
Head commit of repository steam-overlay: b21d724e69a176a398cae2db70172cb9dfede48a
sh bash 5.1_p12
ld GNU ld (Gentoo 2.37_p1 p1) 2.37
app-shells/bash: 5.1_p12::gentoo
dev-java/java-config: 2.3.1::gentoo
dev-lang/perl: 5.34.0-r5::gentoo
dev-lang/python: 2.7.18_p13::gentoo, 3.8.12_p1::gentoo, 3.9.9::gentoo, 3.10.0_p1::gentoo, 3.11.0_alpha2::gentoo
dev-lang/rust: 1.56.1::gentoo
dev-util/cmake: 3.22.0::gentoo
sys-apps/baselayout: 2.8::gentoo
sys-apps/openrc: 0.44.8::gentoo
sys-apps/sandbox: 2.29::gentoo
sys-devel/autoconf: 2.13-r1::gentoo, 2.71-r1::gentoo
sys-devel/automake: 1.13.4-r2::gentoo, 1.16.5::gentoo
sys-devel/binutils: 2.37_p1-r1::gentoo
sys-devel/gcc: 11.2.0::gentoo
sys-devel/gcc-config: 2.5-r1::gentoo
sys-devel/libtool: 2.4.6-r6::gentoo
sys-devel/make: 4.3::gentoo
sys-kernel/linux-headers: 5.15::gentoo (virtual/os-headers)
sys-libs/glibc: 2.34-r2::gentoo
Repositories:
gentoo
location: /var/db/repos/gentoo
sync-type: rsync
sync-uri: rsync://rsync.gentoo.org/gentoo-portage
priority: -1000
sync-rsync-verify-jobs: 1
sync-rsync-extra-opts:
sync-rsync-verify-max-age: 24
sync-rsync-verify-metamanifest: yes
steam-overlay
location: /var/db/repos/steam-overlay
sync-type: git
sync-uri: https://github.com/gentoo-mirror/steam-overlay.git
masters: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE NVIDIA-r2"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -pipe -march=native"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--jobs=16 --load-average=20.00"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe -march=native"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch parallel-install pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=native"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j16"
PKGDIR="/var/cache/binpkgs"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 bluetooth branding bzip2 cairo cdda cdr cli colord context crypt cuda cups dbus dri dts dvd dvdr eds elogind emboss encode epspdf evo exif extra fat ffmpeg flac fortran gdbm gif gnome gnome-keyring gnome-online-accounts gpm graphics gstreamer gtk gtk3 gui iconv icu id3tag introspection ipv6 jack jpeg lame lcms libglvnd libnotify libsecret libtirpc luatex mad metapost mng mp3 mp4 mpeg mtp multilib nautilus ncurses networkmanager nls nptl ntfs nvidia ogg opengl openmp pam pango pcre pdf pdfannotextractor png policykit postscript ppds pstricks publishers pulseaudio readline samba science sdl seccomp sensord spell split-usr ssl startup-notification svg sysprof tex4ht tiff tracker truetype udev udisks unicode upower usb vorbis wxwidgets x264 x265 xattr xcb xetex xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2020" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev libinput" KERNEL="linux" L10N="en_GB pl en en-GB" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="NVPTX BPF X86" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" RUBY_TARGETS="ruby26 ruby27" USERLAND="GNU" VIDEO_CARDS="nvidia" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS
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Here is the log:
| Code: | | cat /var/tmp/portage/sci-mathematics/rstudio-1.3.1093-r1/temp/build.log |
https://dpaste.com/F4ZXT2CKE
any help appreciated...
Last edited by kj184050 on Mon Dec 06, 2021 2:03 am; edited 1 time in total |
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fedeliallalinea
Administrator
Joined: 08 Mar 2003
Posts: 31272
Location: here
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| Posted: Sat Dec 04, 2021 9:38 am Post subject: |
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| Code: | /var/tmp/portage/sci-mathematics/rstudio-1.3.1093-r1/work/rstudio-1.3.1093/src/cpp/tests/cpp/tests/vendor/catch.hpp:6470:33: error: size of array ‘altStackMem’ is not an integral constant-expression
6470 | static char altStackMem[SIGSTKSZ];
| ^~~~~~~~
/var/tmp/portage/sci-mathematics/rstudio-1.3.1093-r1/work/rstudio-1.3.1093/src/cpp/tests/cpp/tests/vendor/catch.hpp:6521:45: error: size of array ‘altStackMem’ is not an integral constant-expression
6521 | char FatalConditionHandler::altStackMem[SIGSTKSZ] = {};
| |
The problem is >=glibc-2.34 that SIGSTKSZ is no longer a constant.
A dirty but fast patch is to change SIGSTKSZ with 32768, see here
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kj184050
Apprentice
Joined: 29 Sep 2021
Posts: 164
Location: Devon
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| Posted: Sat Dec 04, 2021 10:50 am Post subject: |
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Thank you @fedeliallalinea
But how can I fix this? |
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wjb
l33t
Joined: 10 Jul 2005
Posts: 631
Location: Fife, Scotland
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| Posted: Sat Dec 04, 2021 11:46 am Post subject: |
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| Use something like this to patch a build: /etc/portage/patches (Gentoo wiki) |
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fedeliallalinea
Administrator
Joined: 08 Mar 2003
Posts: 31272
Location: here
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| Posted: Sat Dec 04, 2021 11:46 am Post subject: |
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Try this patch, you can apply user patch through /etc/portage/patches.
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kj184050
Apprentice
Joined: 29 Sep 2021
Posts: 164
Location: Devon
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| Posted: Sat Dec 04, 2021 12:42 pm Post subject: |
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Well... guys...
Thank you 
It worked.
But why does this problem exist... |
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wjb
l33t
Joined: 10 Jul 2005
Posts: 631
Location: Fife, Scotland
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| Posted: Sat Dec 04, 2021 3:11 pm Post subject: |
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| kj184050 wrote: | | But why does this problem exist... |
There are problems with current glib because it's a year old version of rstudio. Also, it's only "~arch", so it's more of priority to it's users than Gentoo as a whole. There's a quite busy bug (766294) about getting rstudio updated. |
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Chris1969
Tux's lil' helper
Joined: 31 Dec 2017
Posts: 88
Location: switzerland
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| Posted: Sat Dec 04, 2021 5:41 pm Post subject: |
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I just followed the installation instructions of the mentioned bug and successfully updated to rstudio-1.4.1717. I didn't want to open a new account to tell Silvio of the problems I encountered during installation so I do here (problems might be only related to my local repo, but I do not understand them).
These are the installation instructions as mentioned in the posts of the bug:
| Quote: | Silvio 2021-11-29 21:26:15 UTC
For one who wants to try adams version.
1. If you don't have install eselect repository command
# emerge -u eselect-repository
2. If you dont' have one yet, create a local repository
# eselect repository create localrepo
3. Create a directory for rstudio in your local repository
# mkdir -p /var/db/repos/localrepo/sci-mathematics/rstudio
4. Download the last Adam's version:
go to: https://downgit.github.io/#/home
and put in the form the url of the git repository:
https://github.com/awenocur/asw-custom-software-gentoo/tree/master/sci-mathematics/rstudio
5. Unzip the zip file in the directory created in point 3
6. Download the soci package here
https://github.com/gentoo/gentoo/pull/20575/files
7. Create dir in localrepo
mkdir -p /var/db/repos/localrepo/dev-db/soci
8. Copy all soci file in this directory
9. emerge rstudio |
Here is what I additionally did, to get a working rstudio update:
Portage seems to not recognise my soci files in the local repo so I did install it manually
Then I manually installed yaml-cpp and only the following version worked (as also mentioned in the posts of the bug
| Code: | | emerge -1av =yaml-cpp-0.6.3-r3 |
lsof was also not pulled by portage due to the mentioned problem with soci
Then rstudio was successfully compiled, and as far I can tell it works for me. |
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Chris1969
Tux's lil' helper
Joined: 31 Dec 2017
Posts: 88
Location: switzerland
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| Posted: Sat Dec 11, 2021 1:26 pm Post subject: |
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| probably soci should be under dev-libs/ instead of dev-db/ , at least the rstudio ebuild asks so |
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kj184050
Apprentice
Joined: 29 Sep 2021
Posts: 164
Location: Devon
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| Posted: Sun Dec 12, 2021 1:10 pm Post subject: |
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I wonder if just compiling source code (not using ebuilds) would solve these issues...
Did anyone try? |
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Hu
Administrator
Joined: 06 Mar 2007
Posts: 22686
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| Posted: Sun Dec 12, 2021 5:27 pm Post subject: |
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| Unless the ebuild is actively breaking the source code with a bad patch, compiling outside Portage should produce the same result. As I read the posts from Chris1969, it can be made to work from an ebuild by installing the appropriate prerequisites. |
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Chris1969
Tux's lil' helper
Joined: 31 Dec 2017
Posts: 88
Location: switzerland
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| Posted: Fri Dec 17, 2021 1:41 pm Post subject: |
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I just installed on a second computer, using soci in dev-libs/, then just a simple
pulled and installed all the necessary dependencies.
Seem to work without any problems. |
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astaines
Tux's lil' helper
Joined: 18 Apr 2004
Posts: 101
Location: Ireland
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| Posted: Sun May 22, 2022 3:27 pm Post subject: Patch for SIGSTKSZ issue with rstudio-1.3.1093-r1 |
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This is the SIGSTKSZ patch - it was originally generated by fedeliallalinea but that file has fallen off dpaste, so I copied their advice and this is what I got - errors are mine, praise is theirs. Seems to work for me.
| Code: |
--- rstudio-1.3.95_orig/src/cpp/tests/cpp/tests/vendor/catch.hpp 2022-05-22 15:26:53.179789245 +0100
+++ rstudio-1.3.95/src/cpp/tests/cpp/tests/vendor/catch.hpp 2022-05-22 15:27:56.523248025 +0100
@@ -6467,7 +6467,7 @@
static bool isSet;
static struct sigaction oldSigActions [sizeof(signalDefs)/sizeof(SignalDefs)];
static stack_t oldSigStack;
- static char altStackMem[SIGSTKSZ];
+ static char altStackMem[32768];
static void handleSignal( int sig ) {
std::string name = "<unknown signal>";
@@ -6487,7 +6487,7 @@
isSet = true;
stack_t sigStack;
sigStack.ss_sp = altStackMem;
- sigStack.ss_size = SIGSTKSZ;
+ sigStack.ss_size = 32768;
sigStack.ss_flags = 0;
sigaltstack(&sigStack, &oldSigStack);
struct sigaction sa = { 0 };
@@ -6518,7 +6518,7 @@
bool FatalConditionHandler::isSet = false;
struct sigaction FatalConditionHandler::oldSigActions[sizeof(signalDefs)/sizeof(SignalDefs)] = {};
stack_t FatalConditionHandler::oldSigStack = {};
- char FatalConditionHandler::altStackMem[SIGSTKSZ] = {};
+ char FatalConditionHandler::altStackMem[32768] = {};
} // namespace Catch
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Chris1969
Tux's lil' helper
Joined: 31 Dec 2017
Posts: 88
Location: switzerland
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| Posted: Sun Jul 31, 2022 10:10 am Post subject: |
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| Chris1969 wrote: | I just installed on a second computer, using soci in dev-libs/, then just a simple
pulled and installed all the necessary dependencies.
Seem to work without any problems. |
To anyone who is interested and maybe working on a solution to bring rstudio back.
I just recompiled my setup mentioned in the post above by switching the java system-vm from openjdk-bin-17 back to openjdk-bin-8 (with openjdk-bin-17 compilation stopped with an error). After successful recompilation I got this "white window problem" some people mentioned. |
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Chris1969
Tux's lil' helper
Joined: 31 Dec 2017
Posts: 88
Location: switzerland
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| Posted: Sun Jul 31, 2022 10:11 am Post subject: |
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| kj184050 wrote: | I wonder if just compiling source code (not using ebuilds) would solve these issues...
Did anyone try? |
How do I have to do this? I would be willing to try it. |
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mimosinnet
l33t
Joined: 10 Aug 2006
Posts: 717
Location: Barcelona, Spain
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| Posted: Tue Nov 19, 2024 10:37 pm Post subject: |
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I have come to the same issue. I found the solution in this bug: use the jgenco repository.
1) Create destination dir in the repos directory:
# mkdir /var/db/repos/jgenco
2) Add repository to your list
# eselect repository add jgenco git https://github.com/jgenco/jgenco-overlay
3) Sync repository:
# emaint sync -r jgenco
4) Install rstudio
# emerge rstudio
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