R aborts abruptly on Centos7 (Error in `/usr/lib64/R/bin/exec/R': free(): invalid pointer)

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dkaur
Posts: 1
Joined: 2017/07/11 19:56:19

R aborts abruptly on Centos7 (Error in `/usr/lib64/R/bin/exec/R': free(): invalid pointer)

Post by dkaur » 2020/06/03 00:00:01

I have been trying to run a .R script on Centos7. The script was running fine till yesterday. But when I tried to run it today, R keeps crashing.

The script that I'm trying to run is: 'IF1_theta.R'

Code: Select all

require(plotrix)

#frames is the number of frames of simulation analyzed.
frames<-18000

#n is the number of resiudes in the protein.
 res=71

 # The displacement vectors that show significant correlated direction will be read into A.
 # Significance criteria have already been applied to this matrix.
 A<-matrix(scan("./IF1_wt_allres-theta-sig2.dat",n=res*res),res,res,byrow=TRUE)

 # The contact matrix computed in VMD will be read into the matrix contact.
 contact<-matrix(scan("../contact/contact-matrix-IF1_wt_11-100ns_combined.dat",n=res*res),res,res,byrow=TRUE)

 ##########################################################################
 ## You should not need to alter anything below this line unless you are ##
 ## changing analysis parameters. If you are, then have fun :)           ##
 ##########################################################################



##################################################
## Now we will incorporate contact information. ##
##################################################

#The contact matrix contains the number of frames in which residues are within 4.5A
# of each other over the simulation.
#We need to calculate the probability of a contact between residues i and j by dividing the contact matrix by the number of frames.
#residues in contact for 75% of the simulation or more will be counted as edges in the graph
 cprob<-matrix(0,71,71)
 for (i in c(1:res)) {
     for (j in c(1:res))  { if (contact[i,j]/frames>=0.75) {cprob[i,j]=1}
        }
                         }


          Mat<-matrix(0,res,res)
    for (i in c(1:res)) {
    for (j in c(1:res)) {Mat[i,j]=cprob[i,j]*A[i,j]}
                      }

require(igraph, warn.conflicts=FALSE)

#write the adjacency matrix A to a graph object, which can be read by igraph
g<-graph.adjacency(Mat,mode=c("undirected"),weighted="undirected")
eb<-estimate_betweenness(g,vids=V(g),directed=FALSE,cutoff=0,weights=NULL,nobigint=TRUE)
b<-betweenness(g)
ed<-edge_betweenness(g)

And the error that I'm getting is:

Code: Select all

> source(file="./IF1_theta.R")
Loading required package: plotrix
Read 5041 items
Read 4970 items
Loading required package: igraph
*** Error in `/usr/lib64/R/bin/exec/R': free(): invalid pointer: 0x00000000036116f0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7f91d5dab489]
/usr/lib64/R/library/igraph/libs/igraph.so(igraph_vector_destroy+0x11)[0x7f91c84cfc01]
/usr/lib64/R/library/igraph/libs/igraph.so(R_igraph_community_edge_betweenness+0x19a)[0x7f91c8514e0a]
/usr/lib64/R/lib/libR.so(+0xfb625)[0x7f91d8b28625]
/usr/lib64/R/lib/libR.so(+0x13b67a)[0x7f91d8b6867a]
/usr/lib64/R/lib/libR.so(Rf_eval+0x258)[0x7f91d8b75338]
/usr/lib64/R/lib/libR.so(+0x149b12)[0x7f91d8b76b12]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x7f91d8b77827]
/usr/lib64/R/lib/libR.so(Rf_eval+0x35c)[0x7f91d8b7543c]
/usr/lib64/R/lib/libR.so(+0x14c296)[0x7f91d8b79296]
/usr/lib64/R/lib/libR.so(Rf_eval+0x58d)[0x7f91d8b7566d]
/usr/lib64/R/lib/libR.so(+0x14d9ab)[0x7f91d8b7a9ab]
/usr/lib64/R/lib/libR.so(+0x134dfa)[0x7f91d8b61dfa]
/usr/lib64/R/lib/libR.so(Rf_eval+0x258)[0x7f91d8b75338]
/usr/lib64/R/lib/libR.so(+0x149b12)[0x7f91d8b76b12]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x7f91d8b77827]
/usr/lib64/R/lib/libR.so(+0x13c6a7)[0x7f91d8b696a7]
/usr/lib64/R/lib/libR.so(Rf_eval+0x258)[0x7f91d8b75338]
/usr/lib64/R/lib/libR.so(+0x148bee)[0x7f91d8b75bee]
/usr/lib64/R/lib/libR.so(Rf_eval+0x830)[0x7f91d8b75910]
/usr/lib64/R/lib/libR.so(+0x14dc61)[0x7f91d8b7ac61]
/usr/lib64/R/lib/libR.so(+0x186f69)[0x7f91d8bb3f69]
/usr/lib64/R/lib/libR.so(+0x136133)[0x7f91d8b63133]
/usr/lib64/R/lib/libR.so(Rf_eval+0x258)[0x7f91d8b75338]
/usr/lib64/R/lib/libR.so(+0x149b12)[0x7f91d8b76b12]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x7f91d8b77827]
/usr/lib64/R/lib/libR.so(+0x13c6a7)[0x7f91d8b696a7]
/usr/lib64/R/lib/libR.so(Rf_eval+0x258)[0x7f91d8b75338]
/usr/lib64/R/lib/libR.so(+0x149b12)[0x7f91d8b76b12]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x7f91d8b77827]
/usr/lib64/R/lib/libR.so(Rf_eval+0x35c)[0x7f91d8b7543c]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x232)[0x7f91d8ba65d2]
/usr/lib64/R/lib/libR.so(+0x179941)[0x7f91d8ba6941]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0x4f)[0x7f91d8ba69ff]
/usr/lib64/R/bin/exec/R(main+0x1b)[0x40075b]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f91d5d4c3d5]
/usr/lib64/R/bin/exec/R[0x40078b]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:02 16515462                           /usr/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 08:02 16515462                           /usr/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 08:02 16515462                           /usr/lib64/R/bin/exec/R
01dee000-04f63000 rw-p 00000000 00:00 0                                  [heap]
7f91c0000000-7f91c0021000 rw-p 00000000 00:00 0 
7f91c0021000-7f91c4000000 ---p 00000000 00:00 0 
7f91c7f32000-7f91c8091000 r-xp 00000000 08:02 10356554                   /usr/lib64/libxml2.so.2.9.1
7f91c8091000-7f91c8290000 ---p 0015f000 08:02 10356554                   /usr/lib64/libxml2.so.2.9.1
7f91c8290000-7f91c8298000 r--p 0015e000 08:02 10356554                   /usr/lib64/libxml2.so.2.9.1
7f91c8298000-7f91c829a000 rw-p 00166000 08:02 10356554                   /usr/lib64/libxml2.so.2.9.1
7f91c829a000-7f91c829c000 rw-p 00000000 00:00 0 
7f91c829c000-7f91c85d9000 r-xp 00000000 08:02 16521143                   /usr/lib64/R/library/igraph/libs/igraph.so
7f91c85d9000-7f91c87d9000 ---p 0033d000 08:02 16521143                   /usr/lib64/R/library/igraph/libs/igraph.so
7f91c87d9000-7f91c87dd000 r--p 0033d000 08:02 16521143                   /usr/lib64/R/library/igraph/libs/igraph.so
7f91c87dd000-7f91c87e4000 rw-p 00341000 08:02 16521143                   /usr/lib64/R/library/igraph/libs/igraph.so
7f91c87e4000-7f91c87e9000 rw-p 00000000 00:00 0 
7f91c87e9000-7f91c89df000 r-xp 00000000 08:02 16515476                   /usr/lib64/R/lib/libRlapack.so
7f91c89df000-7f91c8bde000 ---p 001f6000 08:02 16515476                   /usr/lib64/R/lib/libRlapack.so
7f91c8bde000-7f91c8bdf000 r--p 001f5000 08:02 16515476                   /usr/lib64/R/lib/libRlapack.so
7f91c8bdf000-7f91c8be0000 rw-p 001f6000 08:02 16515476                   /usr/lib64/R/lib/libRlapack.so
7f91c8be0000-7f91c8bfa000 rw-p 00000000 00:00 0 
7f91c8bfa000-7f91c8c9f000 r-xp 00000000 08:02 16518874                   /usr/lib64/R/library/stats/libs/stats.so
7f91c8c9f000-7f91c8e9f000 ---p 000a5000 08:02 16518874                   /usr/lib64/R/library/stats/libs/stats.so
7f91c8e9f000-7f91c8ea1000 r--p 000a5000 08:02 16518874                   /usr/lib64/R/library/stats/libs/stats.so
7f91c8ea1000-7f91c8ea3000 rw-p 000a7000 08:02 16518874                   /usr/lib64/R/library/stats/libs/stats.so
7f91c8ea3000-7f91c8ee9000 r-xp 00000000 08:02 16517289                   /usr/lib64/R/library/graphics/libs/graphics.so
7f91c8ee9000-7f91c90e9000 ---p 00046000 08:02 16517289                   /usr/lib64/R/library/graphics/libs/graphics.so
7f91c90e9000-7f91c90ea000 r--p 00046000 08:02 16517289                   /usr/lib64/R/library/graphics/libs/graphics.so
7f91c90ea000-7f91c90eb000 rw-p 00047000 08:02 16517289                   /usr/lib64/R/library/graphics/libs/graphics.so
7f91c90eb000-7f91c90f7000 r-xp 00000000 08:02 16519717                   /usr/lib64/R/library/utils/libs/utils.so
7f91c90f7000-7f91c92f6000 ---p 0000c000 08:02 16519717                   /usr/lib64/R/library/utils/libs/utils.so
7f91c92f6000-7f91c92f7000 r--p 0000b000 08:02 16519717                   /usr/lib64/R/library/utils/libs/utils.so
7f91c92f7000-7f91c92f8000 rw-p 0000c000 08:02 16519717                   /usr/lib64/R/library/utils/libs/utils.so
7f91c92f8000-7f91c92f9000 rw-p 00000000 00:00 0 
7f91c946a000-7f91c94a0000 r-xp 00000000 08:02 16517174                   /usr/lib64/R/library/grDevices/libs/grDevices.so
7f91c94a0000-7f91c969f000 ---p 00036000 08:02 16517174                   /usr/lib64/R/library/grDevices/libs/grDevices.so
7f91c969f000-7f91c96a4000 r--p 00035000 08:02 16517174                   /usr/lib64/R/library/grDevices/libs/grDevices.so
7f91c96a4000-7f91c96a6000 rw-p 0003a000 08:02 16517174                   /usr/lib64/R/library/grDevices/libs/grDevices.so
7f91c96a6000-7f91cad35000 rw-p 00000000 00:00 0 
7f91cad35000-7f91cad37000 r-xp 00000000 08:02 10749715                   /usr/lib64/gconv/ISO8859-1.so
7f91cad37000-7f91caf36000 ---p 00002000 08:02 10749715                   /usr/lib64/gconv/ISO8859-1.so
7f91caf36000-7f91caf37000 r--p 00001000 08:02 10749715                   /usr/lib64/gconv/ISO8859-1.so
7f91caf37000-7f91caf38000 rw-p 00002000 08:02 10749715                   /usr/lib64/gconv/ISO8859-1.so
7f91cb004000-7f91cb144000 rw-p 00000000 00:00 0 
7f91cb144000-7f91cb14c000 r-xp 00000000 08:02 16517679                   /usr/lib64/R/library/methods/libs/methods.so
7f91cb14c000-7f91cb34c000 ---p 00008000 08:02 16517679                   /usr/lib64/R/library/methods/libs/methods.so
7f91cb34c000-7f91cb34d000 r--p 00008000 08:02 16517679                   /usr/lib64/R/library/methods/libs/methods.so
7f91cb34d000-7f91cb34e000 rw-p 00009000 08:02 16517679                   /usr/lib64/R/library/methods/libs/methods.so
7f91cb37d000-7f91cb786000 rw-p 00000000 00:00 0 
7f91cb786000-7f91d1cb0000 r--p 00000000 08:02 10757993                   /usr/lib/locale/locale-archive
7f91d1cb0000-7f91d1d99000 r-xp 00000000 08:02 10354712                   /usr/lib64/libstdc++.so.6.0.19
7f91d1d99000-7f91d1f98000 ---p 000e9000 08:02 10354712                   /usr/lib64/libstdc++.so.6.0.19
7f91d1f98000-7f91d1fa0000 r--p 000e8000 08:02 10354712                   /usr/lib64/libstdc++.so.6.0.19
7f91d1fa0000-7f91d1fa2000 rw-p 000f0000 08:02 10354712                   /usr/lib64/libstdc++.so.6.0.19
7f91d1fa2000-7f91d1fb7000 rw-p 00000000 00:00 0 
7f91d1fb7000-7f91d338a000 r-xp 00000000 08:02 10356692                   /usr/lib64/libicudata.so.50.1.2
7f91d338a000-7f91d3589000 ---p 013d3000 08:02 10356692                   /usr/lib64/libicudata.so.50.1.2
7f91d3589000-7f91d358a000 r--p 013d2000 08:02 10356692                   /usr/lib64/libicudata.so.50.1.2
7f91d358a000-7f91d358b000 rw-p 013d3000 08:02 10356692                   /usr/lib64/libicudata.so.50.1.2
7f91d358b000-7f91d35b0000 r-xp 00000000 08:02 10356506                   /usr/lib64/libtinfo.so.5.9
7f91d35b0000-7f91d37b0000 ---p 00025000 08:02 10356506                   /usr/lib64/libtinfo.so.5.9
7f91d37b0000-7f91d37b4000 r--p 00025000 08:02 10356506                   /usr/lib64/libtinfo.so.5.9
7f91d37b4000-7f91d37b5000 rw-p 00029000 08:02 10356506                   /usr/lib64/libtinfo.so.5.9
7f91d37b5000-7f91d37ca000 r-xp 00000000 08:02 10360824                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f91d37ca000-7f91d39c9000 ---p 00015000 08:02 10360824                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f91d39c9000-7f91d39ca000 r--p 00014000 08:02 10360824                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f91d39ca000-7f91d39cb000 rw-p 00015000 08:02 10360824                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f91d39cb000-7f91d3bbb000 r-xp 00000000 08:02 10356694                   /usr/lib64/libicui18n.so.50.1.2
7f91d3bbb000-7f91d3dbb000 ---p 001f0000 08:02 10356694                   /usr/lib64/libicui18n.so.50.1.2
7f91d3dbb000-7f91d3dc7000 r--p 001f0000 08:02 10356694                   /usr/lib64/libicui18n.so.50.1.2
7f91d3dc7000-7f91d3dc9000 rw-p 001fc000 08:02 10356694                   /usr/lib64/libicui18n.so.50.1.2
7f91d3dc9000-7f91d3dca000 rw-p 00000000 00:00 0 
7f91d3dca000-7f91d3f2e000 r-xp 00000000 08:02 10356706                   /usr/lib64/libicuuc.so.50.1.2
7f91d3f2e000-7f91d412e000 ---p 00164000 08:02 10356706                   /usr/lib64/libicuuc.so.50.1.2
7f91d412e000-7f91d413e000 r--p 00164000 08:02 10356706                   /usr/lib64/libicuuc.so.50.1.2
7f91d413e000-7f91d413f000 rw-p 00174000 08:02 10356706                   /usr/lib64/libicuuc.so.50.1.2
7f91d413f000-7f91d4143000 rw-p 00000000 00:00 0 
7f91d4143000-7f91d4145000 r-xp 00000000 08:02 10365211                   /usr/lib64/libdl-2.17.so
7f91d4145000-7f91d4345000 ---p 00002000 08:02 10365211                   /usr/lib64/libdl-2.17.so
7f91d4345000-7f91d4346000 r--p 00002000 08:02 10365211                   /usr/lib64/libdl-2.17.so
7f91d4346000-7f91d4347000 rw-p 00003000 08:02 10365211                   /usr/lib64/libdl-2.17.so
7f91d4347000-7f91d434e000 r-xp 00000000 08:02 10365702                   /usr/lib64/librt-2.17.so
7f91d434e000-7f91d454d000 ---p 00007000 08:02 10365702                   /usr/lib64/librt-2.17.so
7f91d454d000-7f91d454e000 r--p 00006000 08:02 10365702                   /usr/lib64/librt-2.17.so
7f91d454e000-7f91d454f000 rw-p 00007000 08:02 10365702                   /usr/lib64/librt-2.17.so
7f91d454f000-7f91d4564000 r-xp 00000000 08:02 10356550                   /usr/lib64/libz.so.1.2.7
7f91d4564000-7f91d4763000 ---p 00015000 08:02 10356550                   /usr/lib64/libz.so.1.2.7
7f91d4763000-7f91d4764000 r--p 00014000 08:02 10356550                   /usr/lib64/libz.so.1.2.7
7f91d4764000-7f91d4765000 rw-p 00015000 08:02 10356550                   /usr/lib64/libz.so.1.2.7
7f91d4765000-7f91d4774000 r-xp 00000000 08:02 10356610                   /usr/lib64/libbz2.so.1.0.6
7f91d4774000-7f91d4973000 ---p 0000f000 08:02 10356610                   /usr/lib64/libbz2.so.1.0.6
7f91d4973000-7f91d4974000 r--p 0000e000 08:02 10356610                   /usr/lib64/libbz2.so.1.0.6
7f91d4974000-7f91d4975000 rw-p 0000f000 08:02 10356610                   /usr/lib64/libbz2.so.1.0.6
7f91d4975000-7f91d499a000 r-xp 00000000 08:02 10356535                   /usr/lib64/liblzma.so.5.2.2
7f91d499a000-7f91d4b99000 ---p 00025000 08:02 10356535                   /usr/lib64/liblzma.so.5.2.2
7f91d4b99000-7f91d4b9a000 r--p 00024000 08:02 10356535                   /usr/lib64/liblzma.so.5.2.2
7f91d4b9a000-7f91d4b9b000 rw-p 00025000 08:02 10356535                   /usr/lib64/liblzma.so.5.2.2
7f91d4b9b000-7f91d4bfb000 r-xp 00000000 08:02 10365084                   /usr/lib64/libpcre.so.1.2.0
7f91d4bfb000-7f91d4dfb000 ---p 00060000 08:02 10365084                   /usr/lib64/libpcre.so.1.2.0
7f91d4dfb000-7f91d4dfc000 r--p 00060000 08:02 10365084                   /usr/lib64/libpcre.so.1.2.0
7f91d4dfc000-7f91d4dfd000 rw-p 00061000 08:02 10365084                   /usr/lib64/libpcre.so.1.2.0
7f91d4dfd000-7f91d4e73000 r-xp 00000000 08:02 10371493                   /usr/lib64/libpcre2-8.so.0.5.0
7f91d4e73000-7f91d5072000 ---p 00076000 08:02 10371493                   /usr/lib64/libpcre2-8.so.0.5.0
7f91d5072000-7f91d5073000 r--p 00075000 08:02 10371493                   /usr/lib64/libpcre2-8.so.0.5.0
7f91d5073000-7f91d5074000 rw-p 00076000 08:02 10371493                   /usr/lib64/libpcre2-8.so.0.5.0
7f91d5074000-7f91d5083000 r-xp 00000000 08:02 10367294                   /usr/lib64/libtre.so.5.0.0
7f91d5083000-7f91d5282000 ---p 0000f000 08:02 10367294                   /usr/lib64/libtre.so.5.0.0
7f91d5282000-7f91d5283000 r--p 0000e000 08:02 10367294                   /usr/lib64/libtre.so.5.0.0
7f91d5283000-7f91d5284000 rw-p 0000f000 08:02 10367294                   /usr/lib64/libtre.so.5.0.0
7f91d5284000-7f91d52c0000 r-xp 00000000 08:02 10356649                   /usr/lib64/libreadline.so.6.2
7f91d52c0000-7f91d54c0000 ---p 0003c000 08:02 10356649                   /usr/lib64/libreadline.so.6.2
7f91d54c0000-7f91d54c2000 r--p 0003c000 08:02 10356649                   /usr/lib64/libreadline.so.6.2
7f91d54c2000-7f91d54c8000 rw-p 0003e000 08:02 10356649                   /usr/lib64/libreadline.so.6.2
7f91d54c8000-7f91d54ca000 rw-p 00000000 00:00 0 
7f91d54ca000-7f91d5505000 r-xp 00000000 08:02 10356764                   /usr/lib64/libquadmath.so.0.0.0
7f91d5505000-7f91d5704000 ---p 0003b000 08:02 10356764                   /usr/lib64/libquadmath.so.0.0.0
7f91d5704000-7f91d5705000 r--p 0003a000 08:02 10356764                   /usr/lib64/libquadmath.so.0.0.0
7f91d5705000-7f91d5706000 rw-p 0003b000 08:02 10356764                   /usr/lib64/libquadmath.so.0.0.0
7f91d5706000-7f91d5807000 r-xp 00000000 08:02 10365634                   /usr/lib64/libm-2.17.so
7f91d5807000-7f91d5a06000 ---p 00101000 08:02 10365634                   /usr/lib64/libm-2.17.so
7f91d5a06000-7f91d5a07000 r--p 00100000 08:02 10365634                   /usr/lib64/libm-2.17.so
7f91d5a07000-7f91d5a08000 rw-p 00101000 08:02 10365634                   /usr/lib64/libm-2.17.so
7f91d5a08000-7f91d5b27000 r-xp 00000000 08:02 10367748                   /usr/lib64/libgfortran.so.3.0.0
7f91d5b27000-7f91d5d27000 ---p 0011f000 08:02 10367748                   /usr/lib64/libgfortran.so.3.0.0
7f91d5d27000-7f91d5d28000 r--p 0011f000 08:02 10367748                   /usr/lib64/libgfortran.so.3.0.0
7f91d5d28000-7f91d5d2a000 rw-p 00120000 08:02 10367748                   /usr/lib64/libgfortran.so.3.0.0
7f91d5d2a000-7f91d5eec000 r-xp 00000000 08:02 10356429                   /usr/lib64/libc-2.17.so
7f91d5eec000-7f91d60ec000 ---p 001c2000 08:02 10356429                   /usr/lib64/libc-2.17.so
7f91d60ec000-7f91d60f0000 r--p 001c2000 08:02 10356429                   /usr/lib64/libc-2.17.so
7f91d60f0000-7f91d60f2000 rw-p 001c6000 08:02 10356429                   /usr/lib64/libc-2.17.so
7f91d60f2000-7f91d60f7000 rw-p 00000000 00:00 0 
7f91d60f7000-7f91d610e000 r-xp 00000000 08:02 10356459                   /usr/lib64/libpthread-2.17.so
7f91d610e000-7f91d630d000 ---p 00017000 08:02 10356459                   /usr/lib64/libpthread-2.17.so
7f91d630d000-7f91d630e000 r--p 00016000 08:02 10356459                   /usr/lib64/libpthread-2.17.so
7f91d630e000-7f91d630f000 rw-p 00017000 08:02 10356459                   /usr/lib64/libpthread-2.17.so
7f91d630f000-7f91d6313000 rw-p 00000000 00:00 0 
7f91d6313000-7f91d6338000 r-xp 00000000 08:02 10357222                   /usr/lib64/libgomp.so.1.0.0
7f91d6338000-7f91d6537000 ---p 00025000 08:02 10357222                   /usr/lib64/libgomp.so.1.0.0
7f91d6537000-7f91d6538000 r--p 00024000 08:02 10357222                   /usr/lib64/libgomp.so.1.0.0
7f91d6538000-7f91d6539000 rw-p 00025000 08:02 10357222                   /usr/lib64/libgomp.so.1.0.0
7f91d6539000-7f91d8805000 r-xp 00000000 08:02 16515075                   /usr/lib64/R/lib/libRblas.so
7f91d8805000-7f91d8a04000 ---p 022cc000 08:02 16515075                   /usr/lib64/R/lib/libRblas.so
7f91d8a04000-7f91d8a08000 r--p 022cb000 08:02 16515075                   /usr/lib64/R/lib/libRblas.so
7f91d8a08000-7f91d8a22000 rw-p 022cf000 08:02 16515075                   /usr/lib64/R/lib/libRblas.so
7f91d8a22000-7f91d8a2d000 rw-p 00000000 00:00 0 
7f91d8a2d000-7f91d8d2f000 r-xp 00000000 08:02 16515475                   /usr/lib64/R/lib/libR.so
7f91d8d2f000-7f91d8f2f000 ---p 00302000 08:02 16515475                   /usr/lib64/R/lib/libR.so
7f91d8f2f000-7f91d8f4d000 r--p 00302000 08:02 16515475                   /usr/lib64/R/lib/libR.so
7f91d8f4d000-7f91d8f59000 rw-p 00320000 08:02 16515475                   /usr/lib64/R/lib/libR.so
7f91d8f59000-7f91d90ab000 rw-p 00000000 00:00 0 
7f91d90ab000-7f91d90cd000 r-xp 00000000 08:02 10356422                   /usr/lib64/ld-2.17.so
7f91d9153000-7f91d92a6000 rw-p 00000000 00:00 0 
7f91d92c0000-7f91d92c1000 rw-p 00000000 00:00 0 
7f91d92c1000-7f91d92c2000 r--p 00000000 08:02 16519282                   /usr/lib64/R/library/translations/en/LC_MESSAGES/R.mo
7f91d92c2000-7f91d92c9000 r--s 00000000 08:02 10749792                   /usr/lib64/gconv/gconv-modules.cache
7f91d92c9000-7f91d92cc000 rw-p 00000000 00:00 0 
7f91d92cc000-7f91d92cd000 r--p 00021000 08:02 10356422                   /usr/lib64/ld-2.17.so
7f91d92cd000-7f91d92ce000 rw-p 00022000 08:02 10356422                   /usr/lib64/ld-2.17.so
7f91d92ce000-7f91d92cf000 rw-p 00000000 00:00 0 
7fff5484d000-7fff54889000 rw-p 00000000 00:00 0                          [stack]
7fff5491f000-7fff54921000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

I have been running the same script previously and it ran successfully. But is started giving me this error since today morning. I tried updating R but it didn't help.
Any help is highly appreciated.

Thanks.

chemal
Posts: 674
Joined: 2013/12/08 19:44:49

Re: R aborts abruptly on Centos7 (Error in `/usr/lib64/R/bin/exec/R': free(): invalid pointer)

Post by chemal » 2020/06/04 04:00:19

R isn't shipped by CentOS.

Your script is reading a couple of files. I guess they changed before you ran your script again this morning.

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