On Tue, Nov 22, 2011 at 02:41:42PM +0100, Sebastian Reitenbach wrote:
> Hi,
> On Tuesday, November 22, 2011 14:32 CET, Benjamin Nadland
> <[email protected]> wrote:
>
> > I can not use any tested graphical features of R without it crashing
> > because of some pthread issue.
> >
> > Is this a known problem? Any ideas, solutions or workarounds?
> >
> > I run a -current i386 machine and have installed a fresh snapshot and
> > fresh packages before reporting.
>
> see the other thread with subject: glib2: libgthread-2.0 linked without
> pthread support
>
> maybe this helps when you do::
>
> export LD_PRELOAD=libpthread.so
>
> before starting R.
This seems completely messy.
Why isn't R compile with -pthread instead?
> >
> >
> > How to reproduce:
> > -----------------
> >
> > (14:05:50)[~]$ R
> > R version 2.8.1 (2008-12-22)
> > Copyright (C) 2008 The R Foundation for Statistical Computing
> > ISBN 3-900051-07-0
> >
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under certain conditions.
> > Type 'license()' or 'licence()' for distribution details.
> >
> > R is a collaborative project with many contributors.
> > Type 'contributors()' for more information and
> > 'citation()' on how to cite R or R packages in publications.
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> > > demo(graphics)
> >
> >
> > demo(graphics)
> > ---- ~~~~~~~~
> >
> > Type <Return> to start :
> >
> > > require(datasets)
> >
> > > require(grDevices); require(graphics)
> >
> > > oask <- devAskNewPage(dev.interactive(orNone = TRUE))
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_attr_destroy'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_create'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_attr_init'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_getschedparam'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_attr_setscope'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_setschedparam'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_attr_setstacksize'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'sched_get_priority_max'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'sched_get_priority_min'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_mutex_trylock'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_attr_setschedparam'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_attr_setdetachstate'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_join'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.2992.0:
> > undefined symbol 'pthread_attr_getschedparam'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libcairo.so.11.1: undefined
> > symbol 'pthread_mutexattr_destroy'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libcairo.so.11.1: undefined
> > symbol 'pthread_mutexattr_settype'
> > /usr/local/lib/R/bin/exec/R:/usr/local/lib/libcairo.so.11.1: undefined
> > symbol 'pthread_mutexattr_init'
> >
> > *** caught segfault ***
> > address 0x23, cause 'memory not mapped'
> >
> > Traceback:
> > 1: function (display = "", width, height, pointsize, gamma, bg,
> > canvas, fonts, xpos, ypos, title, type, antialias) { if (display == ""
> > && .Platform$GUI == "AQUA" && is.na(Sys.getenv("DISPLAY", NA)))
> > Sys.setenv(DISPLAY = ":0") new <- list() if (!missing(display))
> > new$display <- display if (!missing(width)) new$width <-
> > width if (!missing(height)) new$height <- height if
> > (!missing(gamma)) new$gamma <- gamma if (!missing(pointsize))
> > new$pointsize <- pointsize if (!missing(bg)) new$bg <- bg
> > if (!missing(canvas)) new$canvas <- canvas if (!missing(xpos))
> > new$xpos <- xpos if (!missing(ypos)) new$ypos <- ypos
> > if (!missing(title)) new$title <- title if
> > (!checkIntFormat(new$title)) stop("invalid 'title'") if
> > (!missing(type)) new$type <- match.arg(type, c("Xlib", "cairo",
> > "nbcairo")) if (!missing(antialias)) { new$anti
> alias <- pmatch(antialias, c("default", "none", "gray",
> "subpixel")) if (is.na(new$antialias)) stop("invalid value
> for 'antialias'") } d <- check.options(new, name.opt = ".X11.Options",
> envir = .X11env) type <- if (capabilities("cairo")) switch(d$type,
> cairo = 1, nbcairo = 2, 0) else 0 if (display == "XImage") type
> <- 0 .Internal(X11(d$display, d$width, d$height, d$pointsize,
> d$gamma, d$colortype, d$maxcubesize, d$bg, d$canvas, d$fonts,
> NA_integer_, d$xpos, d$ypos, d$title, type, d$antialias))}()
> > 2: devAskNewPage(dev.interactive(orNone = TRUE))
> > 3: eval.with.vis(expr, envir, enclos)
> > 4: eval.with.vis(ei, envir)
> > 5: source(available, echo = TRUE, max.deparse.length = 250, keep.source =
> > TRUE)
> > 6: demo(graphics)
> >
> > Possible actions:
> > 1: abort (with core dump, if enabled)
> > 2: normal R exit
> > 3: exit R without saving workspace
> > 4: exit R saving workspace
> >
> > dmesg:
> >
> > OpenBSD 5.0-current (GENERIC.MP) #126: Sun Nov 20 16:48:02 MST 2011
> > [email protected]:/usr/src/sys/arch/i386/compile/GENERIC.MP
> > cpu0: Intel(R) Atom(TM) CPU N270 @ 1.60GHz ("GenuineIntel" 686-class) 1.60
> > GHz
> > cpu0:
> > FPU,V86,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,CFLUSH,DS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,SBF,SSE3,MWAIT,DS-CPL,EST,TM2,SSSE3,xTPR,PDCM,MOVBE,LAHF
> > real mem = 1060130816 (1011MB)
> > avail mem = 1032691712 (984MB)
> > mainbus0 at root
> > bios0 at mainbus0: AT/286+ BIOS, date 05/09/08, SMBIOS rev. 2.4 @ 0xe8e70
> > (32 entries)
> > bios0: vendor Acer version "v0.3114" date 05/09/2008
> > bios0: Acer AOA150
> > acpi0 at bios0: rev 2
> > acpi0: sleep states S0 S3 S4 S5
> > acpi0: tables DSDT FACP SSDT HPET APIC MCFG ASF! SLIC BOOT
> > acpi0: wakeup devices P32_(S4) UHC1(S3) UHC2(S3) UHC3(S3) UHC4(S3) ECHI(S3)
> > EXP1(S4) EXP2(S4) EXP3(S4) EXP4(S4) AZAL(S0) MODM(S0)
> > acpitimer0 at acpi0: 3579545 Hz, 24 bits
> > acpihpet0 at acpi0: 14318179 Hz
> > acpimadt0 at acpi0 addr 0xfee00000: PC-AT compat
> > cpu0 at mainbus0: apid 0 (boot processor)
> > cpu0: apic clock running at 132MHz
> > cpu1 at mainbus0: apid 1 (application processor)
> > cpu1: Intel(R) Atom(TM) CPU N270 @ 1.60GHz ("GenuineIntel" 686-class) 1.60
> > GHz
> > cpu1:
> > FPU,V86,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,CFLUSH,DS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,SBF,SSE3,MWAIT,DS-CPL,EST,TM2,SSSE3,xTPR,PDCM,MOVBE,LAHF
> > ioapic0 at mainbus0: apid 4 pa 0xfec00000, version 20, 24 pins
> > ioapic0: misconfigured as apic 0, remapped to apid 4
> > acpimcfg0 at acpi0 addr 0xe0000000, bus 0-255
> > acpiprt0 at acpi0: bus 0 (PCI0)
> > acpiprt1 at acpi0: bus 4 (P32_)
> > acpiprt2 at acpi0: bus 1 (EXP1)
> > acpiprt3 at acpi0: bus 2 (EXP2)
> > acpiprt4 at acpi0: bus -1 (EXP3)
> > acpiprt5 at acpi0: bus 3 (EXP4)
> > acpiec0 at acpi0
> > acpicpu0 at acpi0: C3, C2, C1, PSS
> > acpicpu1 at acpi0: C3, C2, C1, PSS
> > acpibtn0 at acpi0: PWRB
> > acpibtn1 at acpi0: LID0
> > acpibtn2 at acpi0: SLPB
> > acpibat0 at acpi0: BAT1 not present
> > acpiac0 at acpi0: AC unit offline
> > acpivideo0 at acpi0: OVGA
> > bios0: ROM list: 0xc0000/0xec00! 0xcf000/0x1000
> > cpu0: Enhanced SpeedStep 1596 MHz: speeds: 1600, 1333, 1066, 800 MHz
> > pci0 at mainbus0 bus 0: configuration mode 1 (bios)
> > pchb0 at pci0 dev 0 function 0 "Intel 82945GME Host" rev 0x03
> > vga1 at pci0 dev 2 function 0 "Intel 82945GME Video" rev 0x03
> > wsdisplay0 at vga1 mux 1: console (80x25, vt100 emulation)
> > wsdisplay0: screen 1-5 added (80x25, vt100 emulation)
> > intagp0 at vga1
> > agp0 at intagp0: aperture at 0x40000000, size 0x10000000
> > inteldrm0 at vga1: apic 4 int 16
> > drm0 at inteldrm0
> > "Intel 82945GM Video" rev 0x03 at pci0 dev 2 function 1 not configured
> > azalia0 at pci0 dev 27 function 0 "Intel 82801GB HD Audio" rev 0x02: msi
> > azalia0: codecs: Realtek ALC268
> > audio0 at azalia0
> > ppb0 at pci0 dev 28 function 0 "Intel 82801GB PCIE" rev 0x02: apic 4 int 16
> > pci1 at ppb0 bus 1
> > ppb1 at pci0 dev 28 function 1 "Intel 82801GB PCIE" rev 0x02: apic 4 int 17
> > pci2 at ppb1 bus 2
> > re0 at pci2 dev 0 function 0 "Realtek 8101E" rev 0x02: RTL8102EL (0x2480),
> > apic 4 int 17, address 00:1e:68:ab:b0:0b
> > rlphy0 at re0 phy 7: RTL8201L 10/100 PHY, rev. 1
> > ppb2 at pci0 dev 28 function 3 "Intel 82801GB PCIE" rev 0x02: apic 4 int 19
> > pci3 at ppb2 bus 3
> > "JMicron SD/MMC" rev 0x00 at pci3 dev 0 function 0 not configured
> > sdhc0 at pci3 dev 0 function 2 "JMicron SD Host Controller" rev 0x00: apic
> > 4 int 19
> > sdmmc0 at sdhc0
> > "JMicron Memory Stick" rev 0x00 at pci3 dev 0 function 3 not configured
> > "JMicron xD" rev 0x00 at pci3 dev 0 function 4 not configured
> > uhci0 at pci0 dev 29 function 0 "Intel 82801GB USB" rev 0x02: apic 4 int 16
> > uhci1 at pci0 dev 29 function 1 "Intel 82801GB USB" rev 0x02: apic 4 int 17
> > uhci2 at pci0 dev 29 function 2 "Intel 82801GB USB" rev 0x02: apic 4 int 18
> > uhci3 at pci0 dev 29 function 3 "Intel 82801GB USB" rev 0x02: apic 4 int 19
> > ehci0 at pci0 dev 29 function 7 "Intel 82801GB USB" rev 0x02: apic 4 int 16
> > usb0 at ehci0: USB revision 2.0
> > uhub0 at usb0 "Intel EHCI root hub" rev 2.00/1.00 addr 1
> > ppb3 at pci0 dev 30 function 0 "Intel 82801BAM Hub-to-PCI" rev 0xe2
> > pci4 at ppb3 bus 4
> > ichpcib0 at pci0 dev 31 function 0 "Intel 82801GBM LPC" rev 0x02: PM
> > disabled
> > pciide0 at pci0 dev 31 function 2 "Intel 82801GBM SATA" rev 0x02: DMA,
> > channel 0 wired to compatibility, channel 1 wired to compatibility
> > wd0 at pciide0 channel 0 drive 0: <ST9120817AS>
> > wd0: 16-sector PIO, LBA48, 114473MB, 234441648 sectors
> > wd0(pciide0:0:0): using PIO mode 4, Ultra-DMA mode 6
> > ichiic0 at pci0 dev 31 function 3 "Intel 82801GB SMBus" rev 0x02: apic 4
> > int 17
> > iic0 at ichiic0
> > spdmem0 at iic0 addr 0x51: 512MB DDR2 SDRAM non-parity PC2-5300CL5 SO-DIMM
> > usb1 at uhci0: USB revision 1.0
> > uhub1 at usb1 "Intel UHCI root hub" rev 1.00/1.00 addr 1
> > usb2 at uhci1: USB revision 1.0
> > uhub2 at usb2 "Intel UHCI root hub" rev 1.00/1.00 addr 1
> > usb3 at uhci2: USB revision 1.0
> > uhub3 at usb3 "Intel UHCI root hub" rev 1.00/1.00 addr 1
> > usb4 at uhci3: USB revision 1.0
> > uhub4 at usb4 "Intel UHCI root hub" rev 1.00/1.00 addr 1
> > isa0 at ichpcib0
> > isadma0 at isa0
> > pckbc0 at isa0 port 0x60/5
> > pckbd0 at pckbc0 (kbd slot)
> > pckbc0: using irq 1 for kbd slot
> > wskbd0 at pckbd0: console keyboard, using wsdisplay0
> > pms0 at pckbc0 (aux slot)
> > pckbc0: using irq 12 for aux slot
> > wsmouse0 at pms0 mux 0
> > pms0: Synaptics touchpad, firmware 7.2
> > pcppi0 at isa0 port 0x61
> > spkr0 at pcppi0
> > npx0 at isa0 port 0xf0/16: reported by CPUID; using exception 16
> > mtrr: Pentium Pro MTRR support
> > uvideo0 at uhub0 port 5 configuration 1 interface 0 "Sonix Technology Co.,
> > Ltd. USB 2.0 Camera" rev 2.00/1.00 addr 2
> > video0 at uvideo0
> > urtw0 at uhub0 port 7 "Realtek RTL8187B" rev 2.00/2.00 addr 3
> > urtw0: RTL8187B rev E, address 00:24:d2:2f:6d:1d
> > vscsi0 at root
> > scsibus0 at vscsi0: 256 targets
> > softraid0 at root
> > scsibus1 at softraid0: 256 targets
> > root on wd0a (1fe2cf3bec0653fe.a) swap on wd0b dump on wd0b
> > sd0 at scsibus1 targ 1 lun 0: <OPENBSD, SR CRYPTO, 005> SCSI2 0/direct fixed
> > sd0: 86811MB, 512 bytes/sector, 177790827 sectors
> > video0 detached
> > uvideo0 detached
> >
>
>
>
>
>
--
Antoine
