Comments (16)
bryteise
commented on May 29, 2024
Hrm I expect this to be set to westmere. @fenrus75 any thoughts on that?
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VictorRodriguez
commented on May 29, 2024
@ghuls thanks for the report, let me take a look :). BTW what platform do you have?
cat /proc/cpuinfo | grep avx2
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ghuls
commented on May 29, 2024
# No results
$ cat /proc/cpuinfo | grep avx2
$ cat /proc/cpuinfo | grep -c processor
60
$ gcc -march=native -Q --help=target
The following options are target specific:
-m128bit-long-double [enabled]
-m16 [disabled]
-m32 [disabled]
-m3dnow [disabled]
-m3dnowa [disabled]
-m64 [enabled]
-m80387 [enabled]
-m8bit-idiv [disabled]
-m96bit-long-double [disabled]
-mabi= sysv
-mabm [disabled]
-maccumulate-outgoing-args [disabled]
-maddress-mode= long
-madx [disabled]
-maes [enabled]
-malign-data= compat
-malign-double [disabled]
-malign-functions= 0
-malign-jumps= 0
-malign-loops= 0
-malign-stringops [enabled]
-mandroid [disabled]
-march= ivybridge
-masm= att
-mavx [enabled]
-mavx2 [disabled]
-mavx256-split-unaligned-load [enabled]
-mavx256-split-unaligned-store [enabled]
-mavx5124fmaps [disabled]
-mavx5124vnniw [disabled]
-mavx512bw [disabled]
-mavx512cd [disabled]
-mavx512dq [disabled]
-mavx512er [disabled]
-mavx512f [disabled]
-mavx512ifma [disabled]
-mavx512pf [disabled]
-mavx512vbmi [disabled]
-mavx512vl [disabled]
-mavx512vpopcntdq [disabled]
-mbionic [disabled]
-mbmi [disabled]
-mbmi2 [disabled]
-mbranch-cost= 3
-mcld [disabled]
-mclflushopt [disabled]
-mclwb [disabled]
-mclzero [disabled]
-mcmodel= [default]
-mcpu=
-mcrc32 [disabled]
-mcx16 [enabled]
-mdispatch-scheduler [disabled]
-mdump-tune-features [disabled]
-mf16c [enabled]
-mfancy-math-387 [enabled]
-mfentry [disabled]
-mfma [disabled]
-mfma4 [disabled]
-mforce-drap [disabled]
-mfp-ret-in-387 [enabled]
-mfpmath= sse
-mfsgsbase [enabled]
-mfunction-return= keep
-mfused-madd
-mfxsr [enabled]
-mgeneral-regs-only [disabled]
-mglibc [enabled]
-mhard-float [enabled]
-mhle [disabled]
-miamcu [disabled]
-mieee-fp [enabled]
-mincoming-stack-boundary= 0
-mindirect-branch-register [disabled]
-mindirect-branch= keep
-minline-all-stringops [disabled]
-minline-stringops-dynamically [disabled]
-mintel-syntax
-mlarge-data-threshold=<number> 65536
-mlong-double-128 [disabled]
-mlong-double-64 [disabled]
-mlong-double-80 [enabled]
-mlwp [disabled]
-mlzcnt [disabled]
-mmemcpy-strategy=
-mmemset-strategy=
-mmitigate-rop [disabled]
-mmmx [enabled]
-mmovbe [disabled]
-mmpx [disabled]
-mms-bitfields [disabled]
-mmusl [disabled]
-mmwaitx [disabled]
-mno-align-stringops [disabled]
-mno-default [disabled]
-mno-fancy-math-387 [disabled]
-mno-push-args [disabled]
-mno-red-zone [disabled]
-mno-sse4 [disabled]
-mnop-mcount [disabled]
-momit-leaf-frame-pointer [disabled]
-mpc32 [disabled]
-mpc64 [disabled]
-mpc80 [disabled]
-mpclmul [enabled]
-mpcommit [disabled]
-mpku [disabled]
-mpopcnt [enabled]
-mprefer-avx128 [disabled]
-mprefer-avx256 [disabled]
-mpreferred-stack-boundary= 0
-mprefetchwt1 [disabled]
-mprfchw [disabled]
-mpush-args [enabled]
-mrdpid [disabled]
-mrdrnd [enabled]
-mrdseed [disabled]
-mrecip [disabled]
-mrecip=
-mrecord-mcount [disabled]
-mred-zone [enabled]
-mregparm= 6
-mrtd [disabled]
-mrtm [disabled]
-msahf [enabled]
-msgx [disabled]
-msha [disabled]
-mskip-rax-setup [disabled]
-msoft-float [disabled]
-msse [enabled]
-msse2 [enabled]
-msse2avx [disabled]
-msse3 [enabled]
-msse4 [enabled]
-msse4.1 [enabled]
-msse4.2 [enabled]
-msse4a [disabled]
-msse5
-msseregparm [disabled]
-mssse3 [enabled]
-mstack-arg-probe [disabled]
-mstack-protector-guard= tls
-mstackrealign [disabled]
-mstringop-strategy= [default]
-mstv [enabled]
-mtbm [disabled]
-mtls-dialect= gnu
-mtls-direct-seg-refs [enabled]
-mtune-ctrl=
-mtune= ivybridge
-muclibc [disabled]
-mveclibabi= [default]
-mvect8-ret-in-mem [disabled]
-mvzeroupper [enabled]
-mx32 [disabled]
-mxop [disabled]
-mxsave [enabled]
-mxsavec [disabled]
-mxsaveopt [enabled]
-mxsaves [disabled]
-mzero-caller-saved-regs [disabled]
Known assembler dialects (for use with the -masm= option):
att intel
Known ABIs (for use with the -mabi= option):
ms sysv
Known code models (for use with the -mcmodel= option):
32 kernel large medium small
Valid arguments to -mfpmath=:
387 387+sse 387,sse both sse sse+387 sse,387
Known indirect branch choices (for use with the -mindirect-branch=/-mfunction-return= options):
keep thunk thunk-extern thunk-inline
Known data alignment choices (for use with the -malign-data= option):
abi cacheline compat
Known vectorization library ABIs (for use with the -mveclibabi= option):
acml svml
Known address mode (for use with the -maddress-mode= option):
long short
Known stack protector guard (for use with the -mstack-protector-guard= option):
global tls
Valid arguments to -mstringop-strategy=:
byte_loop libcall loop rep_4byte rep_8byte rep_byte unrolled_loop vector_loop
Known TLS dialects (for use with the -mtls-dialect= option):
gnu gnu2
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 62
model name : Intel(R) Xeon(R) CPU E7-4880 v2 @ 2.50GHz
stepping : 7
microcode : 0x70d
cpu MHz : 1392.285
cache size : 38400 KB
physical id : 0
siblings : 15
core id : 0
cpu cores : 15
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
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 pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts
bugs :
bogomips : 5000.00
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
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fenrus75
commented on May 29, 2024
that's an Ivybridge... while not having AVX2, it should still fully work
correctly.
Looks like we have a bug where some AVX2 bins/libs get installed even for
non-AVX2
likely the install order in the spec file is incorrect or something like
that
…On Fri, Mar 9, 2018 at 2:21 PM, Gert Hulselmans ***@***.***> wrote:
# No results
$ cat /proc/cpuinfo | grep avx2
$ cat /proc/cpuinfo | grep -c processor
60
$ gcc -march=native -Q --help=target
The following options are target specific:
-m128bit-long-double [enabled]
-m16 [disabled]
-m32 [disabled]
-m3dnow [disabled]
-m3dnowa [disabled]
-m64 [enabled]
-m80387 [enabled]
-m8bit-idiv [disabled]
-m96bit-long-double [disabled]
-mabi= sysv
-mabm [disabled]
-maccumulate-outgoing-args [disabled]
-maddress-mode= long
-madx [disabled]
-maes [enabled]
-malign-data= compat
-malign-double [disabled]
-malign-functions= 0
-malign-jumps= 0
-malign-loops= 0
-malign-stringops [enabled]
-mandroid [disabled]
-march= ivybridge
-masm= att
-mavx [enabled]
-mavx2 [disabled]
-mavx256-split-unaligned-load [enabled]
-mavx256-split-unaligned-store [enabled]
-mavx5124fmaps [disabled]
-mavx5124vnniw [disabled]
-mavx512bw [disabled]
-mavx512cd [disabled]
-mavx512dq [disabled]
-mavx512er [disabled]
-mavx512f [disabled]
-mavx512ifma [disabled]
-mavx512pf [disabled]
-mavx512vbmi [disabled]
-mavx512vl [disabled]
-mavx512vpopcntdq [disabled]
-mbionic [disabled]
-mbmi [disabled]
-mbmi2 [disabled]
-mbranch-cost= 3
-mcld [disabled]
-mclflushopt [disabled]
-mclwb [disabled]
-mclzero [disabled]
-mcmodel= [default]
-mcpu=
-mcrc32 [disabled]
-mcx16 [enabled]
-mdispatch-scheduler [disabled]
-mdump-tune-features [disabled]
-mf16c [enabled]
-mfancy-math-387 [enabled]
-mfentry [disabled]
-mfma [disabled]
-mfma4 [disabled]
-mforce-drap [disabled]
-mfp-ret-in-387 [enabled]
-mfpmath= sse
-mfsgsbase [enabled]
-mfunction-return= keep
-mfused-madd
-mfxsr [enabled]
-mgeneral-regs-only [disabled]
-mglibc [enabled]
-mhard-float [enabled]
-mhle [disabled]
-miamcu [disabled]
-mieee-fp [enabled]
-mincoming-stack-boundary= 0
-mindirect-branch-register [disabled]
-mindirect-branch= keep
-minline-all-stringops [disabled]
-minline-stringops-dynamically [disabled]
-mintel-syntax
-mlarge-data-threshold=<number> 65536
-mlong-double-128 [disabled]
-mlong-double-64 [disabled]
-mlong-double-80 [enabled]
-mlwp [disabled]
-mlzcnt [disabled]
-mmemcpy-strategy=
-mmemset-strategy=
-mmitigate-rop [disabled]
-mmmx [enabled]
-mmovbe [disabled]
-mmpx [disabled]
-mms-bitfields [disabled]
-mmusl [disabled]
-mmwaitx [disabled]
-mno-align-stringops [disabled]
-mno-default [disabled]
-mno-fancy-math-387 [disabled]
-mno-push-args [disabled]
-mno-red-zone [disabled]
-mno-sse4 [disabled]
-mnop-mcount [disabled]
-momit-leaf-frame-pointer [disabled]
-mpc32 [disabled]
-mpc64 [disabled]
-mpc80 [disabled]
-mpclmul [enabled]
-mpcommit [disabled]
-mpku [disabled]
-mpopcnt [enabled]
-mprefer-avx128 [disabled]
-mprefer-avx256 [disabled]
-mpreferred-stack-boundary= 0
-mprefetchwt1 [disabled]
-mprfchw [disabled]
-mpush-args [enabled]
-mrdpid [disabled]
-mrdrnd [enabled]
-mrdseed [disabled]
-mrecip [disabled]
-mrecip=
-mrecord-mcount [disabled]
-mred-zone [enabled]
-mregparm= 6
-mrtd [disabled]
-mrtm [disabled]
-msahf [enabled]
-msgx [disabled]
-msha [disabled]
-mskip-rax-setup [disabled]
-msoft-float [disabled]
-msse [enabled]
-msse2 [enabled]
-msse2avx [disabled]
-msse3 [enabled]
-msse4 [enabled]
-msse4.1 [enabled]
-msse4.2 [enabled]
-msse4a [disabled]
-msse5
-msseregparm [disabled]
-mssse3 [enabled]
-mstack-arg-probe [disabled]
-mstack-protector-guard= tls
-mstackrealign [disabled]
-mstringop-strategy= [default]
-mstv [enabled]
-mtbm [disabled]
-mtls-dialect= gnu
-mtls-direct-seg-refs [enabled]
-mtune-ctrl=
-mtune= ivybridge
-muclibc [disabled]
-mveclibabi= [default]
-mvect8-ret-in-mem [disabled]
-mvzeroupper [enabled]
-mx32 [disabled]
-mxop [disabled]
-mxsave [enabled]
-mxsavec [disabled]
-mxsaveopt [enabled]
-mxsaves [disabled]
-mzero-caller-saved-regs [disabled]
Known assembler dialects (for use with the -masm= option):
att intel
Known ABIs (for use with the -mabi= option):
ms sysv
Known code models (for use with the -mcmodel= option):
32 kernel large medium small
Valid arguments to -mfpmath=:
387 387+sse 387,sse both sse sse+387 sse,387
Known indirect branch choices (for use with the -mindirect-branch=/-mfunction-return= options):
keep thunk thunk-extern thunk-inline
Known data alignment choices (for use with the -malign-data= option):
abi cacheline compat
Known vectorization library ABIs (for use with the -mveclibabi= option):
acml svml
Known address mode (for use with the -maddress-mode= option):
long short
Known stack protector guard (for use with the -mstack-protector-guard= option):
global tls
Valid arguments to -mstringop-strategy=:
byte_loop libcall loop rep_4byte rep_8byte rep_byte unrolled_loop vector_loop
Known TLS dialects (for use with the -mtls-dialect= option):
gnu gnu2
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 62
model name : Intel(R) Xeon(R) CPU E7-4880 v2 @ 2.50GHz
stepping : 7
microcode : 0x70d
cpu MHz : 1392.285
cache size : 38400 KB
physical id : 0
siblings : 15
core id : 0
cpu cores : 15
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
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 pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts
bugs :
bogomips : 5000.00
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
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VictorRodriguez
commented on May 29, 2024
Makeconf keeps the latest CFLAGS that was used to build R . I am proposing this patch :
https://hastebin.com/upikigegav.sql
by setting -march=native , the libraries will be optimized for the platform the user has
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ghuls
commented on May 29, 2024
Would it be possible to generate both "*.so" (with and without avx2) files for user installed packages, like done for some default R packages?
$ ls -l /usr/lib64/R/library/Matrix/libs/Matrix.so*
-rwxr-xr-x 1 root root 996808 Jun 4 2017 /usr/lib64/R/library/Matrix/libs/Matrix.so
-rwxr-xr-x 1 root root 1099216 Jun 4 2017 /usr/lib64/R/library/Matrix/libs/Matrix.so.avx2
Or does this require manual work?
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fenrus75
commented on May 29, 2024
that's.... a bit harder.
for python we managed to tweak the buildsystem for it. R's build system is
a bit more free form so it's not nearly as easy.
for our packages we have our autopackager write the (too) complicated
pattern.
…On Fri, Mar 9, 2018 at 4:16 PM, Gert Hulselmans ***@***.***> wrote:
Would it be possible to generate both "*.so" (with and without avx2) files
for user installed packages, like done for some default R packages?
$ ls -l /usr/lib64/R/library/Matrix/libs/Matrix.so*
-rwxr-xr-x 1 root root 996808 Jun 4 2017 /usr/lib64/R/library/Matrix/libs/Matrix.so
-rwxr-xr-x 1 root root 1099216 Jun 4 2017 /usr/lib64/R/library/Matrix/libs/Matrix.so.avx2
Or does this require manual work?
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fenrus75
commented on May 29, 2024
btw if you give us a list of CRAN packages we lack we'll likely just
package them (and then you get the avx2 for free);
we can auto-package CRAN so it's very easy for us to do this
On Fri, Mar 9, 2018 at 4:25 PM, Arjan van de Ven <[email protected]>
wrote:
… that's.... a bit harder.
for python we managed to tweak the buildsystem for it. R's build system is
a bit more free form so it's not nearly as easy.
for our packages we have our autopackager write the (too) complicated
pattern.
On Fri, Mar 9, 2018 at 4:16 PM, Gert Hulselmans ***@***.***>
wrote:
> Would it be possible to generate both "*.so" (with and without avx2)
> files for user installed packages, like done for some default R packages?
>
> $ ls -l /usr/lib64/R/library/Matrix/libs/Matrix.so*
> -rwxr-xr-x 1 root root 996808 Jun 4 2017 /usr/lib64/R/library/Matrix/libs/Matrix.so
> -rwxr-xr-x 1 root root 1099216 Jun 4 2017 /usr/lib64/R/library/Matrix/libs/Matrix.so.avx2
>
> Or does this require manual work?
>
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> <#41 (comment)>,
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ghuls
commented on May 29, 2024
@fenrus75 I am happy to hear this. It will save me a lot of time in the future.
We have a huge list of R packages that we need (mainly from BioConductor).
This should be a list of packages that I need from CRAN:
acepack
ape
assertthat
backports
base64enc
bayesm
BH
bindr
bindrcpp
bit
bit64
bitops
blob
brew
Cairo
car
caret
caTools
checkmate
colorspace
commonmark
compositions
corrplot
cowplot
crayon
crosstalk
curl
CVST
data.table
DBI
ddalpha
dendextend
DEoptimR
desc
devtools
dichromat
diffusionMap
digest
dimRed
diptest
doMC
doParallel
doRNG
doSNOW
dplyr
DRR
DT
dtw
e1071
energy
evaluate
fastcluster
fitdistrplus
flexmix
FNN
foreach
formatR
Formula
fpc
futile.logger
futile.options
gdata
getopt
ggjoy
ggplot2
ggridges
git2r
glue
gower
gplots
gridBase
gridExtra
gtable
gtools
hexbin
highr
Hmisc
htmlTable
htmltools
htmlwidgets
httpuv
httr
ica
igraph
ipred
IRdisplay
irlba
iterators
jsonlite
kernlab
knitr
labeling
laeken
lambda.r
lars
lattice
latticeExtra
lava
lazyeval
lda
lme4
lmtest
lubridate
magrittr
markdown
MASS
Matrix
MatrixModels
mclust
memoise
mime
minqa
mixtools
mnormt
ModelMetrics
modeltools
munsell
mvtnorm
nloptr
NMF
NMOF
numDeriv
openssl
optparse
pbapply
pbdZMQ
pbkrtest
phylogram
pkgconfig
pkgmaker
plogr
plotly
plotrix
plyr
png
prabclus
praise
prodlim
proxy
purrr
quantreg
R.methodsS3
R.oo
R.utils
R6
ranger
RColorBrewer
Rcpp
RcppArmadillo
RcppEigen
RcppProgress
RcppRoll
RCurl
recipes
registry
repr
reshape2
RJSONIO
rlang
rmarkdown
rngtools
robustbase
ROCR
roxygen2
rprojroot
RSQLite
rstudioapi
Rtsne
RUnit
scales
scatterplot3d
SDMTools
segmented
shape
shiny
slam
smoother
sn
snow
sourcetools
sp
SparseM
stringi
stringr
survival
tclust
tensorA
testthat
tibble
tidyr
tidyselect
timeDate
topicmodels
trimcluster
tsne
TTR
uuid
vcd
VGAM
VIM
viridis
viridisLite
visNetwork
whisker
withr
XML
xml2
xtable
xts
yaml
zoo
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VictorRodriguez
commented on May 29, 2024
Thanks a lot for this request @ghuls, I will take care of this and as soon as I get a bundle with this packages I let you know. So far part of these are in R-extras:
https://github.com/clearlinux/clr-bundles/blob/master/bundles/R-extras
and they are optimized for avx2:
https://github.com/clearlinux-pkgs/R-zoo/blob/master/R-zoo.spec#L138
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ghuls
commented on May 29, 2024
@VictorRodriguez Thanks for the effort. I already have R-extras installed. I just didn't exclude those packages from the list.
We also use RStudio server:
https://www.rstudio.com/products/rstudio/download/
https://github.com/rstudio/rstudio/
For now we install the RPM package as the current version is difficult to compile from source (needs wget for Linux, but uses Curl on MacOs), so the build scripts should be rewritten.
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ghuls
commented on May 29, 2024
I had a problem compiling "Rgraphviz" from Bioconductor:
$ R
source("https://bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
...
ar: `u' modifier ignored since `D' is the default (see `U')
ar: arrows.o: plugin needed to handle lto object
ar: colxlate.o: plugin needed to handle lto object
ar: fontmetrics.o: plugin needed to handle lto object
ar: args.o: plugin needed to handle lto object
ar: memory.o: plugin needed to handle lto object
ar: globals.o: plugin needed to handle lto object
ar: htmllex.o: plugin needed to handle lto object
ar: htmlparse.o: plugin needed to handle lto object
ar: htmltable.o: plugin needed to handle lto object
ar: input.o: plugin needed to handle lto object
ar: pointset.o: plugin needed to handle lto object
ar: postproc.o: plugin needed to handle lto object
ar: routespl.o: plugin needed to handle lto object
ar: splines.o: plugin needed to handle lto object
ar: psusershape.o: plugin needed to handle lto object
ar: timing.o: plugin needed to handle lto object
ar: labels.o: plugin needed to handle lto object
ar: ns.o: plugin needed to handle lto object
ar: shapes.o: plugin needed to handle lto object
ar: utils.o: plugin needed to handle lto object
ar: geom.o: plugin needed to handle lto object
ar: output.o: plugin needed to handle lto object
ar: emit.o: plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(arrows.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(colxlate.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(fontmetrics.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(args.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(memory.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(globals.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(htmllex.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(htmlparse.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(htmltable.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(input.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(pointset.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(postproc.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(routespl.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(splines.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(psusershape.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(timing.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(labels.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(ns.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(shapes.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(utils.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(geom.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(output.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(emit.o): plugin needed to handle lto object
...
gcc -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/tmp/RtmpBITMJX/R.INSTALL14bbd758cdcb8/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -march=ivybridge -flto=12 -flto -c doLayout.c -o doLayout.o
gcc -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/tmp/RtmpBITMJX/R.INSTALL14bbd758cdcb8/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -march=ivybridge -flto=12 -flto -c graphvizVersion.c -o graphvizVersion.o
gcc -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/tmp/RtmpBITMJX/R.INSTALL14bbd758cdcb8/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -march=ivybridge -flto=12 -flto -c init.c -o init.o
gcc -g -shared -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -march=ivybridge -flto=12 -flto -fpic -L/usr/lib64/R/lib -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -L/usr/lib64/R/lib -lR
installing to /home/ghuls/R/x86_64-generic-linux-gnu-library/3.4/Rgraphviz/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘Rgraphviz’:
.onLoad failed in loadNamespace() for 'Rgraphviz', details:
call: value[[3L]](cond)
error: unable to load shared object '/home/ghuls/R/x86_64-generic-linux-gnu-library/3.4/Rgraphviz/libs/Rgraphviz.so':
/home/ghuls/R/x86_64-generic-linux-gnu-library/3.4/Rgraphviz/libs/Rgraphviz.so: undefined symbol: gvplugin_dot_layout_LTX_library
Rgraphviz is unable to be loaded. This typically is a symptom of an
installation problem. From 2.x.x onwards, Graphviz ought to come
bundled with Rgraphviz.
If you are trying to use an external Graphviz, see additional
instructions in the 'README' file of the Rgraphviz 'source'
distribution, available at
http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
Ask further questions on the Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Rgraphviz is unable to be loaded. This typically is a symptom of an
installation problem. From 2.x.x onwards, Graphviz ought to come
bundled with Rgraphviz.
If you are trying to use an external Graphviz, see additional
instructions in the 'README' file of the Rgraphviz 'source'
distribution, available at
http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
Ask further questions on the Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/ghuls/R/x86_64-generic-linux-gnu-library/3.4/Rgraphviz’
The downloaded source packages are in
‘/tmp/RtmpxpHZUy/downloaded_packages’
I had to remove the LTO flags in CFLAGS before I could compile this package:
CFLAGS = -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -march=ivybridge
from clr-bundles.
fenrus75
commented on May 29, 2024
I now how to fix this but I'm in airplanes for some time to come
Victor: We may need to always set the RANLIB environment variable in the
profile file in the filesystem package similar to how autospec set it for
LTO packages.
…On Tue, Mar 13, 2018 at 6:30 PM, Gert Hulselmans ***@***.***> wrote:
I had a problem compiling "Rgraphviz" from Bioconductor:
$ R
source("https://bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
...
ar: `u' modifier ignored since `D' is the default (see `U')
ar: arrows.o: plugin needed to handle lto object
ar: colxlate.o: plugin needed to handle lto object
ar: fontmetrics.o: plugin needed to handle lto object
ar: args.o: plugin needed to handle lto object
ar: memory.o: plugin needed to handle lto object
ar: globals.o: plugin needed to handle lto object
ar: htmllex.o: plugin needed to handle lto object
ar: htmlparse.o: plugin needed to handle lto object
ar: htmltable.o: plugin needed to handle lto object
ar: input.o: plugin needed to handle lto object
ar: pointset.o: plugin needed to handle lto object
ar: postproc.o: plugin needed to handle lto object
ar: routespl.o: plugin needed to handle lto object
ar: splines.o: plugin needed to handle lto object
ar: psusershape.o: plugin needed to handle lto object
ar: timing.o: plugin needed to handle lto object
ar: labels.o: plugin needed to handle lto object
ar: ns.o: plugin needed to handle lto object
ar: shapes.o: plugin needed to handle lto object
ar: utils.o: plugin needed to handle lto object
ar: geom.o: plugin needed to handle lto object
ar: output.o: plugin needed to handle lto object
ar: emit.o: plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(arrows.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(colxlate.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(fontmetrics.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(args.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(memory.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(globals.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(htmllex.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(htmlparse.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(htmltable.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(input.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(pointset.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(postproc.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(routespl.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(splines.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(psusershape.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(timing.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(labels.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(ns.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(shapes.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(utils.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(geom.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(output.o): plugin needed to handle lto object
ranlib: .libs/libcommon_C.a(emit.o): plugin needed to handle lto object
...
gcc -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/tmp/RtmpBITMJX/R.INSTALL14bbd758cdcb8/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -march=ivybridge -flto=12 -flto -c doLayout.c -o doLayout.o
gcc -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/tmp/RtmpBITMJX/R.INSTALL14bbd758cdcb8/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -march=ivybridge -flto=12 -flto -c graphvizVersion.c -o graphvizVersion.o
gcc -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/tmp/RtmpBITMJX/R.INSTALL14bbd758cdcb8/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -march=ivybridge -flto=12 -flto -c init.c -o init.o
gcc -g -shared -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -march=ivybridge -flto=12 -flto -fpic -L/usr/lib64/R/lib -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -L/usr/lib64/R/lib -lR
installing to /home/ghuls/R/x86_64-generic-linux-gnu-library/3.4/Rgraphviz/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘Rgraphviz’:
.onLoad failed in loadNamespace() for 'Rgraphviz', details:
call: value[[3L]](cond)
error: unable to load shared object '/home/ghuls/R/x86_64-generic-linux-gnu-library/3.4/Rgraphviz/libs/Rgraphviz.so':
/home/ghuls/R/x86_64-generic-linux-gnu-library/3.4/Rgraphviz/libs/Rgraphviz.so: undefined symbol: gvplugin_dot_layout_LTX_library
Rgraphviz is unable to be loaded. This typically is a symptom of an
installation problem. From 2.x.x onwards, Graphviz ought to come
bundled with Rgraphviz.
If you are trying to use an external Graphviz, see additional
instructions in the 'README' file of the Rgraphviz 'source'
distribution, available at
http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
Ask further questions on the Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Rgraphviz is unable to be loaded. This typically is a symptom of an
installation problem. From 2.x.x onwards, Graphviz ought to come
bundled with Rgraphviz.
If you are trying to use an external Graphviz, see additional
instructions in the 'README' file of the Rgraphviz 'source'
distribution, available at
http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
Ask further questions on the Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/ghuls/R/x86_64-generic-linux-gnu-library/3.4/Rgraphviz’
The downloaded source packages are in
‘/tmp/RtmpxpHZUy/downloaded_packages’
I had to remove the LTO flags in CFLAGS before I could compile this
package:
CFLAGS = -O2 -fPIC -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,--copy-dt-needed-entries -Wno-error -Wl,-z -Wl,now -Wl,-z -Wl,relro -Wl,-z,max-page-size=0x1000 -ftree-vectorize -m64 -mtune=skylake -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -march=ivybridge
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#41 (comment)>,
or mute the thread
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.
from clr-bundles.
fenrus75
commented on May 29, 2024
(I created a helper script to auto package a CRAN package, recursively for its dependencies. the script is chugging through your list now, but since we also run all tests and package the dependencies for the tests, the recursion is a tad deep and takes a while)
from clr-bundles.
bryteise
commented on May 29, 2024
Packages should be in latest release in R-extras bundle.
from clr-bundles.
alecz20
commented on May 29, 2024
Was this supposed to be fixed? This still happens with the 2019 version of clear-linux.
/usr/lib64/R/etc/Makeconf has: -march=haswell -mtune=haswell even though I have a westmere architecture.
This caused a simple fread to crash with:
*** caught illegal operation ***
address 0x7fa41f60b274, cause 'illegal operand'
from clr-bundles.
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