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Problem with metaMDS and large input file #152

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V-Z opened this Issue Jan 4, 2016 · 10 comments

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@V-Z

V-Z commented Jan 4, 2016

library(vegan)
metab.pos.root1.concat.mrbayes.nmds <- metaMDS(comm=metab.pos.root1.concat.mrbayes,
distance="manhattan", k=2, trymax=10000, engine="monoMDS", autotransform=FALSE, 
noshare=FALSE, stepacross=FALSE, wascores=FALSE, expand=FALSE, plot=TRUE)

metab.pos.root1.concat.mrbayes has over 14000 columns and 18 rows
R console does not produce any output, it just hangs.

When I force quit R window, I get:

Message code: r_engine_has_died
Connection closed unexpectedly. Last error was: QLocalSocket: Remote closed

The R backend will be shut down immediately. This means, you can not use any more functions that rely on it. I.e. you can do hardly anything at all, not even save the workspace (but if you're lucky, R already did that). What you can do, however, is save any open command-files, the output, or copy data out of open data editors.

I use openSUSE Linux R binary and vegan is compiled locally.

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jarioksa Jan 4, 2016

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You may not tell us all relevant details of your environment. You say that "R backend will shut down" -- so what is your front-end? (R Studio, Rcmdr, emacs?). When starting a session directly from a command shell (bash in terminal window), I can analyse data with similar dimensionality of 18 rows x 14000 columns lightning fast. However, if I have the dimensions reversed (i.e., 14000 rows), then the resulting dissimilarity object has 98 million elements, and analysis will be very slow. It won't hang (if you have sufficient memory: 12 GB looks enough), but it will take very long time to get any results, and you need patience. A lot of patience, and perhaps also a retirement plan if you want to run 10000 tries.

Contributor

jarioksa commented Jan 4, 2016

You may not tell us all relevant details of your environment. You say that "R backend will shut down" -- so what is your front-end? (R Studio, Rcmdr, emacs?). When starting a session directly from a command shell (bash in terminal window), I can analyse data with similar dimensionality of 18 rows x 14000 columns lightning fast. However, if I have the dimensions reversed (i.e., 14000 rows), then the resulting dissimilarity object has 98 million elements, and analysis will be very slow. It won't hang (if you have sufficient memory: 12 GB looks enough), but it will take very long time to get any results, and you need patience. A lot of patience, and perhaps also a retirement plan if you want to run 10000 tries.

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V-Z Jan 4, 2016

Sorry, here are the details. I use to use Rkward and in such case, it crashes (see reported bug, but people there think this is vegan's problem), in console (bash) it just hangs (overnight, no progress). The computer has altogether 16 GB RAM, 4.2 GHz i7 CPU and SSD, so it should work. :-) And yes, I understand it can take really long time, but it doesn't seem to be the case (I has been able to handle bigger tasks on that machine).

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE 13.2 (Harlequin) (x86_64)

locale:
 [1] LC_CTYPE=cs_CZ.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=cs_CZ.UTF-8        LC_COLLATE=cs_CZ.UTF-8
 [5] LC_MONETARY=cs_CZ.UTF-8    LC_MESSAGES=cs_CZ.UTF-8
 [7] LC_PAPER=cs_CZ.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

> rk.sessionInfo()
-- Frontend --
RKWard version: 0.6.3
KDE version (runtime): 4.14.9
KDE version (compile time): 4.14.2
Qt build key: x86_64 linux g++-4 full-config
Local KDE directory: /home/vojta/.kde4/
RKWard storage directory: /home/vojta/.rkward/
Backend version (as known to the frontend): 3.2.3

Debug message file (this may contain relevant diagnostic output in case of trouble):
/tmp/rkward.frontend.rA7644

-- Backend --
Debug message file (this may contain relevant diagnostic output in case of trouble):
/tmp/rkward.rbackend.TJ7649

R version (compile time): 3.2.3  (2015-12-10 r69752)
R runtime session info:
R version 3.2.3 (2015-12-10)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE 13.2 (Harlequin) (x86_64)

locale:
 [1] LC_CTYPE=cs_CZ.UTF-8          LC_NUMERIC=C                  LC_TIME=cs_CZ.UTF-8          
 [4] LC_COLLATE=cs_CZ.UTF-8        LC_MONETARY=cs_CZ.UTF-8       LC_MESSAGES=cs_CZ.UTF-8      
 [7] LC_PAPER=cs_CZ.UTF-8          LC_NAME=cs_CZ.UTF-8           LC_ADDRESS=cs_CZ.UTF-8       
[10] LC_TELEPHONE=cs_CZ.UTF-8      LC_MEASUREMENT=cs_CZ.UTF-8    LC_IDENTIFICATION=cs_CZ.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rkward_0.6.3

loaded via a namespace (and not attached):
[1] tools_3.2.3

The R binary is from openSUSE repository.

V-Z commented Jan 4, 2016

Sorry, here are the details. I use to use Rkward and in such case, it crashes (see reported bug, but people there think this is vegan's problem), in console (bash) it just hangs (overnight, no progress). The computer has altogether 16 GB RAM, 4.2 GHz i7 CPU and SSD, so it should work. :-) And yes, I understand it can take really long time, but it doesn't seem to be the case (I has been able to handle bigger tasks on that machine).

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE 13.2 (Harlequin) (x86_64)

locale:
 [1] LC_CTYPE=cs_CZ.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=cs_CZ.UTF-8        LC_COLLATE=cs_CZ.UTF-8
 [5] LC_MONETARY=cs_CZ.UTF-8    LC_MESSAGES=cs_CZ.UTF-8
 [7] LC_PAPER=cs_CZ.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

> rk.sessionInfo()
-- Frontend --
RKWard version: 0.6.3
KDE version (runtime): 4.14.9
KDE version (compile time): 4.14.2
Qt build key: x86_64 linux g++-4 full-config
Local KDE directory: /home/vojta/.kde4/
RKWard storage directory: /home/vojta/.rkward/
Backend version (as known to the frontend): 3.2.3

Debug message file (this may contain relevant diagnostic output in case of trouble):
/tmp/rkward.frontend.rA7644

-- Backend --
Debug message file (this may contain relevant diagnostic output in case of trouble):
/tmp/rkward.rbackend.TJ7649

R version (compile time): 3.2.3  (2015-12-10 r69752)
R runtime session info:
R version 3.2.3 (2015-12-10)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE 13.2 (Harlequin) (x86_64)

locale:
 [1] LC_CTYPE=cs_CZ.UTF-8          LC_NUMERIC=C                  LC_TIME=cs_CZ.UTF-8          
 [4] LC_COLLATE=cs_CZ.UTF-8        LC_MONETARY=cs_CZ.UTF-8       LC_MESSAGES=cs_CZ.UTF-8      
 [7] LC_PAPER=cs_CZ.UTF-8          LC_NAME=cs_CZ.UTF-8           LC_ADDRESS=cs_CZ.UTF-8       
[10] LC_TELEPHONE=cs_CZ.UTF-8      LC_MEASUREMENT=cs_CZ.UTF-8    LC_IDENTIFICATION=cs_CZ.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rkward_0.6.3

loaded via a namespace (and not attached):
[1] tools_3.2.3

The R binary is from openSUSE repository.

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jarioksa Jan 4, 2016

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I cannot reproduce your problem, and you do not provide a reproducible example. Please (1) provide a reproducible example, or (2) try without rkward by starting a terminal window and start there R, or (3) check your data and the result of dist(<your-data>, "manhattan").

Here is what I get:

> x <- matrix(runif(18*14000), nrow=18)
> m <- metaMDS(x, dist="man", k=2, try=2, auto =FALSE, noshare=FALSE, 
   step=FALSE, wascores=FALSE)
Run 0 stress 0.2533868 
Run 1 stress 0.2808658 
Run 2 stress 0.2556608 

Runs smoothly and swiftly.

Contributor

jarioksa commented Jan 4, 2016

I cannot reproduce your problem, and you do not provide a reproducible example. Please (1) provide a reproducible example, or (2) try without rkward by starting a terminal window and start there R, or (3) check your data and the result of dist(<your-data>, "manhattan").

Here is what I get:

> x <- matrix(runif(18*14000), nrow=18)
> m <- metaMDS(x, dist="man", k=2, try=2, auto =FALSE, noshare=FALSE, 
   step=FALSE, wascores=FALSE)
Run 0 stress 0.2533868 
Run 1 stress 0.2808658 
Run 2 stress 0.2556608 

Runs smoothly and swiftly.

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V-Z Jan 4, 2016

Hello

  1. I can provide the file, but I'd like to avoid public posting on the "wild" internet... What would be the best way for You?
  2. In plain terminal window it runs like this:
> metab.pos.root1.concat.mrbayes.nmds <- 
  metaMDS(comm=metab.pos.root1.concat.mrbayes, distance="manhattan", k=2, 
  trymax=10000, engine="monoMDS", autotransform=FALSE, noshare=FALSE, 
  stepacross=FALSE, wascores=FALSE, expand=FALSE, plot=TRUE)
*** Error in `/usr/lib64/R/bin/exec/R': double free or corruption (!prev): 0x000000000d671080 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7283f)[0x7f9768eb083f]
/lib64/libc.so.6(+0x780ae)[0x7f9768eb60ae]
/lib64/libc.so.6(+0x78db6)[0x7f9768eb6db6]
/usr/lib64/R/lib/libR.so(+0x149821)[0x7f976954b821]
/usr/lib64/R/lib/libR.so(CONS_NR+0x8c)[0x7f976954d12c]
/usr/lib64/R/lib/libR.so(+0x10cfaa)[0x7f976950efaa]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(+0x14f3a4)[0x7f97695513a4]
/usr/lib64/R/lib/libR.so(+0x14f7e0)[0x7f97695517e0]
/usr/lib64/R/lib/libR.so(+0x14fab2)[0x7f9769551ab2]
/usr/lib64/R/lib/libR.so(+0x10ce44)[0x7f976950ee44]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(+0x11400c)[0x7f976951600c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(R_forceAndCall+0x14c)[0x7f97695210ac]
/usr/lib64/R/lib/libR.so(+0x7a69a)[0x7f976947c69a]
/usr/lib64/R/lib/libR.so(+0x14d689)[0x7f976954f689]
/usr/lib64/R/lib/libR.so(+0x10ce44)[0x7f976950ee44]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(+0x11400c)[0x7f976951600c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(+0x1090c6)[0x7f976950b0c6]
/usr/lib64/R/lib/libR.so(+0x1ac521)[0x7f97695ae521]
/usr/lib64/R/lib/libR.so(Rf_eval+0x643)[0x7f976951d993]
/usr/lib64/R/lib/libR.so(+0x11ebce)[0x7f9769520bce]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(+0x11daf0)[0x7f976951faf0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2df)[0x7f976951d62f]
/usr/lib64/R/lib/libR.so(+0x11ebce)[0x7f9769520bce]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(+0x11daf0)[0x7f976951faf0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(+0x11daf0)[0x7f976951faf0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2df)[0x7f976951d62f]
/usr/lib64/R/lib/libR.so(+0x11ebce)[0x7f9769520bce]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x232)[0x7f97695449c2]
/usr/lib64/R/lib/libR.so(+0x142d11)[0x7f9769544d11]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0x44)[0x7f9769544dc4]
/usr/lib64/R/bin/exec/R(main+0x1b)[0x40089b]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f9768e5fb05]
/usr/lib64/R/bin/exec/R[0x4008cb]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fe:01 3028083                            /usr/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 fe:01 3028083                            /usr/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 fe:01 3028083                            /usr/lib64/R/bin/exec/R
01226000-11916000 rw-p 00000000 00:00 0                                  [heap]
7f97470ac000-7f97470ce000 r--p 00000000 fe:01 2512551                    /usr/share/fonts/texlive-tex-gyre/texgyreheros-bold.otf
7f97470ce000-7f97470ef000 r--p 00000000 fe:01 2512554                    /usr/share/fonts/texlive-tex-gyre/texgyreheros-regular.otf
7f97470ef000-7f97470f2000 r-xp 00000000 fe:01 1967065                    /usr/lib64/pango/1.8.0/modules/pango-basic-fc.so
7f97470f2000-7f97472f1000 ---p 00003000 fe:01 1967065                    /usr/lib64/pango/1.8.0/modules/pango-basic-fc.so
7f97472f1000-7f97472f2000 r--p 00002000 fe:01 1967065                    /usr/lib64/pango/1.8.0/modules/pango-basic-fc.so
7f97472f2000-7f97472f3000 rw-p 00003000 fe:01 1967065                    /usr/lib64/pango/1.8.0/modules/pango-basic-fc.so
7f97472f3000-7f974730d000 r--s 00000000 fe:03 2149445020                 /home/vojta/.cache/fontconfig/81ee38b02c7c21d5c726a9a4eca0938f-x86_64.cache-4
7f974730d000-7f974730f000 r--s 00000000 fe:03 2149445019                 /home/vojta/.cache/fontconfig/97f77127cac57354e0504a53f5e6468d-x86_64.cache-4
7f974730f000-7f9747318000 r--s 00000000 fe:03 2149445018                 /home/vojta/.cache/fontconfig/f92bba027e85f20cf4ed008ecdc40abd-x86_64.cache-4
7f9747318000-7f9747321000 r--s 00000000 fe:03 2149445011                 /home/vojta/.cache/fontconfig/1adb6c01d5471348247f3f21c44e3b1e-x86_64.cache-4
7f9747321000-7f9747324000 r--s 00000000 fe:03 2149445010                 /home/vojta/.cache/fontconfig/2a2f4d248b40c6231a06619e2d3c41e1-x86_64.cache-4
7f9747324000-7f9747344000 r--s 00000000 fe:03 2149445009                 /home/vojta/.cache/fontconfig/cdf663b38b074286b0594bd8aa823790-x86_64.cache-4
7f9747344000-7f9747395000 r--s 00000000 fe:03 2149445008                 /home/vojta/.cache/fontconfig/ec6411fee082fe8de5c80b3b3b428adc-x86_64.cache-4
7f9747395000-7f97473a1000 r--s 00000000 fe:03 2149445007                 /home/vojta/.cache/fontconfig/ec30bf3c9389a9130f071263ba010d07-x86_64.cache-4
7f97473a1000-7f97473a5000 r--s 00000000 fe:03 2149391572                 /home/vojta/.cache/fontconfig/101736a6b19f07022070fe0561c5bd7a-x86_64.cache-4
7f97473a5000-7f97473b9000 r--s 00000000 fe:03 2149391571                 /home/vojta/.cache/fontconfig/b1745dcecbf8e43497254b728d0b076d-x86_64.cache-4
7f97473b9000-7f97473c5000 r--s 00000000 fe:03 2149391570                 /home/vojta/.cache/fontconfig/af0fc35b89e3122fd2842bcb6e895a1e-x86_64.cache-4
7f97473c5000-7f97473eb000 r--s 00000000 fe:03 2149391569                 /home/vojta/.cache/fontconfig/e034a016a6b68e1a54567066b496ab95-x86_64.cache-4
7f97473eb000-7f9747406000 r--s 00000000 fe:03 2149391568                 /home/vojta/.cache/fontconfig/4a507c0bfc5b5d9f456dc4a69df4ec80-x86_64.cache-4
7f9747406000-7f9747425000 r--s 00000000 fe:03 2149391563                 /home/vojta/.cache/fontconfig/5dcc5d8d93de3eec1837020af8cae73a-x86_64.cache-4
7f9747425000-7f9747438000 r--s 00000000 fe:03 2149391562                 /home/vojta/.cache/fontconfig/21e296f96eb206ccd855b9b28328fe94-x86_64.cache-4
7f9747438000-7f974743c000 r--s 00000000 fe:03 2149391561                 /home/vojta/.cache/fontconfig/30a748b12d5d4f614914a3e4cd358af7-x86_64.cache-4
7f974743c000-7f9747450000 r--s 00000000 fe:03 2149391560                 /home/vojta/.cache/fontconfig/c87031a1de2576bfadad5a26174bdef2-x86_64.cache-4
7f9747450000-7f974746d000 r--s 00000000 fe:03 2149391559                 /home/vojta/.cache/fontconfig/43a72e8cb0767c982e1f312b37fca0c1-x86_64.cache-4
7f974746d000-7f97474ab000 r--s 00000000 fe:03 2149391558                 /home/vojta/.cache/fontconfig/073a9e98eb7e02f6711eb18f3cce0a44-x86_64.cache-4
7f97474ab000-7f97474e2000 r--s 00000000 fe:03 2149391557                 /home/vojta/.cache/fontconfig/b885105119255e05554f946da59e8821-x86_64.cache-4
7f97474e2000-7f97474fd000 r--s 00000000 fe:03 2149391556                 /home/vojta/.cache/fontconfig/72ac980c2d4e53000c7ba1ae4696dd09-x86_64.cache-4
7f97474fd000-7f974751a000 r--s 00000000 fe:03 2149391555                 /home/vojta/.cache/fontconfig/1a823246853fcc6ceb351b48cf1cdbfa-x86_64.cache-4
7f974751a000-7f974757c000 r--s 00000000 fe:03 2149391553                 /home/vojta/.cache/fontconfig/3dcc8a8d60036b1dffde63ffca89d63a-x86_64.cache-4
7f974757c000-7f97475bd000 r--s 00000000 fe:03 2149391552                 /home/vojta/.cache/fontconfig/1be83550c1aaad2ea620533c141c798e-x86_64.cache-4
7f97475bd000-7f97475e6000 r--s 00000000 fe:03 2149391538                 /home/vojta/.cache/fontconfig/49b36a0a829654628f9a05a7ef277292-x86_64.cache-4
7f97475e6000-7f97475e9000 r--s 00000000 fe:01 132356                     /var/cache/fontconfig/d458be102e54cf534d1eef0dcbb02d07-x86_64.cache-4
7f97475e9000-7f97476ca000 r--s 00000000 fe:01 142984                     /var/cache/fontconfig/7ef2298fde41cc6eeb7af42e48b7d293-x86_64.cache-4
7f97476ca000-7f97476cb000 r--s 00000000 fe:01 142983                     /var/cache/fontconfig/fb8341411dac03919a6f30c61d3ee363-x86_64.cache-4
7f97476cb000-7f97476cc000 r--s 00000000 fe:01 142982                     /var/cache/fontconfig/31d258c26849b1f3b28618b43aef0df4-x86_64.cache-4
7f97476cc000-7f97476cd000 r--s 00000000 fe:01 142981                     /var/cache/fontconfig/8aefcdceaf7081f7a76e5c97af6ee8fa-x86_64.cache-4
7f97476cd000-7f97476d4000 r--s 00000000 fe:01 142980                     /var/cache/fontconfig/2b4c5ecca09e2930001c0780a4ec3c17-x86_64.cache-4
7f97476d4000-7f97476d7000 r--s 00000000 fe:01 142979                     /var/cache/fontconfig/72cfb3223c4327e0479d681c7a7c488c-x86_64.cache-4
7f97476d7000-7f97476da000 r--s 00000000 fe:01 142978                     /var/cache/fontconfig/4eaf058b0b0e9ae7a516c8d5db143b2f-x86_64.cache-4
7f97476da000-7f97476dc000 r--s 00000000 fe:01 142977                     /var/cache/fontconfig/d5324d870fcb6fde6925cc576c7f8278-x86_64.cache-4
7f97476dc000-7f9747719000 r--s 00000000 fe:01 142976                     /var/cache/fontconfig/4c50721ef3546eb2746d415117216e74-x86_64.cache-4
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7f9747d84000-7f9747d85000 r--s 00000000 fe:01 142809                     /var/cache/fontconfig/e424636388af50ef9639a0f16e5f0d4a-x86_64.cache-4
7f9747d85000-7f9747d90000 r--s 00000000 fe:01 142808                     /var/cache/fontconfig/41b519e25b977b215e4abe1709e102f7-x86_64.cache-4
7f9747d90000-7f9747d91000 r--s 00000000 fe:01 142807                     /var/cache/fontconfig/f69cae16ba8a085d94c47be99adaed02-x86_64.cache-4
7f9747d91000-7f9747d92000 r--s 00000000 fe:01 142806                     /var/cache/fontconfig/a1cead28b916eb5e8a9f7115e80164d3-x86_64.cache-4
7f9747d92000-7f9747d94000 r--s 00000000 fe:01 142805                     /var/cache/fontconfig/e0e88faed98482da20589e6b339038d0-x86_64.cache-4
7f9747d94000-7f9747d96000 r--s 00000000 fe:01 142804                     /var/cache/fontconfig/f78daf97bf6ded3365a98f648103de77-x86_64.cache-4
7f9747d96000-7f9747d97000 r--s 00000000 fe:01 142803                     /var/cache/fontconfig/e07708c12730c753c7c5cf123ed41ee7-x86_64.cache-4
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7f9747d9a000-7f9747da0000 r--s 00000000 fe:01 142801                     /var/cache/fontconfig/ad0310ab6ad93acf2cca852dcf221b47-x86_64.cache-4
7f9747da0000-7f9747da3000 r--s 00000000 fe:01 142800                     /var/cache/fontconfig/3c457729e4e5a9ff04779ca857c5fddb-x86_64.cache-4
7f9747da3000-7f9747da6000 r--s 00000000 fe:01 142799                     /var/cache/fontconfig/9c12ca98c493673165835b63c738c49b-x86_64.cache-4
7f9747da6000-7f9747da7000 r--s 00000000 fe:01 142798                     /var/cache/fontconfig/db6e63289fe30c011702b7c3a928b8b0-x86_64.cache-4
7f9747da7000-7f9747daa000 r--s 00000000 fe:01 142797                     /var/cache/fontconfig/18c25f757222b98f7bacc3fae81146ea-x86_64.cache-4
7f9747daa000-7f9747dac000 r--s 00000000 fe:01 142796                     /var/cache/fontconfig/b3fa9fd32724f0350a02bafe292b0126-x86_64.cache-4
7f9747dac000-7f9747dae000 r--s 00000000 fe:01 142795                     /var/cache/fontconfig/37e3bf11a789d8d924261b25fce532e5-x86_64.cache-4
7f9747dae000-7f9747db5000 r--s 00000000 fe:01 142794                     /var/cache/fontconfig/141a9a0106469e198565079c43f20b37-x86_64.cache-4
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7f9747e2d000-7f9747e30000 r--s 00000000 fe:01 142788                     /var/cache/fontconfig/6cf00169a16fb597391ebfbef639229e-x86_64.cache-4
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7f9747e32000-7f9747e37000 r--s 00000000 fe:01 142786                     /var/cache/fontconfig/03efd6fb310bfa342c884ba2b37408a2-x86_64.cache-4
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7f9747e98000-7f9747eb3000 r--s 00000000 fe:01 142776                     /var/cache/fontconfig/27a3783234a582e9b0f5395f12814b1f-x86_64.cache-4
7f9747eb3000-7f9747f27000 r--s 00000000 fe:01 134581                     /var/cache/fontconfig/17090aa38d5c6f09fb8c5c354938f1d7-x86_64.cache-4
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7f9748155000-7f9748156000 rw-p 00000000 00:00 0 
7f9748156000-7f9748160000 r-xp 00000000 fe:01 1966971                    /usr/lib64/libXcursor.so.1.0.2
7f9748160000-7f974835f000 ---p 0000a000 fe:01 1966971                    /usr/lib64/libXcursor.so.1.0.2
7f974835f000-7f9748360000 r--p 00009000 fe:01 1966971                    /usr/lib64/libXcursor.so.1.0.2
7f9748360000-7f9748361000 rw-p 0000a000 fe:01 1966971                    /usr/lib64/libXcursor.so.1.0.2
7f9748361000-7f9748386000 r-xp 00000000 fe:01 1976206                    /usr/lib64/libgraphite2.so.3.0.1
7f9748386000-7f9748585000 ---p 00025000 fe:01 1976206                    /usr/lib64/libgraphite2.so.3.0.1
7f9748585000-7f9748587000 r--p 00024000 fe:01 1976206                    /usr/lib64/libgraphite2.so.3.0.1
7f9748587000-7f9748588000 rw-p 00026000 fe:01 1976206                    /usr/lib64/libgraphite2.so.3.0.1
7f9748588000-7f974858c000 r-xp 00000000 fe:01 1980935                    /usr/lib64/libuuid.so.1.3.0
7f974858c000-7f974878b000 ---p 00004000 fe:01 1980935                    /usr/lib64/libuuid.so.1.3.0
7f974878b000-7f974878c000 r--p 00003000 fe:01 1980935                    /usr/lib64/libuuid.so.1.3.0
7f974878c000-7f974878d000 rw-p 00004000 fe:01 1980935                    /usr/lib64/libuuid.so.1.3.0
7f974878d000-7f9748792000 r-xp 00000000 fe:01 1966937                    /usr/lib64/libXxf86vm.so.1.0.0
7f9748792000-7f9748991000 ---p 00005000 fe:01 1966937                    /usr/lib64/libXxf86vm.so.1.0.0
7f9748991000-7f9748992000 r--p 00004000 fe:01 1966937                    /usr/lib64/libXxf86vm.so.1.0.0
7f9748992000-7f9748993000 rw-p 00005000 fe:01 1966937                    /usr/lib64/libXxf86vm.so.1.0.0
7f9748993000-7f9748994000 r-xp 00000000 fe:01 1966254                    /usr/lib64/libxshmfence.so.1.0.0
7f9748994000-7f9748b94000 ---p 00001000 fe:01 1966254                    /usr/lib64/libxshmfence.so.1.0.0
7f9748b94000-7f9748b95000 r--p 00001000 fe:01 1966254                    /usr/lib64/libxshmfence.so.1.0.0
7f9748b95000-7f9748b96000 rw-p 00002000 fe:01 1966254                    /usr/lib64/libxshmfence.so.1.0.0
7f9748b96000-7f9748b9b000 r-xp 00000000 fe:01 1977423                    /usr/lib64/libxcb-sync.so.1.0.0
7f9748b9b000-7f9748d9a000 ---p 00005000 fe:01 1977423                    /usr/lib64/libxcb-sync.so.1.0.0
7f9748d9a000-7f9748d9b000 r--p 00004000 fe:01 1977423                    /usr/lib64/libxcb-sync.so.1.0.0
7f9748d9b000-7f9748d9c000 rw-p 00005000 fe:01 1977423                    /usr/lib64/libxcb-sync.so.1.0.0
7f9748d9c000-7f9748d9e000 r-xp 00000000 fe:01 1978006                    /usr/lib64/libxcb-present.so.0.0.0
7f9748d9e000-7f9748f9d000 ---p 00002000 fe:01 1978006                    /usr/lib64/libxcb-present.so.0.0.0
7f9748f9d000-7f9748f9e000 r--p 00001000 fe:01 1978006                    /usr/lib64/libxcb-present.so.0.0.0
7f9748f9e000-7f9748f9f000 rw-p 00002000 fe:01 1978006                    /usr/lib64/libxcb-present.so.0.0.0
7f9748f9f000-7f9748fa1000 r-xp 00000000 fe:01 1978256                    /usr/lib64/libxcb-dri3.so.0.0.0
7f9748fa1000-7f97491a0000 ---p 00002000 fe:01 1978256                    /usr/lib64/libxcb-dri3.so.0.0.0
7f97491a0000-7f97491a1000 r--p 00001000 fe:01 1978256                    /usr/lib64/libxcb-dri3.so.0.0.0
7f97491a1000-7f97491a2000 rw-p 00002000 fe:01 1978256                    /usr/lib64/libxcb-dri3.so.0.0.0
7f97491a2000-7f97491b8000 r-xp 00000000 fe:01 1977931                    /usr/lib64/libxcb-glx.so.0.0.0
7f97491b8000-7f97493b7000 ---p 00016000 fe:01 1977931                    /usr/lib64/libxcb-glx.so.0.0.0
7f97493b7000-7f97493b9000 r--p 00015000 fe:01 1977931                    /usr/lib64/libxcb-glx.so.0.0.0
7f97493b9000-7f97493ba000 rw-p 00017000 fe:01 1977931                    /usr/lib64/libxcb-glx.so.0.0.0
7f97493ba000-7f97493bf000 r-xp 00000000 fe:01 1966088                    /usr/lib64/libXfixes.so.3.1.0
7f97493bf000-7f97495be000 ---p 00005000 fe:01 1966088                    /usr/lib64/libXfixes.so.3.1.0
7f97495be000-7f97495bf000 r--p 00004000 fe:01 1966088                    /usr/lib64/libXfixes.so.3.1.0
7f97495bf000-7f97495c0000 rw-p 00005000 fe:01 1966088                    /usr/lib64/libXfixes.so.3.1.0
7f97495c0000-7f97495c2000 r-xp 00000000 fe:01 1966295                    /usr/lib64/libXdamage.so.1.1.0
7f97495c2000-7f97497c1000 ---p 00002000 fe:01 1966295                    /usr/lib64/libXdamage.so.1.1.0
7f97497c1000-7f97497c2000 r--p 00001000 fe:01 1966295                    /usr/lib64/libXdamage.so.1.1.0
7f97497c2000-7f97497c3000 rw-p 00002000 fe:01 1966295                    /usr/lib64/libXdamage.so.1.1.0
7f97497c3000-7f97497e8000 r-xp 00000000 fe:01 1977250                    /usr/lib64/libglapi.so.0.0.0
7f97497e8000-7f97499e8000 ---p 00025000 fe:01 1977250                    /usr/lib64/libglapi.so.0.0.0
7f97499e8000-7f97499eb000 r--p 00025000 fe:01 1977250                    /usr/lib64/libglapi.so.0.0.0
7f97499eb000-7f97499ec000 rw-p 00028000 fe:01 1977250                    /usr/lib64/libglapi.so.0.0.0
7f97499ec000-7f97499ed000 rw-p 00000000 00:00 0 
7f97499ed000-7f97499f0000 r-xp 00000000 fe:01 1968308                    /usr/lib64/libXau.so.6.0.0
7f97499f0000-7f9749bef000 ---p 00003000 fe:01 1968308                    /usr/lib64/libXau.so.6.0.0
7f9749bef000-7f9749bf0000 r--p 00002000 fe:01 1968308                    /usr/lib64/libXau.so.6.0.0
7f9749bf0000-7f9749bf1000 rw-p 00003000 fe:01 1968308                    /usr/lib64/libXau.so.6.0.0
7f9749bf1000-7f9749bfc000 r-xp 00000000 fe:01 1968340                    /usr/lib64/libdrm.so.2.4.0
7f9749bfc000-7f9749dfb000 ---p 0000b000 fe:01 1968340                    /usr/lib64/libdrm.so.2.4.0
7f9749dfb000-7f9749dfc000 r--p 0000a000 fe:01 1968340                    /usr/lib64/libdrm.so.2.4.0
7f9749dfc000-7f9749dfd000 rw-p 0000b000 fe:01 1968340                    /usr/lib64/libdrm.so.2.4.0
7f9749dfd000-7f9749e0c000 r-xp 00000000 fe:01 1968453                    /usr/lib64/libwayland-server.so.0.1.0
7f9749e0c000-7f974a00c000 ---p 0000f000 fe:01 1968453                    /usr/lib64/libwayland-server.so.0.1.0
7f974a00c000-7f974a00e000 r--p 0000f000 fe:01 1968453                    /usr/lib64/libwayland-server.so.0.1.0
7f974a00e000-7f974a00f000 rw-p 00011000 fe:01 1968453                    /usr/lib64/libwayland-server.so.0.1.0
7f974a00f000-7f974a01b000 r-xp 00000000 fe:01 1967071                    /usr/lib64/libwayland-client.so.0.3.0
7f974a01b000-7f974a21a000 ---p 0000c000 fe:01 1967071                    /usr/lib64/libwayland-client.so.0.3.0
7f974a21a000-7f974a21c000 r--p 0000b000 fe:01 1967071                    /usr/lib64/libwayland-client.so.0.3.0
7f974a21c000-7f974a21d000 rw-p 0000d000 fe:01 1967071                    /usr/lib64/libwayland-client.so.0.3.0
7f974a21d000-7f974a229000 r-xp 00000000 fe:01 1967097                    /usr/lib64/libgbm.so.1.0.0
7f974a229000-7f974a429000 ---p 0000c000 fe:01 1967097                    /usr/lib64/libgbm.so.1.0.0
7f974a429000-7f974a42a000 r--p 0000c000 fe:01 1967097                    /usr/lib64/libgbm.so.1.0.0
7f974a42a000-7f974a42b000 rw-p 0000d000 fe:01 1967097                    /usr/lib64/libgbm.so.1.0.0
7f974a42b000-7f974a431000 r-xp 00000000 fe:01 1977547                    /usr/lib64/libxcb-xfixes.so.0.0.0
7f974a431000-7f974a630000 ---p 00006000 fe:01 1977547                    /usr/lib64/libxcb-xfixes.so.0.0.0
7f974a630000-7f974a631000 r--p 00005000 fe:01 1977547                    /usr/lib64/libxcb-xfixes.so.0.0.0
7f974a631000-7f974a632000 rw-p 00006000 fe:01 1977547                    /usr/lib64/libxcb-xfixes.so.0.0.0
7f974a632000-7f974a636000 r-xp 00000000 fe:01 1977932                    /usr/lib64/libxcb-dri2.so.0.0.0
7f974a636000-7f974a835000 ---p 00004000 fe:01 1977932                    /usr/lib64/libxcb-dri2.so.0.0.0
7f974a835000-7f974a836000 r--p 00003000 fe:01 1977932                    /usr/lib64/libxcb-dri2.so.0.0.0
7f974a836000-7f974a837000 rw-p 00004000 fe:01 1977932                    /usr/lib64/libxcb-dri2.so.0.0.0
7f974a837000-7f974a838000 r-xp 00000000 fe:01 1977512                    /usr/lib64/libX11-xcb.so.1.0.0
7f974a838000-7f974aa37000 ---p 00001000 fe:01 1977512                    /usr/lib64/libX11-xcb.so.1.0.0
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7f974aa38000-7f974aa39000 rw-p 00001000 fe:01 1977512                    /usr/lib64/libX11-xcb.so.1.0.0
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7f9769a0f000-7f9769a12000 r--s 00000000 fe:01 142778                     /var/cache/fontconfig/26ba52b4ad2b884e09b2ecee609fe7da-x86_64.cache-4
7f9769a12000-7f9769a21000 r--s 00000000 fe:01 134577                     /var/cache/fontconfig/d42e465d3d703735db7577b46e8d64be-x86_64.cache-4
7f9769a21000-7f9769a46000 r--p 00000000 fe:01 2372869                    /usr/share/locale/cs/LC_MESSAGES/libc.mo
7f9769a46000-7f9769a7b000 r--s 00000000 00:11 26644                      /run/nscd/passwd
7f9769a7b000-7f9769b87000 rw-p 00000000 00:00 0
7f9769b87000-7f9769bc6000 r--p 00000000 fe:01 3146605                    /usr/lib/locale/cs_CZ.utf8/LC_CTYPE
7f9769bc6000-7f9769bd1000 rw-p 00000000 00:00 0
7f9769bd1000-7f9769bd2000 r--s 00000000 fe:01 142790                     /var/cache/fontconfig/3b4b00f4c8729b30bd8cdecb656b4e7b-x86_64.cache-4
7f9769bd2000-7f9769bd3000 r--s 00000000 fe:01 142781                     /var/cache/fontconfig/0a206c5b12450cf4d909a9c36ddc121b-x86_64.cache-4
7f9769bd3000-7f9769bd4000 r--s 00000000 fe:01 142775                     /var/cache/fontconfig/457be539316e49d90db894a2e1bcaebe-x86_64.cache-4
7f9769bd4000-7f9769bd5000 r--s 00000000 fe:01 142774                     /var/cache/fontconfig/f8b76d193bb79c238a2703949d308530-x86_64.cache-4
7f9769bd5000-7f9769bd9000 r--s 00000000 fe:01 142773                     /var/cache/fontconfig/55e3aa00b6b2f1727d4400f2004120e9-x86_64.cache-4
7f9769bd9000-7f9769bda000 r--s 00000000 fe:01 142772                     /var/cache/fontconfig/913dda57dbe22c714e9ee05535b1786a-x86_64.cache-4
7f9769bda000-7f9769be3000 r--s 00000000 fe:01 134583                     /var/cache/fontconfig/d62e99ef547d1d24cdb1bd22ec1a2976-x86_64.cache-4
7f9769be3000-7f9769be4000 rw-p 00000000 00:00 0
7f9769be4000-7f9769be5000 r--p 00000000 fe:01 3150917                    /usr/lib/locale/cs_CZ.utf8/LC_MEASUREMENT
7f9769be5000-7f9769be6000 r--p 00000000 fe:01 3146609                    /usr/lib/locale/cs_CZ.utf8/LC_PAPER
7f9769be6000-7f9769be7000 r--p 00000000 fe:01 3028874                    /usr/lib/locale/cs_CZ.utf8/LC_MONETARY
7f9769be7000-7f9769be8000 r--p 00000000 fe:01 3028879                    /usr/lib/locale/cs_CZ.utf8/LC_TIME
7f9769be8000-7f9769c04000 r--p 00000000 fe:01 3146663                    /usr/lib/locale/cs_CZ.utf8/LC_COLLATE
7f9769c04000-7f9769c0b000 r--s 00000000 fe:01 2103454                    /usr/lib64/gconv/gconv-modules.cache
7f9769c0b000-7f9769c0c000 r--p 00000000 fe:01 3028803                    /usr/lib/locale/cs_CZ.utf8/LC_MESSAGES/SYS_LC_MESSAGES
7f9769c0c000-7f9769c0d000 rw-p 00000000 00:00 0
7f9769c0d000-7f9769c0e000 r--p 00020000 fe:01 3148005                    /lib64/ld-2.19.so
7f9769c0e000-7f9769c0f000 rw-p 00021000 fe:01 3148005                    /lib64/ld-2.19.so
7f9769c0f000-7f9769c10000 rw-p 00000000 00:00 0
7ffd5dba9000-7ffd5dbdc000 rw-p 00000000 00:00 0                          [stack]
7ffd5dbf6000-7ffd5dbf8000 r-xp 00000000 00:00 0                          [vdso]
7ffd5dbf8000-7ffd5dbfa000 r--p 00000000 00:00 0                          [vvar]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
SIGABRT

Crashing this time
If I run it like

metab.pos.root1.concat.mrbayes.nmds <-
  metaMDS(comm=scale(x=metab.pos.root1.concat.mrbayes, center=TRUE, 
  scale=TRUE), distance="manhattan", k=2, trymax=10000, engine="monoMDS", 
  autotransform=FALSE, noshare=FALSE, stepacross=FALSE, wascores=FALSE, 
  expand=FALSE, plot=TRUE)

it works fine, so that the problem can be within the data.

V-Z commented Jan 4, 2016

Hello

  1. I can provide the file, but I'd like to avoid public posting on the "wild" internet... What would be the best way for You?
  2. In plain terminal window it runs like this:
> metab.pos.root1.concat.mrbayes.nmds <- 
  metaMDS(comm=metab.pos.root1.concat.mrbayes, distance="manhattan", k=2, 
  trymax=10000, engine="monoMDS", autotransform=FALSE, noshare=FALSE, 
  stepacross=FALSE, wascores=FALSE, expand=FALSE, plot=TRUE)
*** Error in `/usr/lib64/R/bin/exec/R': double free or corruption (!prev): 0x000000000d671080 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7283f)[0x7f9768eb083f]
/lib64/libc.so.6(+0x780ae)[0x7f9768eb60ae]
/lib64/libc.so.6(+0x78db6)[0x7f9768eb6db6]
/usr/lib64/R/lib/libR.so(+0x149821)[0x7f976954b821]
/usr/lib64/R/lib/libR.so(CONS_NR+0x8c)[0x7f976954d12c]
/usr/lib64/R/lib/libR.so(+0x10cfaa)[0x7f976950efaa]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(+0x14f3a4)[0x7f97695513a4]
/usr/lib64/R/lib/libR.so(+0x14f7e0)[0x7f97695517e0]
/usr/lib64/R/lib/libR.so(+0x14fab2)[0x7f9769551ab2]
/usr/lib64/R/lib/libR.so(+0x10ce44)[0x7f976950ee44]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(+0x11400c)[0x7f976951600c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(R_forceAndCall+0x14c)[0x7f97695210ac]
/usr/lib64/R/lib/libR.so(+0x7a69a)[0x7f976947c69a]
/usr/lib64/R/lib/libR.so(+0x14d689)[0x7f976954f689]
/usr/lib64/R/lib/libR.so(+0x10ce44)[0x7f976950ee44]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(+0x11400c)[0x7f976951600c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x160)[0x7f976951d4b0]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(+0x1090c6)[0x7f976950b0c6]
/usr/lib64/R/lib/libR.so(+0x1ac521)[0x7f97695ae521]
/usr/lib64/R/lib/libR.so(Rf_eval+0x643)[0x7f976951d993]
/usr/lib64/R/lib/libR.so(+0x11ebce)[0x7f9769520bce]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(+0x11daf0)[0x7f976951faf0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2df)[0x7f976951d62f]
/usr/lib64/R/lib/libR.so(+0x11ebce)[0x7f9769520bce]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(+0x11daf0)[0x7f976951faf0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(+0x11daf0)[0x7f976951faf0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x597)[0x7f976951eb87]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2df)[0x7f976951d62f]
/usr/lib64/R/lib/libR.so(+0x11ebce)[0x7f9769520bce]
/usr/lib64/R/lib/libR.so(Rf_eval+0x503)[0x7f976951d853]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x232)[0x7f97695449c2]
/usr/lib64/R/lib/libR.so(+0x142d11)[0x7f9769544d11]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0x44)[0x7f9769544dc4]
/usr/lib64/R/bin/exec/R(main+0x1b)[0x40089b]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f9768e5fb05]
/usr/lib64/R/bin/exec/R[0x4008cb]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fe:01 3028083                            /usr/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 fe:01 3028083                            /usr/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 fe:01 3028083                            /usr/lib64/R/bin/exec/R
01226000-11916000 rw-p 00000000 00:00 0                                  [heap]
7f97470ac000-7f97470ce000 r--p 00000000 fe:01 2512551                    /usr/share/fonts/texlive-tex-gyre/texgyreheros-bold.otf
7f97470ce000-7f97470ef000 r--p 00000000 fe:01 2512554                    /usr/share/fonts/texlive-tex-gyre/texgyreheros-regular.otf
7f97470ef000-7f97470f2000 r-xp 00000000 fe:01 1967065                    /usr/lib64/pango/1.8.0/modules/pango-basic-fc.so
7f97470f2000-7f97472f1000 ---p 00003000 fe:01 1967065                    /usr/lib64/pango/1.8.0/modules/pango-basic-fc.so
7f97472f1000-7f97472f2000 r--p 00002000 fe:01 1967065                    /usr/lib64/pango/1.8.0/modules/pango-basic-fc.so
7f97472f2000-7f97472f3000 rw-p 00003000 fe:01 1967065                    /usr/lib64/pango/1.8.0/modules/pango-basic-fc.so
7f97472f3000-7f974730d000 r--s 00000000 fe:03 2149445020                 /home/vojta/.cache/fontconfig/81ee38b02c7c21d5c726a9a4eca0938f-x86_64.cache-4
7f974730d000-7f974730f000 r--s 00000000 fe:03 2149445019                 /home/vojta/.cache/fontconfig/97f77127cac57354e0504a53f5e6468d-x86_64.cache-4
7f974730f000-7f9747318000 r--s 00000000 fe:03 2149445018                 /home/vojta/.cache/fontconfig/f92bba027e85f20cf4ed008ecdc40abd-x86_64.cache-4
7f9747318000-7f9747321000 r--s 00000000 fe:03 2149445011                 /home/vojta/.cache/fontconfig/1adb6c01d5471348247f3f21c44e3b1e-x86_64.cache-4
7f9747321000-7f9747324000 r--s 00000000 fe:03 2149445010                 /home/vojta/.cache/fontconfig/2a2f4d248b40c6231a06619e2d3c41e1-x86_64.cache-4
7f9747324000-7f9747344000 r--s 00000000 fe:03 2149445009                 /home/vojta/.cache/fontconfig/cdf663b38b074286b0594bd8aa823790-x86_64.cache-4
7f9747344000-7f9747395000 r--s 00000000 fe:03 2149445008                 /home/vojta/.cache/fontconfig/ec6411fee082fe8de5c80b3b3b428adc-x86_64.cache-4
7f9747395000-7f97473a1000 r--s 00000000 fe:03 2149445007                 /home/vojta/.cache/fontconfig/ec30bf3c9389a9130f071263ba010d07-x86_64.cache-4
7f97473a1000-7f97473a5000 r--s 00000000 fe:03 2149391572                 /home/vojta/.cache/fontconfig/101736a6b19f07022070fe0561c5bd7a-x86_64.cache-4
7f97473a5000-7f97473b9000 r--s 00000000 fe:03 2149391571                 /home/vojta/.cache/fontconfig/b1745dcecbf8e43497254b728d0b076d-x86_64.cache-4
7f97473b9000-7f97473c5000 r--s 00000000 fe:03 2149391570                 /home/vojta/.cache/fontconfig/af0fc35b89e3122fd2842bcb6e895a1e-x86_64.cache-4
7f97473c5000-7f97473eb000 r--s 00000000 fe:03 2149391569                 /home/vojta/.cache/fontconfig/e034a016a6b68e1a54567066b496ab95-x86_64.cache-4
7f97473eb000-7f9747406000 r--s 00000000 fe:03 2149391568                 /home/vojta/.cache/fontconfig/4a507c0bfc5b5d9f456dc4a69df4ec80-x86_64.cache-4
7f9747406000-7f9747425000 r--s 00000000 fe:03 2149391563                 /home/vojta/.cache/fontconfig/5dcc5d8d93de3eec1837020af8cae73a-x86_64.cache-4
7f9747425000-7f9747438000 r--s 00000000 fe:03 2149391562                 /home/vojta/.cache/fontconfig/21e296f96eb206ccd855b9b28328fe94-x86_64.cache-4
7f9747438000-7f974743c000 r--s 00000000 fe:03 2149391561                 /home/vojta/.cache/fontconfig/30a748b12d5d4f614914a3e4cd358af7-x86_64.cache-4
7f974743c000-7f9747450000 r--s 00000000 fe:03 2149391560                 /home/vojta/.cache/fontconfig/c87031a1de2576bfadad5a26174bdef2-x86_64.cache-4
7f9747450000-7f974746d000 r--s 00000000 fe:03 2149391559                 /home/vojta/.cache/fontconfig/43a72e8cb0767c982e1f312b37fca0c1-x86_64.cache-4
7f974746d000-7f97474ab000 r--s 00000000 fe:03 2149391558                 /home/vojta/.cache/fontconfig/073a9e98eb7e02f6711eb18f3cce0a44-x86_64.cache-4
7f97474ab000-7f97474e2000 r--s 00000000 fe:03 2149391557                 /home/vojta/.cache/fontconfig/b885105119255e05554f946da59e8821-x86_64.cache-4
7f97474e2000-7f97474fd000 r--s 00000000 fe:03 2149391556                 /home/vojta/.cache/fontconfig/72ac980c2d4e53000c7ba1ae4696dd09-x86_64.cache-4
7f97474fd000-7f974751a000 r--s 00000000 fe:03 2149391555                 /home/vojta/.cache/fontconfig/1a823246853fcc6ceb351b48cf1cdbfa-x86_64.cache-4
7f974751a000-7f974757c000 r--s 00000000 fe:03 2149391553                 /home/vojta/.cache/fontconfig/3dcc8a8d60036b1dffde63ffca89d63a-x86_64.cache-4
7f974757c000-7f97475bd000 r--s 00000000 fe:03 2149391552                 /home/vojta/.cache/fontconfig/1be83550c1aaad2ea620533c141c798e-x86_64.cache-4
7f97475bd000-7f97475e6000 r--s 00000000 fe:03 2149391538                 /home/vojta/.cache/fontconfig/49b36a0a829654628f9a05a7ef277292-x86_64.cache-4
7f97475e6000-7f97475e9000 r--s 00000000 fe:01 132356                     /var/cache/fontconfig/d458be102e54cf534d1eef0dcbb02d07-x86_64.cache-4
7f97475e9000-7f97476ca000 r--s 00000000 fe:01 142984                     /var/cache/fontconfig/7ef2298fde41cc6eeb7af42e48b7d293-x86_64.cache-4
7f97476ca000-7f97476cb000 r--s 00000000 fe:01 142983                     /var/cache/fontconfig/fb8341411dac03919a6f30c61d3ee363-x86_64.cache-4
7f97476cb000-7f97476cc000 r--s 00000000 fe:01 142982                     /var/cache/fontconfig/31d258c26849b1f3b28618b43aef0df4-x86_64.cache-4
7f97476cc000-7f97476cd000 r--s 00000000 fe:01 142981                     /var/cache/fontconfig/8aefcdceaf7081f7a76e5c97af6ee8fa-x86_64.cache-4
7f97476cd000-7f97476d4000 r--s 00000000 fe:01 142980                     /var/cache/fontconfig/2b4c5ecca09e2930001c0780a4ec3c17-x86_64.cache-4
7f97476d4000-7f97476d7000 r--s 00000000 fe:01 142979                     /var/cache/fontconfig/72cfb3223c4327e0479d681c7a7c488c-x86_64.cache-4
7f97476d7000-7f97476da000 r--s 00000000 fe:01 142978                     /var/cache/fontconfig/4eaf058b0b0e9ae7a516c8d5db143b2f-x86_64.cache-4
7f97476da000-7f97476dc000 r--s 00000000 fe:01 142977                     /var/cache/fontconfig/d5324d870fcb6fde6925cc576c7f8278-x86_64.cache-4
7f97476dc000-7f9747719000 r--s 00000000 fe:01 142976                     /var/cache/fontconfig/4c50721ef3546eb2746d415117216e74-x86_64.cache-4
7f9747719000-7f9747739000 r--s 00000000 fe:01 142975                     /var/cache/fontconfig/57f8ef3d0e053c7736a4f21b064a90d1-x86_64.cache-4
7f9747739000-7f974774c000 r--s 00000000 fe:01 142974                     /var/cache/fontconfig/f37b5b8c806b42a8fede030aff7185af-x86_64.cache-4
7f974774c000-7f974775d000 r--s 00000000 fe:01 142973                     /var/cache/fontconfig/a3d9fc77b234768faa6666bd507d86ff-x86_64.cache-4
7f974775d000-7f974775f000 r--s 00000000 fe:01 142972                     /var/cache/fontconfig/b7c4333675e0ca84d9af12927db7f5e5-x86_64.cache-4
7f974775f000-7f9747767000 r--s 00000000 fe:01 142971                     /var/cache/fontconfig/608cbb6b07224ca9644d1e29768c82b7-x86_64.cache-4
7f9747767000-7f974776a000 r--s 00000000 fe:01 142970                     /var/cache/fontconfig/30e4d7c8cc6ed7f380c9cdeca050b132-x86_64.cache-4
7f974776a000-7f9747775000 r--s 00000000 fe:01 142969                     /var/cache/fontconfig/b6565330f3cba832d0b61036a78e2648-x86_64.cache-4
7f9747775000-7f9747778000 r--s 00000000 fe:01 142968                     /var/cache/fontconfig/d5a1373a263cdb8790605d67526a2542-x86_64.cache-4
7f9747778000-7f9747784000 r--s 00000000 fe:01 142967                     /var/cache/fontconfig/c7065e1c7dd0f6b2e3062b6686e0f20f-x86_64.cache-4
7f9747784000-7f9747785000 r--s 00000000 fe:01 142966                     /var/cache/fontconfig/be397df775f3421f8908a388f6fd3b48-x86_64.cache-4
7f9747785000-7f9747798000 r--s 00000000 fe:01 142965                     /var/cache/fontconfig/aea8c537c52b25f9610906e9b4a66191-x86_64.cache-4
7f9747798000-7f974779a000 r--s 00000000 fe:01 142964                     /var/cache/fontconfig/fc21ea1fe6724c15d7343bb68dd7155d-x86_64.cache-4
7f974779a000-7f974779b000 r--s 00000000 fe:01 142963                     /var/cache/fontconfig/af53229f807a5ca02c3447592c0fb5d0-x86_64.cache-4
7f974779b000-7f974779d000 r--s 00000000 fe:01 142962                     /var/cache/fontconfig/2f36c32c6ec3ca87de89a6eb757fa974-x86_64.cache-4
7f974779d000-7f97477b3000 r--s 00000000 fe:01 142961                     /var/cache/fontconfig/b5c7c63143a222d0fb41621bb05e4dd9-x86_64.cache-4
7f97477b3000-7f97477b4000 r--s 00000000 fe:01 142960                     /var/cache/fontconfig/18f7cb0d58aec49a72ec28ba27e364bf-x86_64.cache-4
7f97477b4000-7f97477b5000 r--s 00000000 fe:01 142959                     /var/cache/fontconfig/b248374641ab374d27a47787d24a662a-x86_64.cache-4
7f97477b5000-7f97477b6000 r--s 00000000 fe:01 142958                     /var/cache/fontconfig/60a6a8e2eba8f5e339200398e3020a89-x86_64.cache-4
7f97477b6000-7f97477b7000 r--s 00000000 fe:01 142957                     /var/cache/fontconfig/4aa8d405fbd08bf8a2499b752f9d2fc7-x86_64.cache-4
7f97477b7000-7f97477b9000 r--s 00000000 fe:01 142956                     /var/cache/fontconfig/27de980c8d701e5bddda670399e94a62-x86_64.cache-4
7f97477b9000-7f97477c5000 r--s 00000000 fe:01 142955                     /var/cache/fontconfig/30244d759331c0a54b813efbf0e633d3-x86_64.cache-4
7f97477c5000-7f97477c6000 r--s 00000000 fe:01 142954                     /var/cache/fontconfig/becb74c7d9f440667c883784c464f41c-x86_64.cache-4
7f97477c6000-7f97477c7000 r--s 00000000 fe:01 142953                     /var/cache/fontconfig/62706d4a764b4a084c9db4ad3bdf9660-x86_64.cache-4
7f97477c7000-7f97477d0000 r--s 00000000 fe:01 142952                     /var/cache/fontconfig/2ac5805a383932d69a44bdd73a6a8799-x86_64.cache-4
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7f9747bee000-7f9747c5b000 r--s 00000000 fe:01 142822                     /var/cache/fontconfig/54588b7ff0e34721d54765917d634828-x86_64.cache-4
7f9747c5b000-7f9747c71000 r--s 00000000 fe:01 142821                     /var/cache/fontconfig/c60874c6d6de091a3b7bec468be39454-x86_64.cache-4
7f9747c71000-7f9747c77000 r--s 00000000 fe:01 142820                     /var/cache/fontconfig/957d2f7c3f4fec4572f6ddaf637c8d48-x86_64.cache-4
7f9747c77000-7f9747c78000 r--s 00000000 fe:01 142819                     /var/cache/fontconfig/f32d9b32cbcfc1628160503b2eb0ca01-x86_64.cache-4
7f9747c78000-7f9747c7d000 r--s 00000000 fe:01 142818                     /var/cache/fontconfig/d9604822faca8b18491a0116e1b11b52-x86_64.cache-4
7f9747c7d000-7f9747c7e000 r--s 00000000 fe:01 142817                     /var/cache/fontconfig/a095e39a2aaae6c4fe0aa9a01f032375-x86_64.cache-4
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7f9747c80000-7f9747c81000 r--s 00000000 fe:01 142815                     /var/cache/fontconfig/82ebeecdabfef641cb59f0445aac153c-x86_64.cache-4
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7f9747d80000-7f9747d81000 r--s 00000000 fe:01 142812                     /var/cache/fontconfig/8c13987400cb57444aa5c801cf98e016-x86_64.cache-4
7f9747d81000-7f9747d83000 r--s 00000000 fe:01 142811                     /var/cache/fontconfig/b07de5bdd8f9916199a933a7246b6bc1-x86_64.cache-4
7f9747d83000-7f9747d84000 r--s 00000000 fe:01 142810                     /var/cache/fontconfig/8f3d9a15aa3a9d7644250711f7edeba5-x86_64.cache-4
7f9747d84000-7f9747d85000 r--s 00000000 fe:01 142809                     /var/cache/fontconfig/e424636388af50ef9639a0f16e5f0d4a-x86_64.cache-4
7f9747d85000-7f9747d90000 r--s 00000000 fe:01 142808                     /var/cache/fontconfig/41b519e25b977b215e4abe1709e102f7-x86_64.cache-4
7f9747d90000-7f9747d91000 r--s 00000000 fe:01 142807                     /var/cache/fontconfig/f69cae16ba8a085d94c47be99adaed02-x86_64.cache-4
7f9747d91000-7f9747d92000 r--s 00000000 fe:01 142806                     /var/cache/fontconfig/a1cead28b916eb5e8a9f7115e80164d3-x86_64.cache-4
7f9747d92000-7f9747d94000 r--s 00000000 fe:01 142805                     /var/cache/fontconfig/e0e88faed98482da20589e6b339038d0-x86_64.cache-4
7f9747d94000-7f9747d96000 r--s 00000000 fe:01 142804                     /var/cache/fontconfig/f78daf97bf6ded3365a98f648103de77-x86_64.cache-4
7f9747d96000-7f9747d97000 r--s 00000000 fe:01 142803                     /var/cache/fontconfig/e07708c12730c753c7c5cf123ed41ee7-x86_64.cache-4
7f9747d97000-7f9747d9a000 r--s 00000000 fe:01 142802                     /var/cache/fontconfig/13f4011773c8c35170b3c1ee128a368e-x86_64.cache-4
7f9747d9a000-7f9747da0000 r--s 00000000 fe:01 142801                     /var/cache/fontconfig/ad0310ab6ad93acf2cca852dcf221b47-x86_64.cache-4
7f9747da0000-7f9747da3000 r--s 00000000 fe:01 142800                     /var/cache/fontconfig/3c457729e4e5a9ff04779ca857c5fddb-x86_64.cache-4
7f9747da3000-7f9747da6000 r--s 00000000 fe:01 142799                     /var/cache/fontconfig/9c12ca98c493673165835b63c738c49b-x86_64.cache-4
7f9747da6000-7f9747da7000 r--s 00000000 fe:01 142798                     /var/cache/fontconfig/db6e63289fe30c011702b7c3a928b8b0-x86_64.cache-4
7f9747da7000-7f9747daa000 r--s 00000000 fe:01 142797                     /var/cache/fontconfig/18c25f757222b98f7bacc3fae81146ea-x86_64.cache-4
7f9747daa000-7f9747dac000 r--s 00000000 fe:01 142796                     /var/cache/fontconfig/b3fa9fd32724f0350a02bafe292b0126-x86_64.cache-4
7f9747dac000-7f9747dae000 r--s 00000000 fe:01 142795                     /var/cache/fontconfig/37e3bf11a789d8d924261b25fce532e5-x86_64.cache-4
7f9747dae000-7f9747db5000 r--s 00000000 fe:01 142794                     /var/cache/fontconfig/141a9a0106469e198565079c43f20b37-x86_64.cache-4
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7f9747db6000-7f9747dbc000 r--s 00000000 fe:01 142791                     /var/cache/fontconfig/fb6a1545ec1db38237cb07710395501c-x86_64.cache-4
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7f9747e2d000-7f9747e30000 r--s 00000000 fe:01 142788                     /var/cache/fontconfig/6cf00169a16fb597391ebfbef639229e-x86_64.cache-4
7f9747e30000-7f9747e32000 r--s 00000000 fe:01 142787                     /var/cache/fontconfig/1f8a31a9e1fd742a6671e1df681eabc5-x86_64.cache-4
7f9747e32000-7f9747e37000 r--s 00000000 fe:01 142786                     /var/cache/fontconfig/03efd6fb310bfa342c884ba2b37408a2-x86_64.cache-4
7f9747e37000-7f9747e39000 r--s 00000000 fe:01 142785                     /var/cache/fontconfig/366820697b07ceaea425e1d8b6aab004-x86_64.cache-4
7f9747e39000-7f9747e60000 r--s 00000000 fe:01 142779                     /var/cache/fontconfig/d4fe60d93f2935cff7814e4a010063a1-x86_64.cache-4
7f9747e60000-7f9747e98000 r--s 00000000 fe:01 142777                     /var/cache/fontconfig/2942833114b0ae98dceeb5b92c6f203d-x86_64.cache-4
7f9747e98000-7f9747eb3000 r--s 00000000 fe:01 142776                     /var/cache/fontconfig/27a3783234a582e9b0f5395f12814b1f-x86_64.cache-4
7f9747eb3000-7f9747f27000 r--s 00000000 fe:01 134581                     /var/cache/fontconfig/17090aa38d5c6f09fb8c5c354938f1d7-x86_64.cache-4
7f9747f27000-7f9747f9b000 r--s 00000000 fe:01 132355                     /var/cache/fontconfig/df311e82a1a24c41a75c2c930223552e-x86_64.cache-4
7f9748155000-7f9748156000 rw-p 00000000 00:00 0 
7f9748156000-7f9748160000 r-xp 00000000 fe:01 1966971                    /usr/lib64/libXcursor.so.1.0.2
7f9748160000-7f974835f000 ---p 0000a000 fe:01 1966971                    /usr/lib64/libXcursor.so.1.0.2
7f974835f000-7f9748360000 r--p 00009000 fe:01 1966971                    /usr/lib64/libXcursor.so.1.0.2
7f9748360000-7f9748361000 rw-p 0000a000 fe:01 1966971                    /usr/lib64/libXcursor.so.1.0.2
7f9748361000-7f9748386000 r-xp 00000000 fe:01 1976206                    /usr/lib64/libgraphite2.so.3.0.1
7f9748386000-7f9748585000 ---p 00025000 fe:01 1976206                    /usr/lib64/libgraphite2.so.3.0.1
7f9748585000-7f9748587000 r--p 00024000 fe:01 1976206                    /usr/lib64/libgraphite2.so.3.0.1
7f9748587000-7f9748588000 rw-p 00026000 fe:01 1976206                    /usr/lib64/libgraphite2.so.3.0.1
7f9748588000-7f974858c000 r-xp 00000000 fe:01 1980935                    /usr/lib64/libuuid.so.1.3.0
7f974858c000-7f974878b000 ---p 00004000 fe:01 1980935                    /usr/lib64/libuuid.so.1.3.0
7f974878b000-7f974878c000 r--p 00003000 fe:01 1980935                    /usr/lib64/libuuid.so.1.3.0
7f974878c000-7f974878d000 rw-p 00004000 fe:01 1980935                    /usr/lib64/libuuid.so.1.3.0
7f974878d000-7f9748792000 r-xp 00000000 fe:01 1966937                    /usr/lib64/libXxf86vm.so.1.0.0
7f9748792000-7f9748991000 ---p 00005000 fe:01 1966937                    /usr/lib64/libXxf86vm.so.1.0.0
7f9748991000-7f9748992000 r--p 00004000 fe:01 1966937                    /usr/lib64/libXxf86vm.so.1.0.0
7f9748992000-7f9748993000 rw-p 00005000 fe:01 1966937                    /usr/lib64/libXxf86vm.so.1.0.0
7f9748993000-7f9748994000 r-xp 00000000 fe:01 1966254                    /usr/lib64/libxshmfence.so.1.0.0
7f9748994000-7f9748b94000 ---p 00001000 fe:01 1966254                    /usr/lib64/libxshmfence.so.1.0.0
7f9748b94000-7f9748b95000 r--p 00001000 fe:01 1966254                    /usr/lib64/libxshmfence.so.1.0.0
7f9748b95000-7f9748b96000 rw-p 00002000 fe:01 1966254                    /usr/lib64/libxshmfence.so.1.0.0
7f9748b96000-7f9748b9b000 r-xp 00000000 fe:01 1977423                    /usr/lib64/libxcb-sync.so.1.0.0
7f9748b9b000-7f9748d9a000 ---p 00005000 fe:01 1977423                    /usr/lib64/libxcb-sync.so.1.0.0
7f9748d9a000-7f9748d9b000 r--p 00004000 fe:01 1977423                    /usr/lib64/libxcb-sync.so.1.0.0
7f9748d9b000-7f9748d9c000 rw-p 00005000 fe:01 1977423                    /usr/lib64/libxcb-sync.so.1.0.0
7f9748d9c000-7f9748d9e000 r-xp 00000000 fe:01 1978006                    /usr/lib64/libxcb-present.so.0.0.0
7f9748d9e000-7f9748f9d000 ---p 00002000 fe:01 1978006                    /usr/lib64/libxcb-present.so.0.0.0
7f9748f9d000-7f9748f9e000 r--p 00001000 fe:01 1978006                    /usr/lib64/libxcb-present.so.0.0.0
7f9748f9e000-7f9748f9f000 rw-p 00002000 fe:01 1978006                    /usr/lib64/libxcb-present.so.0.0.0
7f9748f9f000-7f9748fa1000 r-xp 00000000 fe:01 1978256                    /usr/lib64/libxcb-dri3.so.0.0.0
7f9748fa1000-7f97491a0000 ---p 00002000 fe:01 1978256                    /usr/lib64/libxcb-dri3.so.0.0.0
7f97491a0000-7f97491a1000 r--p 00001000 fe:01 1978256                    /usr/lib64/libxcb-dri3.so.0.0.0
7f97491a1000-7f97491a2000 rw-p 00002000 fe:01 1978256                    /usr/lib64/libxcb-dri3.so.0.0.0
7f97491a2000-7f97491b8000 r-xp 00000000 fe:01 1977931                    /usr/lib64/libxcb-glx.so.0.0.0
7f97491b8000-7f97493b7000 ---p 00016000 fe:01 1977931                    /usr/lib64/libxcb-glx.so.0.0.0
7f97493b7000-7f97493b9000 r--p 00015000 fe:01 1977931                    /usr/lib64/libxcb-glx.so.0.0.0
7f97493b9000-7f97493ba000 rw-p 00017000 fe:01 1977931                    /usr/lib64/libxcb-glx.so.0.0.0
7f97493ba000-7f97493bf000 r-xp 00000000 fe:01 1966088                    /usr/lib64/libXfixes.so.3.1.0
7f97493bf000-7f97495be000 ---p 00005000 fe:01 1966088                    /usr/lib64/libXfixes.so.3.1.0
7f97495be000-7f97495bf000 r--p 00004000 fe:01 1966088                    /usr/lib64/libXfixes.so.3.1.0
7f97495bf000-7f97495c0000 rw-p 00005000 fe:01 1966088                    /usr/lib64/libXfixes.so.3.1.0
7f97495c0000-7f97495c2000 r-xp 00000000 fe:01 1966295                    /usr/lib64/libXdamage.so.1.1.0
7f97495c2000-7f97497c1000 ---p 00002000 fe:01 1966295                    /usr/lib64/libXdamage.so.1.1.0
7f97497c1000-7f97497c2000 r--p 00001000 fe:01 1966295                    /usr/lib64/libXdamage.so.1.1.0
7f97497c2000-7f97497c3000 rw-p 00002000 fe:01 1966295                    /usr/lib64/libXdamage.so.1.1.0
7f97497c3000-7f97497e8000 r-xp 00000000 fe:01 1977250                    /usr/lib64/libglapi.so.0.0.0
7f97497e8000-7f97499e8000 ---p 00025000 fe:01 1977250                    /usr/lib64/libglapi.so.0.0.0
7f97499e8000-7f97499eb000 r--p 00025000 fe:01 1977250                    /usr/lib64/libglapi.so.0.0.0
7f97499eb000-7f97499ec000 rw-p 00028000 fe:01 1977250                    /usr/lib64/libglapi.so.0.0.0
7f97499ec000-7f97499ed000 rw-p 00000000 00:00 0 
7f97499ed000-7f97499f0000 r-xp 00000000 fe:01 1968308                    /usr/lib64/libXau.so.6.0.0
7f97499f0000-7f9749bef000 ---p 00003000 fe:01 1968308                    /usr/lib64/libXau.so.6.0.0
7f9749bef000-7f9749bf0000 r--p 00002000 fe:01 1968308                    /usr/lib64/libXau.so.6.0.0
7f9749bf0000-7f9749bf1000 rw-p 00003000 fe:01 1968308                    /usr/lib64/libXau.so.6.0.0
7f9749bf1000-7f9749bfc000 r-xp 00000000 fe:01 1968340                    /usr/lib64/libdrm.so.2.4.0
7f9749bfc000-7f9749dfb000 ---p 0000b000 fe:01 1968340                    /usr/lib64/libdrm.so.2.4.0
7f9749dfb000-7f9749dfc000 r--p 0000a000 fe:01 1968340                    /usr/lib64/libdrm.so.2.4.0
7f9749dfc000-7f9749dfd000 rw-p 0000b000 fe:01 1968340                    /usr/lib64/libdrm.so.2.4.0
7f9749dfd000-7f9749e0c000 r-xp 00000000 fe:01 1968453                    /usr/lib64/libwayland-server.so.0.1.0
7f9749e0c000-7f974a00c000 ---p 0000f000 fe:01 1968453                    /usr/lib64/libwayland-server.so.0.1.0
7f974a00c000-7f974a00e000 r--p 0000f000 fe:01 1968453                    /usr/lib64/libwayland-server.so.0.1.0
7f974a00e000-7f974a00f000 rw-p 00011000 fe:01 1968453                    /usr/lib64/libwayland-server.so.0.1.0
7f974a00f000-7f974a01b000 r-xp 00000000 fe:01 1967071                    /usr/lib64/libwayland-client.so.0.3.0
7f974a01b000-7f974a21a000 ---p 0000c000 fe:01 1967071                    /usr/lib64/libwayland-client.so.0.3.0
7f974a21a000-7f974a21c000 r--p 0000b000 fe:01 1967071                    /usr/lib64/libwayland-client.so.0.3.0
7f974a21c000-7f974a21d000 rw-p 0000d000 fe:01 1967071                    /usr/lib64/libwayland-client.so.0.3.0
7f974a21d000-7f974a229000 r-xp 00000000 fe:01 1967097                    /usr/lib64/libgbm.so.1.0.0
7f974a229000-7f974a429000 ---p 0000c000 fe:01 1967097                    /usr/lib64/libgbm.so.1.0.0
7f974a429000-7f974a42a000 r--p 0000c000 fe:01 1967097                    /usr/lib64/libgbm.so.1.0.0
7f974a42a000-7f974a42b000 rw-p 0000d000 fe:01 1967097                    /usr/lib64/libgbm.so.1.0.0
7f974a42b000-7f974a431000 r-xp 00000000 fe:01 1977547                    /usr/lib64/libxcb-xfixes.so.0.0.0
7f974a431000-7f974a630000 ---p 00006000 fe:01 1977547                    /usr/lib64/libxcb-xfixes.so.0.0.0
7f974a630000-7f974a631000 r--p 00005000 fe:01 1977547                    /usr/lib64/libxcb-xfixes.so.0.0.0
7f974a631000-7f974a632000 rw-p 00006000 fe:01 1977547                    /usr/lib64/libxcb-xfixes.so.0.0.0
7f974a632000-7f974a636000 r-xp 00000000 fe:01 1977932                    /usr/lib64/libxcb-dri2.so.0.0.0
7f974a636000-7f974a835000 ---p 00004000 fe:01 1977932                    /usr/lib64/libxcb-dri2.so.0.0.0
7f974a835000-7f974a836000 r--p 00003000 fe:01 1977932                    /usr/lib64/libxcb-dri2.so.0.0.0
7f974a836000-7f974a837000 rw-p 00004000 fe:01 1977932                    /usr/lib64/libxcb-dri2.so.0.0.0
7f974a837000-7f974a838000 r-xp 00000000 fe:01 1977512                    /usr/lib64/libX11-xcb.so.1.0.0
7f974a838000-7f974aa37000 ---p 00001000 fe:01 1977512                    /usr/lib64/libX11-xcb.so.1.0.0
7f974aa37000-7f974aa38000 r--p 00000000 fe:01 1977512                    /usr/lib64/libX11-xcb.so.1.0.0
7f974aa38000-7f974aa39000 rw-p 00001000 fe:01 1977512                    /usr/lib64/libX11-xcb.so.1.0.0
7f974aa39000-7f974aa60000 r-xp 00000000 fe:01 1968392                    /usr/lib64/libexpat.so.1.6.0
7f974aa60000-7f974ac60000 ---p 00027000 fe:01 1968392                    /usr/lib64/libexpat.so.1.6.0
7f974ac60000-7f974ac62000 r--p 00027000 fe:01 1968392                    /usr/lib64/libexpat.so.1.6.0
7f974ac62000-7f974ac63000 rw-p 00029000 fe:01 1968392                    /usr/lib64/libexpat.so.1.6.0
7f974ac63000-7f974acba000 r-xp 00000000 fe:01 1968468                    /usr/lib64/libharfbuzz.so.0.935.0
7f974acba000-7f974aeba000 ---p 00057000 fe:01 1968468                    /usr/lib64/libharfbuzz.so.0.935.0
7f974aeba000-7f974aebb000 r--p 00057000 fe:01 1968468                    /usr/lib64/libharfbuzz.so.0.935.0
7f974aebb000-7f974aebc000 rw-p 00058000 fe:01 1968468                    /usr/lib64/libharfbuzz.so.0.935.0
7f974aebc000-7f974aec5000 r-xp 00000000 fe:01 1978240                    /usr/lib64/libjbig.so.2.1
7f974aec5000-7f974b0c4000 ---p 00009000 fe:01 1978240                    /usr/lib64/libjbig.so.2.1
7f974b0c4000-7f974b0c5000 r--p 00008000 fe:01 1978240                    /usr/lib64/libjbig.so.2.1
7f974b0c5000-7f974b0c8000 rw-p 00009000 fe:01 1978240                    /usr/lib64/libjbig.so.2.1
7f974b0c8000-7f974b0ef000 r-xp 00000000 fe:01 1977076                    /usr/lib64/liblzma.so.5.2.2
7f974b0ef000-7f974b2ef000 ---p 00027000 fe:01 1977076                    /usr/lib64/liblzma.so.5.2.2
7f974b2ef000-7f974b2f0000 r--p 00027000 fe:01 1977076                    /usr/lib64/liblzma.so.5.2.2
7f974b2f0000-7f974b2f1000 rw-p 00028000 fe:01 1977076                    /usr/lib64/liblzma.so.5.2.2
7f974b2f1000-7f974b308000 r-xp 00000000 fe:01 1967050                    /usr/lib64/libICE.so.6.3.0
7f974b308000-7f974b508000 ---p 00017000 fe:01 1967050                    /usr/lib64/libICE.so.6.3.0
7f974b508000-7f974b509000 r--p 00017000 fe:01 1967050                    /usr/lib64/libICE.so.6.3.0
7f974b509000-7f974b50a000 rw-p 00018000 fe:01 1967050                    /usr/lib64/libICE.so.6.3.0
7f974b50a000-7f974b50e000 rw-p 00000000 00:00 0 
7f974b50e000-7f974b515000 r-xp 00000000 fe:01 1966084                    /usr/lib64/libSM.so.6.0.1
7f974b515000-7f974b714000 ---p 00007000 fe:01 1966084                    /usr/lib64/libSM.so.6.0.1
7f974b714000-7f974b715000 r--p 00006000 fe:01 1966084                    /usr/lib64/libSM.so.6.0.1
7f974b715000-7f974b716000 rw-p 00007000 fe:01 1966084                    /usr/lib64/libSM.so.6.0.1
7f974b716000-7f974b7a2000 r-xp 00000000 fe:01 1975907                    /usr/lib64/libGL.so.1.2.0
7f974b7a2000-7f974b9a1000 ---p 0008c000 fe:01 1975907                    /usr/lib64/libGL.so.1.2.0
7f974b9a1000-7f974b9a4000 r--p 0008b000 fe:01 1975907                    /usr/lib64/libGL.so.1.2.0
7f974b9a4000-7f974b9a5000 rw-p 0008e000 fe:01 1975907                    /usr/lib64/libGL.so.1.2.0
7f974b9a5000-7f974b9a6000 rw-p 00000000 00:00 0 
7f974b9a6000-7f974b9b7000 r-xp 00000000 fe:01 1966941                    /usr/lib64/libXext.so.6.4.0
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7f975f0df000-7f975f0e2000 r-xp 00000000 fe:03 2150941857                 /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/lattice/libs/lattice.so
7f975f0e2000-7f975f2e1000 ---p 00003000 fe:03 2150941857                 /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/lattice/libs/lattice.so
7f975f2e1000-7f975f2e2000 r--p 00002000 fe:03 2150941857                 /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/lattice/libs/lattice.so
7f975f2e2000-7f975f2e3000 rw-p 00003000 fe:03 2150941857                 /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/lattice/libs/lattice.so
7f975f2e3000-7f975f300000 r-xp 00000000 fe:01 3422773                    /usr/lib64/R/library/grid/libs/grid.so
7f975f300000-7f975f500000 ---p 0001d000 fe:01 3422773                    /usr/lib64/R/library/grid/libs/grid.so
7f975f500000-7f975f501000 r--p 0001d000 fe:01 3422773                    /usr/lib64/R/library/grid/libs/grid.so
7f975f501000-7f975f502000 rw-p 0001e000 fe:01 3422773                    /usr/lib64/R/library/grid/libs/grid.so
7f975f502000-7f975f587000 r-xp 00000000 fe:03 6269304                    /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/deSolve/libs/deSolve.so
7f975f587000-7f975f786000 ---p 00085000 fe:03 6269304                    /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/deSolve/libs/deSolve.so
7f975f786000-7f975f787000 r--p 00084000 fe:03 6269304                    /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/deSolve/libs/deSolve.so
7f975f787000-7f975f788000 rw-p 00085000 fe:03 6269304                    /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/deSolve/libs/deSolve.so
7f975f788000-7f975f789000 rw-p 00000000 00:00 0 
7f975f789000-7f975f7a5000 r-xp 00000000 fe:03 3225454428                 /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/digest/libs/digest.so
7f975f7a5000-7f975f9a4000 ---p 0001c000 fe:03 3225454428                 /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/digest/libs/digest.so
7f975f9a4000-7f975f9a5000 r--p 0001b000 fe:03 3225454428                 /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/digest/libs/digest.so
7f975f9a5000-7f975f9a6000 rw-p 0001c000 fe:03 3225454428                 /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/digest/libs/digest.so
7f975f9a6000-7f975f9a8000 rw-p 00000000 00:00 0 
7f975f9a8000-7f975f9ad000 r-xp 00000000 fe:03 53257557                   /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/MASS/libs/MASS.so
7f975f9ad000-7f975fbac000 ---p 00005000 fe:03 53257557                   /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/MASS/libs/MASS.so
7f975fbac000-7f975fbad000 r--p 00004000 fe:03 53257557                   /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/MASS/libs/MASS.so
7f975fbad000-7f975fbae000 rw-p 00005000 fe:03 53257557                   /home/vojta/R/x86_64-suse-linux-gnu-library/3.2/MASS/libs/MASS.so
7f975fbae000-7f9763e10000 rw-p 00000000 00:00 0 
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7f976412a000-7f97642e6000 r-xp 00000000 fe:01 3028059                    /usr/lib64/R/lib/libRlapack.so
7f97642e6000-7f97644e5000 ---p 001bc000 fe:01 3028059                    /usr/lib64/R/lib/libRlapack.so
7f97644e5000-7f97644e6000 r--p 001bb000 fe:01 3028059                    /usr/lib64/R/lib/libRlapack.so
7f97644e6000-7f97644e7000 rw-p 001bc000 fe:01 3028059                    /usr/lib64/R/lib/libRlapack.so
7f97644e7000-7f976458a000 r-xp 00000000 fe:01 3423257                    /usr/lib64/R/library/stats/libs/stats.so
7f976458a000-7f976478a000 ---p 000a3000 fe:01 3423257                    /usr/lib64/R/library/stats/libs/stats.so
7f976478a000-7f976478c000 r--p 000a3000 fe:01 3423257                    /usr/lib64/R/library/stats/libs/stats.so
7f976478c000-7f976478e000 rw-p 000a5000 fe:01 3423257                    /usr/lib64/R/library/stats/libs/stats.so
7f976478e000-7f97647cb000 r-xp 00000000 fe:01 3422696                    /usr/lib64/R/library/graphics/libs/graphics.so
7f97647cb000-7f97649cb000 ---p 0003d000 fe:01 3422696                    /usr/lib64/R/library/graphics/libs/graphics.so
7f97649cb000-7f97649cc000 r--p 0003d000 fe:01 3422696                    /usr/lib64/R/library/graphics/libs/graphics.so
7f97649cc000-7f97649cd000 rw-p 0003e000 fe:01 3422696                    /usr/lib64/R/library/graphics/libs/graphics.so
7f97649cd000-7f9764a01000 r-xp 00000000 fe:01 3421424                    /usr/lib64/R/library/grDevices/libs/grDevices.so
7f9764a01000-7f9764c01000 ---p 00034000 fe:01 3421424                    /usr/lib64/R/library/grDevices/libs/grDevices.so
7f9764c01000-7f9764c06000 r--p 00034000 fe:01 3421424                    /usr/lib64/R/library/grDevices/libs/grDevices.so
7f9764c06000-7f9764c08000 rw-p 00039000 fe:01 3421424                    /usr/lib64/R/library/grDevices/libs/grDevices.so
7f9764c08000-7f9764c09000 rw-p 00000000 00:00 0 
7f9764c09000-7f9764c0a000 r--s 00000000 fe:01 142792                     /var/cache/fontconfig/5ea99a3fd541959964d132d9faa82bab-x86_64.cache-4
7f9764c0a000-7f9764c14000 r--s 00000000 fe:01 142783                     /var/cache/fontconfig/88f861b912d3cae7dc2bacad6e03d372-x86_64.cache-4
7f9764c14000-7f9764c1f000 r--s 00000000 fe:01 142782                     /var/cache/fontconfig/b2fa382366656bfdebb90bef13ca9118-x86_64.cache-4
7f9764c1f000-7f9764c22000 r--s 00000000 fe:01 142780                     /var/cache/fontconfig/1e025244fe03cf7a8f4023cc3ee44356-x86_64.cache-4
7f9764c22000-7f9764c59000 r--s 00000000 fe:01 142771                     /var/cache/fontconfig/8d4af663993b81a124ee82e610bb31f9-x86_64.cache-4
7f9764c59000-7f9764c94000 r-xp 00000000 fe:01 1979238                    /usr/lib64/libquadmath.so.0.0.0
7f9764c94000-7f9764e93000 ---p 0003b000 fe:01 1979238                    /usr/lib64/libquadmath.so.0.0.0
7f9764e93000-7f9764e94000 r--p 0003a000 fe:01 1979238                    /usr/lib64/libquadmath.so.0.0.0
7f9764e94000-7f9764e95000 rw-p 0003b000 fe:01 1979238                    /usr/lib64/libquadmath.so.0.0.0
7f9764e95000-7f9764f8c000 rw-p 00000000 00:00 0 
7f9764f8c000-7f9764f94000 r-xp 00000000 fe:01 3422856                    /usr/lib64/R/library/methods/libs/methods.so
7f9764f94000-7f9765193000 ---p 00008000 fe:01 3422856                    /usr/lib64/R/library/methods/libs/methods.so
7f9765193000-7f9765194000 r--p 00007000 fe:01 3422856                    /usr/lib64/R/library/methods/libs/methods.so
7f9765194000-7f9765195000 rw-p 00008000 fe:01 3422856                    /usr/lib64/R/library/methods/libs/methods.so
7f9765195000-7f976519f000 r-xp 00000000 fe:01 14306                      /usr/lib64/R/library/utils/libs/utils.so
7f976519f000-7f976539f000 ---p 0000a000 fe:01 14306                      /usr/lib64/R/library/utils/libs/utils.so
7f976539f000-7f97653a0000 r--p 0000a000 fe:01 14306                      /usr/lib64/R/library/utils/libs/utils.so
7f97653a0000-7f97653a1000 rw-p 0000b000 fe:01 14306                      /usr/lib64/R/library/utils/libs/utils.so
7f97653a1000-7f976544f000 rw-p 00000000 00:00 0 
7f976544f000-7f97668d7000 r--s 00000000 fe:01 2368875                    /usr/share/icu/53.1/icudt53l.dat
7f97668d7000-7f9766b12000 rw-p 00000000 00:00 0 
7f9766b12000-7f9766b28000 r-xp 00000000 fe:01 3145763                    /lib64/libgcc_s.so.1
7f9766b28000-7f9766d27000 ---p 00016000 fe:01 3145763                    /lib64/libgcc_s.so.1
7f9766d27000-7f9766d28000 r--p 00015000 fe:01 3145763                    /lib64/libgcc_s.so.1
7f9766d28000-7f9766d29000 rw-p 00016000 fe:01 3145763                    /lib64/libgcc_s.so.1
7f9766d29000-7f9766e13000 r-xp 00000000 fe:01 1967094                    /usr/lib64/libstdc++.so.6.0.19
7f9766e13000-7f9767012000 ---p 000ea000 fe:01 1967094                    /usr/lib64/libstdc++.so.6.0.19
7f9767012000-7f976701a000 r--p 000e9000 fe:01 1967094                    /usr/lib64/libstdc++.so.6.0.19
7f976701a000-7f976701c000 rw-p 000f1000 fe:01 1967094                    /usr/lib64/libstdc++.so.6.0.19
7f976701c000-7f9767031000 rw-p 00000000 00:00 0 
7f9767031000-7f9767032000 r--p 00000000 fe:01 1976477                    /usr/lib64/libicudata.so.53.1
7f9767032000-7f9767231000 ---p 00001000 fe:01 1976477                    /usr/lib64/libicudata.so.53.1
7f9767231000-7f9767232000 r--p 00000000 fe:01 1976477                    /usr/lib64/libicudata.so.53.1
7f9767232000-7f976725d000 r-xp 00000000 fe:01 3145820                    /lib64/libtinfo.so.5.9
7f976725d000-7f976745c000 ---p 0002b000 fe:01 3145820                    /lib64/libtinfo.so.5.9
7f976745c000-7f9767460000 r--p 0002a000 fe:01 3145820                    /lib64/libtinfo.so.5.9
7f9767460000-7f9767465000 rw-p 0002e000 fe:01 3145820                    /lib64/libtinfo.so.5.9
7f9767465000-7f9767466000 rw-p 00000000 00:00 0 
7f9767466000-7f9767474000 r-xp 00000000 fe:01 1977089                    /usr/lib64/libgomp.so.1.0.0
7f9767474000-7f9767673000 ---p 0000e000 fe:01 1977089                    /usr/lib64/libgomp.so.1.0.0
7f9767673000-7f9767674000 r--p 0000d000 fe:01 1977089                    /usr/lib64/libgomp.so.1.0.0
7f9767674000-7f9767675000 rw-p 0000e000 fe:01 1977089                    /usr/lib64/libgomp.so.1.0.0
7f9767675000-7f97678a7000 r-xp 00000000 fe:01 1976333                    /usr/lib64/libicui18n.so.53.1
7f97678a7000-7f9767aa7000 ---p 00232000 fe:01 1976333                    /usr/lib64/libicui18n.so.53.1
7f9767aa7000-7f9767ab5000 r--p 00232000 fe:01 1976333                    /usr/lib64/libicui18n.so.53.1
7f9767ab5000-7f9767ab7000 rw-p 00240000 fe:01 1976333                    /usr/lib64/libicui18n.so.53.1
7f9767ab7000-7f9767ab8000 rw-p 00000000 00:00 0 
7f9767ab8000-7f9767c25000 r-xp 00000000 fe:01 1976256                    /usr/lib64/libicuuc.so.53.1
7f9767c25000-7f9767e24000 ---p 0016d000 fe:01 1976256                    /usr/lib64/libicuuc.so.53.1
7f9767e24000-7f9767e35000 r--p 0016c000 fe:01 1976256                    /usr/lib64/libicuuc.so.53.1
7f9767e35000-7f9767e36000 rw-p 0017d000 fe:01 1976256                    /usr/lib64/libicuuc.so.53.1
7f9767e36000-7f9767e3a000 rw-p 00000000 00:00 0 
7f9767e3a000-7f9767e3d000 r-xp 00000000 fe:01 3151450                    /lib64/libdl-2.19.so
7f9767e3d000-7f976803c000 ---p 00003000 fe:01 3151450                    /lib64/libdl-2.19.so
7f976803c000-7f976803d000 r--p 00002000 fe:01 3151450                    /lib64/libdl-2.19.so
7f976803d000-7f976803e000 rw-p 00003000 fe:01 3151450                    /lib64/libdl-2.19.so
7f976803e000-7f9768045000 r-xp 00000000 fe:01 3151459                    /lib64/librt-2.19.so
7f9768045000-7f9768244000 ---p 00007000 fe:01 3151459                    /lib64/librt-2.19.so
7f9768244000-7f9768245000 r--p 00006000 fe:01 3151459                    /lib64/librt-2.19.so
7f9768245000-7f9768246000 rw-p 00007000 fe:01 3151459                    /lib64/librt-2.19.so
7f9768246000-7f976825b000 r-xp 00000000 fe:01 3145815                    /lib64/libz.so.1.2.8
7f976825b000-7f976845a000 ---p 00015000 fe:01 3145815                    /lib64/libz.so.1.2.8
7f976845a000-7f976845b000 r--p 00014000 fe:01 3145815                    /lib64/libz.so.1.2.8
7f976845b000-7f976845c000 rw-p 00015000 fe:01 3145815                    /lib64/libz.so.1.2.8
7f976845c000-7f97684c7000 r-xp 00000000 fe:01 1977913                    /usr/lib64/libpcre.so.1.2.5
7f97684c7000-7f97686c6000 ---p 0006b000 fe:01 1977913                    /usr/lib64/libpcre.so.1.2.5
7f97686c6000-7f97686c7000 r--p 0006a000 fe:01 1977913                    /usr/lib64/libpcre.so.1.2.5
7f97686c7000-7f97686c8000 rw-p 0006b000 fe:01 1977913                    /usr/lib64/libpcre.so.1.2.5
7f97686c8000-7f9768706000 r-xp 00000000 fe:01 3145825                    /lib64/libreadline.so.6.2
7f9768706000-7f9768906000 ---p 0003e000 fe:01 3145825                    /lib64/libreadline.so.6.2
7f9768906000-7f9768908000 r--p 0003e000 fe:01 3145825                    /lib64/libreadline.so.6.2
7f9768908000-7f976890e000 rw-p 00040000 fe:01 3145825                    /lib64/libreadline.so.6.2
7f976890e000-7f9768910000 rw-p 00000000 00:00 0
7f9768910000-7f9768a10000 r-xp 00000000 fe:01 3151451                    /lib64/libm-2.19.so
7f9768a10000-7f9768c0f000 ---p 00100000 fe:01 3151451                    /lib64/libm-2.19.so
7f9768c0f000-7f9768c10000 r--p 000ff000 fe:01 3151451                    /lib64/libm-2.19.so
7f9768c10000-7f9768c11000 rw-p 00100000 fe:01 3151451                    /lib64/libm-2.19.so
7f9768c11000-7f9768c3d000 r-xp 00000000 fe:01 3028058                    /usr/lib64/R/lib/libRblas.so
7f9768c3d000-7f9768e3c000 ---p 0002c000 fe:01 3028058                    /usr/lib64/R/lib/libRblas.so
7f9768e3c000-7f9768e3d000 r--p 0002b000 fe:01 3028058                    /usr/lib64/R/lib/libRblas.so
7f9768e3d000-7f9768e3e000 rw-p 0002c000 fe:01 3028058                    /usr/lib64/R/lib/libRblas.so
7f9768e3e000-7f9768fdc000 r-xp 00000000 fe:01 3145868                    /lib64/libc-2.19.so
7f9768fdc000-7f97691db000 ---p 0019e000 fe:01 3145868                    /lib64/libc-2.19.so
7f97691db000-7f97691df000 r--p 0019d000 fe:01 3145868                    /lib64/libc-2.19.so
7f97691df000-7f97691e1000 rw-p 001a1000 fe:01 3145868                    /lib64/libc-2.19.so
7f97691e1000-7f97691e5000 rw-p 00000000 00:00 0
7f97691e5000-7f97691fd000 r-xp 00000000 fe:01 3145839                    /lib64/libpthread-2.19.so
7f97691fd000-7f97693fc000 ---p 00018000 fe:01 3145839                    /lib64/libpthread-2.19.so
7f97693fc000-7f97693fd000 r--p 00017000 fe:01 3145839                    /lib64/libpthread-2.19.so
7f97693fd000-7f97693fe000 rw-p 00018000 fe:01 3145839                    /lib64/libpthread-2.19.so
7f97693fe000-7f9769402000 rw-p 00000000 00:00 0
7f9769402000-7f97696d5000 r-xp 00000000 fe:01 3028057                    /usr/lib64/R/lib/libR.so
7f97696d5000-7f97698d5000 ---p 002d3000 fe:01 3028057                    /usr/lib64/R/lib/libR.so
7f97698d5000-7f97698f3000 r--p 002d3000 fe:01 3028057                    /usr/lib64/R/lib/libR.so
7f97698f3000-7f9769900000 rw-p 002f1000 fe:01 3028057                    /usr/lib64/R/lib/libR.so
7f9769900000-7f97699ed000 rw-p 00000000 00:00 0
7f97699ed000-7f9769a0d000 r-xp 00000000 fe:01 3148005                    /lib64/ld-2.19.so
7f9769a0d000-7f9769a0f000 r--s 00000000 fe:01 142784                     /var/cache/fontconfig/6f808de34b6f71c1f5991da0b33db31b-x86_64.cache-4
7f9769a0f000-7f9769a12000 r--s 00000000 fe:01 142778                     /var/cache/fontconfig/26ba52b4ad2b884e09b2ecee609fe7da-x86_64.cache-4
7f9769a12000-7f9769a21000 r--s 00000000 fe:01 134577                     /var/cache/fontconfig/d42e465d3d703735db7577b46e8d64be-x86_64.cache-4
7f9769a21000-7f9769a46000 r--p 00000000 fe:01 2372869                    /usr/share/locale/cs/LC_MESSAGES/libc.mo
7f9769a46000-7f9769a7b000 r--s 00000000 00:11 26644                      /run/nscd/passwd
7f9769a7b000-7f9769b87000 rw-p 00000000 00:00 0
7f9769b87000-7f9769bc6000 r--p 00000000 fe:01 3146605                    /usr/lib/locale/cs_CZ.utf8/LC_CTYPE
7f9769bc6000-7f9769bd1000 rw-p 00000000 00:00 0
7f9769bd1000-7f9769bd2000 r--s 00000000 fe:01 142790                     /var/cache/fontconfig/3b4b00f4c8729b30bd8cdecb656b4e7b-x86_64.cache-4
7f9769bd2000-7f9769bd3000 r--s 00000000 fe:01 142781                     /var/cache/fontconfig/0a206c5b12450cf4d909a9c36ddc121b-x86_64.cache-4
7f9769bd3000-7f9769bd4000 r--s 00000000 fe:01 142775                     /var/cache/fontconfig/457be539316e49d90db894a2e1bcaebe-x86_64.cache-4
7f9769bd4000-7f9769bd5000 r--s 00000000 fe:01 142774                     /var/cache/fontconfig/f8b76d193bb79c238a2703949d308530-x86_64.cache-4
7f9769bd5000-7f9769bd9000 r--s 00000000 fe:01 142773                     /var/cache/fontconfig/55e3aa00b6b2f1727d4400f2004120e9-x86_64.cache-4
7f9769bd9000-7f9769bda000 r--s 00000000 fe:01 142772                     /var/cache/fontconfig/913dda57dbe22c714e9ee05535b1786a-x86_64.cache-4
7f9769bda000-7f9769be3000 r--s 00000000 fe:01 134583                     /var/cache/fontconfig/d62e99ef547d1d24cdb1bd22ec1a2976-x86_64.cache-4
7f9769be3000-7f9769be4000 rw-p 00000000 00:00 0
7f9769be4000-7f9769be5000 r--p 00000000 fe:01 3150917                    /usr/lib/locale/cs_CZ.utf8/LC_MEASUREMENT
7f9769be5000-7f9769be6000 r--p 00000000 fe:01 3146609                    /usr/lib/locale/cs_CZ.utf8/LC_PAPER
7f9769be6000-7f9769be7000 r--p 00000000 fe:01 3028874                    /usr/lib/locale/cs_CZ.utf8/LC_MONETARY
7f9769be7000-7f9769be8000 r--p 00000000 fe:01 3028879                    /usr/lib/locale/cs_CZ.utf8/LC_TIME
7f9769be8000-7f9769c04000 r--p 00000000 fe:01 3146663                    /usr/lib/locale/cs_CZ.utf8/LC_COLLATE
7f9769c04000-7f9769c0b000 r--s 00000000 fe:01 2103454                    /usr/lib64/gconv/gconv-modules.cache
7f9769c0b000-7f9769c0c000 r--p 00000000 fe:01 3028803                    /usr/lib/locale/cs_CZ.utf8/LC_MESSAGES/SYS_LC_MESSAGES
7f9769c0c000-7f9769c0d000 rw-p 00000000 00:00 0
7f9769c0d000-7f9769c0e000 r--p 00020000 fe:01 3148005                    /lib64/ld-2.19.so
7f9769c0e000-7f9769c0f000 rw-p 00021000 fe:01 3148005                    /lib64/ld-2.19.so
7f9769c0f000-7f9769c10000 rw-p 00000000 00:00 0
7ffd5dba9000-7ffd5dbdc000 rw-p 00000000 00:00 0                          [stack]
7ffd5dbf6000-7ffd5dbf8000 r-xp 00000000 00:00 0                          [vdso]
7ffd5dbf8000-7ffd5dbfa000 r--p 00000000 00:00 0                          [vvar]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
SIGABRT

Crashing this time
If I run it like

metab.pos.root1.concat.mrbayes.nmds <-
  metaMDS(comm=scale(x=metab.pos.root1.concat.mrbayes, center=TRUE, 
  scale=TRUE), distance="manhattan", k=2, trymax=10000, engine="monoMDS", 
  autotransform=FALSE, noshare=FALSE, stepacross=FALSE, wascores=FALSE, 
  expand=FALSE, plot=TRUE)

it works fine, so that the problem can be within the data.

@jarioksa

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@jarioksa

jarioksa Jan 4, 2016

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You can send the file to my email address. I will run tests and delete file.

Have you run R CMD check on vegan?

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jarioksa commented Jan 4, 2016

You can send the file to my email address. I will run tests and delete file.

Have you run R CMD check on vegan?

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V-Z Jan 4, 2016

cd ~/R/x86_64-suse-linux-gnu-library/3.2
$ R CMD check vegan
* using log directory ‘/home/vojta/R/x86_64-suse-linux-gnu-library/3.2/vegan.Rcheck’
* using R version 3.2.3 (2015-12-10)
* using platform: x86_64-suse-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘vegan/DESCRIPTION’ ... OK
* this is package ‘vegan’ version ‘2.3-3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... ERROR
Only *source* packages can be checked.
* DONE

Well, it doesn't seem to be very useful... vegan was installed using install.packages(). I'm mailing the data file.

V-Z commented Jan 4, 2016

cd ~/R/x86_64-suse-linux-gnu-library/3.2
$ R CMD check vegan
* using log directory ‘/home/vojta/R/x86_64-suse-linux-gnu-library/3.2/vegan.Rcheck’
* using R version 3.2.3 (2015-12-10)
* using platform: x86_64-suse-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘vegan/DESCRIPTION’ ... OK
* this is package ‘vegan’ version ‘2.3-3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... ERROR
Only *source* packages can be checked.
* DONE

Well, it doesn't seem to be very useful... vegan was installed using install.packages(). I'm mailing the data file.

@jarioksa jarioksa added the bug label Jan 5, 2016

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jarioksa Jan 5, 2016

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I confirm this as a bug in vegan.

The underlying problem is that your data are badly scaled, and monoMDS function in vegan does not adequately handle the awkward scaling in your data. Your raw data has values up to 8E84, and the resulting Manhattan dissimilarities are in the range 2E22 to 2E85. Scaling by (e.g.) x/max(x) will solve your problem with the current vegan. I'll take care that vegan will do something similar under the hood in the future versions.

Another problem you have is that your observations are not distinct. Despite large number of columns, your rows (species in this case) are duplicated, and NMDS is under-defined: there are several alternative solutions with zero-stress. You need more different species to be able to use NMDS .

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jarioksa commented Jan 5, 2016

I confirm this as a bug in vegan.

The underlying problem is that your data are badly scaled, and monoMDS function in vegan does not adequately handle the awkward scaling in your data. Your raw data has values up to 8E84, and the resulting Manhattan dissimilarities are in the range 2E22 to 2E85. Scaling by (e.g.) x/max(x) will solve your problem with the current vegan. I'll take care that vegan will do something similar under the hood in the future versions.

Another problem you have is that your observations are not distinct. Despite large number of columns, your rows (species in this case) are duplicated, and NMDS is under-defined: there are several alternative solutions with zero-stress. You need more different species to be able to use NMDS .

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V-Z Jan 5, 2016

I know the data are little bit weird - I'm still struggling with it. Thank You for fixing and advice and I'm sorry it consumes Your time.

V-Z commented Jan 5, 2016

I know the data are little bit weird - I'm still struggling with it. Thank You for fixing and advice and I'm sorry it consumes Your time.

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jarioksa Jan 5, 2016

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No worries, mate. Bug reports are the only way of fixing bugs. Your data are badly scaled, but vegan should handle all valid data. It was good that you selected Manhattan distance, though: Euclidean distance would have been unstable certainly in vegan and when I last checked, also in dist of base R.

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jarioksa commented Jan 5, 2016

No worries, mate. Bug reports are the only way of fixing bugs. Your data are badly scaled, but vegan should handle all valid data. It was good that you selected Manhattan distance, though: Euclidean distance would have been unstable certainly in vegan and when I last checked, also in dist of base R.

@jarioksa jarioksa closed this Jan 5, 2016

@jarioksa jarioksa reopened this Jan 5, 2016

jarioksa added a commit that referenced this issue Jan 6, 2016

monoMDS may crash with badly scaled dissimilarities: scale down
Issue #152 in github reported a case where monoMDS seqfaulted
with data sets where longest  dissimilarities were ~2E85 and shortest
about 2E22. This commit scales down dissimilarities with very long
maxima. In pricinple, this should be handled within the FORTRAN code
of monoMDS, but the current kluge seems to avoid the problem, too.

@jarioksa jarioksa added this to the v2.3-3 milestone Jan 7, 2016

jarioksa added a commit that referenced this issue Jan 8, 2016

monoMDS could crash with huge input dissimilarites
monoMDS needed to set a guard dissimilarity which is longer than
observed dissimilarity, and this could fail if observed dissimilarities
were huge (in the issue #152 dissimilarities were of magnitude 2e85),
and this could crash monoMDS.

Fixes issue #152 reported in github.

jarioksa added a commit that referenced this issue Jan 8, 2016

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jarioksa Jan 8, 2016

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This is now fixed with 62fc1cb

The fundamental problem is that your data are very badly scaled: dissimilarities in magnitude 2E22 are effectively zero and indicate identical observations! I anticipate problems with several R functions with that badly scaled data. Not necessarily crashes or obvious failures, but loss of accuracy in calculations. However, metaMDS now accepts your data, but will not produce nothing useful because you do not have sufficient data to separate 18 observations.

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jarioksa commented Jan 8, 2016

This is now fixed with 62fc1cb

The fundamental problem is that your data are very badly scaled: dissimilarities in magnitude 2E22 are effectively zero and indicate identical observations! I anticipate problems with several R functions with that badly scaled data. Not necessarily crashes or obvious failures, but loss of accuracy in calculations. However, metaMDS now accepts your data, but will not produce nothing useful because you do not have sufficient data to separate 18 observations.

@jarioksa jarioksa closed this Jan 8, 2016

jarioksa added a commit that referenced this issue Jan 8, 2016

monoMDS could crash with huge input dissimilarites
monoMDS needed to set a guard dissimilarity which is longer than
observed dissimilarity, and this could fail if observed dissimilarities
were huge (in the issue #152 dissimilarities were of magnitude 2e85),
and this could crash monoMDS.

Fixes issue #152 reported in github.

(cherry picked from commit 62fc1cb)
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