Your message dated Thu, 27 Nov 2014 13:23:33 -0600
with message-id <[email protected]>
and subject line Re: Bug#770696: r-base-core: R crashes with "*** caught
illegal operation ***"
has caused the Debian Bug report #770696,
regarding r-base-core: R crashes with "*** caught illegal operation ***"
to be marked as done.
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Bug report if necessary, and/or fix the problem forthwith.
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--
770696: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=770696
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: r-base-core
Version: 2.15.1-4
Severity: important
R crashes because it tries to execute an illegal instruction.
This is how you can reproduce:
$ R
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
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.
Natural language support but running in an English locale
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.
> ar.yw(rnorm(4000), aic=F, order.max=100)
*** caught illegal operation ***
address 0x7ff14fbd6d44, cause 'illegal operand'
Traceback:
1: solve.default(toeplitz(drop(xacf)[seq_len(order)]))
2: solve(toeplitz(drop(xacf)[seq_len(order)]))
3: ar.yw.default(rnorm(4000), aic = F, order.max = 100)
4: ar.yw(rnorm(4000), aic = F, order.max = 100)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
aborting ...
Illegal instruction
Here is the /proc/cpuinfo of the machine:
processor : 0
vendor_id : GenuineIntel
cpu family : 15
model : 4
model name : Intel(R) Pentium(R) 4 CPU 2.80GHz
stepping : 1
microcode : 0x17
cpu MHz : 2793.249
cache size : 1024 KB
physical id : 0
siblings : 2
core id : 0
cpu cores : 1
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm
constant_tsc pebs bts nopl pni dtes64 monitor ds_cpl cid cx16 xtpr
bogomips : 5586.49
clflush size : 64
cache_alignment : 128
address sizes : 36 bits physical, 48 bits virtual
power management:
processor : 1
vendor_id : GenuineIntel
cpu family : 15
model : 4
model name : Intel(R) Pentium(R) 4 CPU 2.80GHz
stepping : 1
microcode : 0x17
cpu MHz : 2793.249
cache size : 1024 KB
physical id : 0
siblings : 2
core id : 0
cpu cores : 1
apicid : 1
initial apicid : 1
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm
constant_tsc pebs bts nopl pni dtes64 monitor ds_cpl cid cx16 xtpr
bogomips : 5586.11
clflush size : 64
cache_alignment : 128
address sizes : 36 bits physical, 48 bits virtual
power management:
-- System Information:
Debian Release: 7.7
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'proposed-updates'), (500,
'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 3.2.0-4-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_GB.ISO-8859-1, LC_CTYPE=en_GB.ISO-8859-1 (charmap=ISO-8859-1)
Shell: /bin/sh linked to /bin/dash
Versions of packages r-base-core depends on:
ii libatlas3-base [liblapack.so.3] 3.8.4-9+deb7u1
ii libblas3 [libblas.so.3] 1.2.20110419-5
ii libbz2-1.0 1.0.6-4
ii libc6 2.13-38+deb7u6
ii libcairo2 1.12.2-3
ii libgfortran3 4.7.2-5
ii libglib2.0-0 2.33.12+really2.32.4-5
ii libgomp1 4.7.2-5
ii libice6 2:1.0.8-2
ii libjpeg8 8d-1+deb7u1
ii liblapack3 [liblapack.so.3] 3.4.1+dfsg-1+deb70u1
ii liblzma5 5.1.1alpha+20120614-2
ii libpango1.0-0 1.30.0-1
ii libpaper-utils 1.1.24+nmu2
ii libpcre3 1:8.30-5
ii libpng12-0 1.2.49-1
ii libquadmath0 4.7.2-5
ii libreadline6 6.2+dfsg-0.1
ii libsm6 2:1.2.1-2
ii libtiff4 3.9.6-11
ii libx11-6 2:1.5.0-1+deb7u1
ii libxext6 2:1.3.1-2+deb7u1
ii libxss1 1:1.2.2-1
ii libxt6 1:1.1.3-1+deb7u1
ii tcl8.5 8.5.11-2
ii tk8.5 8.5.11-2
ii ucf 3.0025+nmu3
ii unzip 6.0-8
ii xdg-utils 1.1.0~rc1+git20111210-6+deb7u1
ii zip 3.0-6
ii zlib1g 1:1.2.7.dfsg-13
Versions of packages r-base-core recommends:
pn r-base-dev <none>
ii r-doc-html 2.15.1-4
ii r-recommended 2.15.1-4
Versions of packages r-base-core suggests:
pn ess <none>
pn r-base-html <none>
pn r-doc-info | r-doc-pdf <none>
pn r-mathlib <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
Hi Matti,
On 23 November 2014 at 16:07, Matti Vihola wrote:
| Dear Dirk,
|
| Thank you for your prompt response.
|
| I was unaware that I should not report bugs about packages in the Debian
| stable if there are newer versions in testing/unstable (as there always
| are), sorry.
It is a bit nuanced. "Technically", "Debian as a whole" welcomes this.
At least it is then filed.
Practically, I am the one who has to deal with it, and there really is
nothing I can do. For bugs fixed in newer versions, R Core will just tell
"to use the newer version" -- and I can't argue with that. I just don't have
the time to work out a backport. Most of us use current R versions via the
Debian / Ubuntu repo on CRAN even on older releases.
| Feel free to mark the bug resolved if you wish.
Doing so via a CC.
Thanks for the report though.
Dirk
|
|
| Best,
|
| -- Matti
|
| On Sun, 23 Nov 2014, Dirk Eddelbuettel wrote:
| > On 23 November 2014 at 10:45, Matti Vihola wrote:
| > | Package: r-base-core
| > | Version: 2.15.1-4
| > | Severity: important
| > |
| > | R crashes because it tries to execute an illegal instruction.
| > | This is how you can reproduce:
| > |
| > | $ R
| > |
| > | R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
| > | Copyright (C) 2012 The R Foundation for Statistical Computing
| > | ISBN 3-900051-07-0
| > | Platform: x86_64-pc-linux-gnu (64-bit)
| > |
| > | 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.
| > |
| > | Natural language support but running in an English locale
| > |
| > | 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.
| > |
| > | > ar.yw(rnorm(4000), aic=F, order.max=100)
| >
| > Works fine in the current version, so upstream is not going to be
interested,
| > and I have no time or interest in backporting a fix for a version that
__more
| > that two years behind__ the current release.
| >
| > As you may know, there are backports for Debian stable etc on every CRAN
| > mirror in $CRAN/bin/linux/debian/
| >
| > Feel free to tag this appropriately but *please* remove the tag: important
| > as this simply does not apply for testing or unstable.
| >
| > Dirk
| >
| > |
| > | *** caught illegal operation ***
| > | address 0x7ff14fbd6d44, cause 'illegal operand'
| > |
| > | Traceback:
| > | 1: solve.default(toeplitz(drop(xacf)[seq_len(order)]))
| > | 2: solve(toeplitz(drop(xacf)[seq_len(order)]))
| > | 3: ar.yw.default(rnorm(4000), aic = F, order.max = 100)
| > | 4: ar.yw(rnorm(4000), aic = F, order.max = 100)
| > |
| > | Possible actions:
| > | 1: abort (with core dump, if enabled)
| > | 2: normal R exit
| > | 3: exit R without saving workspace
| > | 4: exit R saving workspace
| > | Selection: 1
| > | aborting ...
| > | Illegal instruction
| > |
| > |
| > | Here is the /proc/cpuinfo of the machine:
| > |
| > | processor : 0
| > | vendor_id : GenuineIntel
| > | cpu family : 15
| > | model : 4
| > | model name : Intel(R) Pentium(R) 4 CPU 2.80GHz
| > | stepping : 1
| > | microcode : 0x17
| > | cpu MHz : 2793.249
| > | cache size : 1024 KB
| > | physical id : 0
| > | siblings : 2
| > | core id : 0
| > | cpu cores : 1
| > | apicid : 0
| > | initial apicid : 0
| > | fpu : yes
| > | fpu_exception : yes
| > | cpuid level : 5
| > | wp : yes
| > | flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca
| > | cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
lm
| > | constant_tsc pebs bts nopl pni dtes64 monitor ds_cpl cid cx16 xtpr
| > | bogomips : 5586.49
| > | clflush size : 64
| > | cache_alignment : 128
| > | address sizes : 36 bits physical, 48 bits virtual
| > | power management:
| > |
| > | processor : 1
| > | vendor_id : GenuineIntel
| > | cpu family : 15
| > | model : 4
| > | model name : Intel(R) Pentium(R) 4 CPU 2.80GHz
| > | stepping : 1
| > | microcode : 0x17
| > | cpu MHz : 2793.249
| > | cache size : 1024 KB
| > | physical id : 0
| > | siblings : 2
| > | core id : 0
| > | cpu cores : 1
| > | apicid : 1
| > | initial apicid : 1
| > | fpu : yes
| > | fpu_exception : yes
| > | cpuid level : 5
| > | wp : yes
| > | flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca
| > | cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
lm
| > | constant_tsc pebs bts nopl pni dtes64 monitor ds_cpl cid cx16 xtpr
| > | bogomips : 5586.11
| > | clflush size : 64
| > | cache_alignment : 128
| > | address sizes : 36 bits physical, 48 bits virtual
| > | power management:
| > |
| > |
| > |
| > |
| > | -- System Information:
| > | Debian Release: 7.7
| > | APT prefers stable-updates
| > | APT policy: (500, 'stable-updates'), (500, 'proposed-updates'), (500,
'stable')
| > | Architecture: amd64 (x86_64)
| > | Foreign Architectures: i386
| > |
| > | Kernel: Linux 3.2.0-4-amd64 (SMP w/2 CPU cores)
| > | Locale: LANG=en_GB.ISO-8859-1, LC_CTYPE=en_GB.ISO-8859-1
(charmap=ISO-8859-1)
| > | Shell: /bin/sh linked to /bin/dash
| > |
| > | Versions of packages r-base-core depends on:
| > | ii libatlas3-base [liblapack.so.3] 3.8.4-9+deb7u1
| > | ii libblas3 [libblas.so.3] 1.2.20110419-5
| > | ii libbz2-1.0 1.0.6-4
| > | ii libc6 2.13-38+deb7u6
| > | ii libcairo2 1.12.2-3
| > | ii libgfortran3 4.7.2-5
| > | ii libglib2.0-0 2.33.12+really2.32.4-5
| > | ii libgomp1 4.7.2-5
| > | ii libice6 2:1.0.8-2
| > | ii libjpeg8 8d-1+deb7u1
| > | ii liblapack3 [liblapack.so.3] 3.4.1+dfsg-1+deb70u1
| > | ii liblzma5 5.1.1alpha+20120614-2
| > | ii libpango1.0-0 1.30.0-1
| > | ii libpaper-utils 1.1.24+nmu2
| > | ii libpcre3 1:8.30-5
| > | ii libpng12-0 1.2.49-1
| > | ii libquadmath0 4.7.2-5
| > | ii libreadline6 6.2+dfsg-0.1
| > | ii libsm6 2:1.2.1-2
| > | ii libtiff4 3.9.6-11
| > | ii libx11-6 2:1.5.0-1+deb7u1
| > | ii libxext6 2:1.3.1-2+deb7u1
| > | ii libxss1 1:1.2.2-1
| > | ii libxt6 1:1.1.3-1+deb7u1
| > | ii tcl8.5 8.5.11-2
| > | ii tk8.5 8.5.11-2
| > | ii ucf 3.0025+nmu3
| > | ii unzip 6.0-8
| > | ii xdg-utils 1.1.0~rc1+git20111210-6+deb7u1
| > | ii zip 3.0-6
| > | ii zlib1g 1:1.2.7.dfsg-13
| > |
| > | Versions of packages r-base-core recommends:
| > | pn r-base-dev <none>
| > | ii r-doc-html 2.15.1-4
| > | ii r-recommended 2.15.1-4
| > |
| > | Versions of packages r-base-core suggests:
| > | pn ess <none>
| > | pn r-base-html <none>
| > | pn r-doc-info | r-doc-pdf <none>
| > | pn r-mathlib <none>
| > |
| > | -- no debconf information
| >
| > --
| > http://dirk.eddelbuettel.com | @eddelbuettel | [email protected]
| >
--
http://dirk.eddelbuettel.com | @eddelbuettel | [email protected]
--- End Message ---
