I am getting a segfault with Rsubread. It appears to finish, but then segfaults and kills R. > library(Rsubread) > fls <- paste0("../data/", dir("../data/", "sam$")) > dat <- featureCounts(fls, annot.inbuilt = "mm10") Mouse annotation NCBI Build 38.1 is used. ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 1.12.0 //========================== featureCounts setting ===========================\ || || || Input files : 24 SAM files || || o ../data/RCP12.sam || || o ../data/RCP14.sam || || o ../data/RCP16.sam || || o ../data/RCP1_REPEAT.sam || || o ../data/RCP20_REPEAT.sam || || o ../data/RCP21.sam || || o ../data/RCP22.sam || || o ../data/RCP2.sam || || o ../data/RCP3.sam || || o ../data/RCP6.sam || || o ../data/RCP7.sam || || o ../data/RCP9.sam || || o ../data/RUP13.sam || || o ../data/RUP15_REPEAT.sam || || o ../data/RUP17.sam || || o ../data/RUP19.sam || || o ../data/RUP1.sam || || o ../data/RUP20.sam || || o ../data/RUP22_REPEAT.sam || || o ../data/RUP23.sam || || o ../data/RUP24.sam || || o ../data/RUP25.sam || || o ../data/RUP26.sam || || o ../data/RUP27.sam || || || || Output file : ./.Rsubread_featureCounts_pid30445 || || Annotations : /data/programs/lib64/R/library/Rsubread/anno ... || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Strand specific : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || || \===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\ || || || Load annotation file /data/programs/lib64/R/library/Rsubread/annot/mm1 ... || || Number of features is 222996 || || Number of meta-features is 27179 || || Number of chromosomes is 43 || <snip> || Process ../data/RUP27.sam ... || || Total number of reads is : 12363805 || || Number of successfully assigned reads is : 6077652 (49.2%) || || Running time : 0.12 minutes || || || || Read assignment finished. || || || \===================== http://subread.sourceforge.net/ ======================// *** Error in `/data/programs/lib64/R/bin/exec/R': double free or corruption (!prev): 0x0000000001e2f8f0 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7aa26)[0x7f7ddc4e3a26] /lib/x86_64-linux-gnu/libc.so.6(+0x7b7a3)[0x7f7ddc4e47a3] /data/programs/lib64/R/library/Rsubread/libs/Rsubread.so(R_readSummary _wrapper+0x110)[0x7f7ddae9eac0] /data/programs/lib64/R/bin/exec/R[0x475226] /data/programs/lib64/R/bin/exec/R(Rf_eval+0x5db)[0x4aefcb] /data/programs/lib64/R/bin/exec/R[0x4b1d90] /data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31] /data/programs/lib64/R/bin/exec/R[0x4b1f50] /data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31] /data/programs/lib64/R/bin/exec/R(Rf_applyClosure+0x34b)[0x4a16cb] /data/programs/lib64/R/bin/exec/R(Rf_eval+0x1ee)[0x4aebde] /data/programs/lib64/R/bin/exec/R[0x4b1d90] /data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31] /data/programs/lib64/R/bin/exec/R[0x4b1f50] /data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31] /data/programs/lib64/R/bin/exec/R(Rf_eval+0x441)[0x4aee31] /data/programs/lib64/R/bin/exec/R(Rf_ReplIteration+0x229)[0x4d0d99] /data/programs/lib64/R/bin/exec/R[0x4d0ff9] /data/programs/lib64/R/bin/exec/R(run_Rmainloop+0x41)[0x4d14b1] /data/programs/lib64/R/bin/exec/R(main+0x18)[0x415c38] /lib/x86_64-linux- gnu/libc.so.6(__libc_start_main+0xf5)[0x7f7ddc48a995] /data/programs/lib64/R/bin/exec/R[0x415b49] ======= Memory map: ======== 00400000-00679000 r-xp 00000000 08:21 100622427 /data/programs/lib64/R/bin/exec/R 00878000-00883000 rw-p 00278000 08:21 100622427 /data/programs/lib64/R/bin/exec/R 00883000-0096e000 rw-p 00000000 00:00 0 01114000-02f0a000 rw-p 00000000 00:00 0 [heap] 7f7dda193000-7f7dda1aa000 r-xp 00000000 08:11 21415 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f7dda1aa000-7f7dda3a9000 ---p 00017000 08:11 21415 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f7dda3a9000-7f7dda3aa000 r--p 00016000 08:11 21415 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f7dda3aa000-7f7dda3ab000 rw-p 00017000 08:11 21415 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f7dda3ab000-7f7dda560000 r-xp 00000000 08:21 100515846 /data/programs/lib64/R/lib/libRlapack.so 7f7dda560000-7f7dda75f000 ---p 001b5000 08:21 100515846 /data/programs/lib64/R/lib/libRlapack.so 7f7dda75f000-7f7dda761000 rw-p 001b4000 08:21 100515846 /data/programs/lib64/R/lib/libRlapack.so 7f7dda761000-7f7dda7fa000 r-xp 00000000 08:21 100524323 /data/programs/lib64/R/library/stats/libs/stats.so 7f7dda7fa000-7f7dda9fa000 ---p 00099000 08:21 100524323 /data/programs/lib64/R/library/stats/libs/stats.so 7f7dda9fa000-7f7dda9fd000 rw-p 00099000 08:21 100524323 /data/programs/lib64/R/library/stats/libs/stats.so 7f7dda9fd000-7f7dda9fe000 rw-p 00000000 00:00 0 7f7dda9fe000-7f7ddaa3c000 r-xp 00000000 08:21 100573350 /data/programs/lib64/R/library/graphics/libs/graphics.so 7f7ddaa3c000-7f7ddac3b000 ---p 0003e000 08:21 100573350 /data/programs/lib64/R/library/graphics/libs/graphics.so 7f7ddac3b000-7f7ddac3d000 rw-p 0003d000 08:21 100573350 /data/programs/lib64/R/library/graphics/libs/graphics.so 7f7ddac3d000-7f7ddac79000 r-xp 00000000 08:21 100524653 /data/programs/lib64/R/library/grDevices/libs/grDevices.so 7f7ddac79000-7f7ddae79000 ---p 0003c000 08:21 100524653 /data/programs/lib64/R/library/grDevices/libs/grDevices.so 7f7ddae79000-7f7ddae7f000 rw-p 0003c000 08:21 100524653 /data/programs/lib64/R/library/grDevices/libs/grDevices.so 7f7ddae7f000-7f7ddae80000 rw-p 00000000 00:00 0 7f7ddae90000-7f7ddaeee000 r-xp 00000000 08:21 103170387 /data/programs/lib64/R/library/Rsubread/libs/Rsubread.so 7f7ddaeee000-7f7ddb0ed000 ---p 0005e000 08:21 103170387 /data/programs/lib64/R/library/Rsubread/libs/Rsubread.so 7f7ddb0ed000-7f7ddb0ef000 rw-p 0005d000 08:21 103170387 /data/programs/lib64/R/library/Rsubread/libs/Rsubread.so 7f7ddb0ef000-7f7ddb0fa000 rw-p 00000000 00:00 0 7f7ddb0fa000-7f7ddb0fc000 r-xp 00000000 08:15 124401 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so 7f7ddb0fc000-7f7ddb2fb000 ---p 00002000 08:15 124401 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so 7f7ddb2fb000-7f7ddb2fc000 r--p 00001000 08:15 124401 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so 7f7ddb2fc000-7f7ddb2fd000 rw-p 00002000 08:15 124401 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so 7f7ddb2fd000-7f7ddb406000 rw-p 00000000 00:00 0 7f7ddb406000-7f7ddb40d000 r-xp 00000000 08:21 100606286 /data/programs/lib64/R/library/methods/libs/methods.so 7f7ddb40d000-7f7ddb60d000 ---p 00007000 08:21 100606286 /data/programs/lib64/R/library/methods/libs/methods.so 7f7ddb60d000-7f7ddb60e000 rw-p 00007000 08:21 100606286 /data/programs/lib64/R/library/methods/libs/methods.so 7f7ddb60e000-7f7ddb618000 r-xp 00000000 08:21 100566155 /data/programs/lib64/R/library/utils/libs/utils.so 7f7ddb618000-7f7ddb818000 ---p 0000a000 08:21 100566155 /data/programs/lib64/R/library/utils/libs/utils.so 7f7ddb818000-7f7ddb819000 rw-p 0000a000 08:21 100566155 /data/programs/lib64/R/library/utils/libs/utils.so 7f7ddb819000-7f7ddb81a000 rw-p 00000000 00:00 0 7f7ddb81a000-7f7ddb821000 r-xp 00000000 08:11 21551 /lib/x86_64-linux-gnu/libnss_sss.so.2 7f7ddb821000-7f7ddba20000 ---p 00007000 08:11 21551 /lib/x86_64-linux-gnu/libnss_sss.so.2 7f7ddba20000-7f7ddba21000 r--p 00006000 08:11 21551 /lib/x86_64-linux-gnu/libnss_sss.so.2 7f7ddba21000-7f7ddba22000 rw-p 00007000 08:11 21551 /lib/x86_64-linux-gnu/libnss_sss.so.2 7f7ddba22000-7f7ddba2e000 r-xp 00000000 08:11 21617 /lib/x86_64-linux-gnu/libnss_files-2.17.so 7f7ddba2e000-7f7ddbc2d000 ---p 0000c000 08:11 21617 /lib/x86_64-linux-gnu/libnss_files-2.17.so 7f7ddbc2d000-7f7ddbc2e000 r--p 0000b000 08:11 21617 /lib/x86_64-linux-gnu/libnss_files-2.17.so 7f7ddbc2e000-7f7ddbc2f000 rw-p 0000c000 08:11 21617 /lib/x86_64-linux-gnu/libnss_files-2.17.so 7f7ddbc2f000-7f7ddbdd8000 rw-p 00000000 00:00 0 7f7ddbdd8000-7f7ddbe1a000 r-xp 00000000 08:11 23573 /lib/libncurses.so.5.7 7f7ddbe1a000-7f7ddc019000 ---p 00042000 08:11 23573 /lib/libncurses.so.5.7 7f7ddc019000-7f7ddc01e000 rw-p 00041000 08:11 23573 /lib/libncurses.so.5.7 7f7ddc01e000-7f7ddc033000 r-xp 00000000 08:11 21583 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f7ddc033000-7f7ddc233000 ---p 00015000 08:11 21583 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f7ddc233000-7f7ddc234000 rw-p 00015000 08:11 21583 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f7ddc234000-7f7ddc269000 r-xp 00000000 08:15 458903 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 7f7ddc269000-7f7ddc468000 ---p 00035000 08:15 458903 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 7f7ddc468000-7f7ddc469000 rw-p 00034000 08:15 458903 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 7f7ddc469000-7f7ddc60b000 r-xp 00000000 08:11 21566 /lib/x86_64-linux-gnu/libc-2.17.so 7f7ddc60b000-7f7ddc80b000 ---p 001a2000 08:11 21566 /lib/x86_64-linux-gnu/libc-2.17.so 7f7ddc80b000-7f7ddc80f000 r--p 001a2000 08:11 21566 /lib/x86_64-linux-gnu/libc-2.17.so 7f7ddc80f0 Process /data/programs/bin/R aborted at Tue Oct 22 12:34:40 2013 And after restarting, > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rsubread_1.12.0 loaded via a namespace (and not attached): [1] compiler_3.0.2 tools_3.0.2 If I split the files up into groups of eight, I could get featureCounts to run. Also please note that I am using the current version of Subread: jmacdon$ subread-align Version 1.4.0 Best, Jim -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099