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.
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$type <- match.arg(type, c("Xlib",
"cairo", "nbcairo")) if (!missing(antialias)) { new$antialias <-
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
