R语言 启动报错 *** glibc detected *** /usr/lib64/R/bin/exec/R: free(): invalid next size (fast): 0x000000000263a420 *** 错误 解决方案
*** glibc detected *** /usr/lib64/R/bin/exec/R: free(): invalid next size (fast): 0x000000000263a420 *** ======= Backtrace: ========= /lib64/libc.so.6[0x313a47dda6] /lib64/libc.so.6[0x313a47f08e] /home/phoxis/Documents/Works/Programming/R/libmetis.so(gk_free+0x9a)[0x7fd5ef3a7eba] /home/phoxis/Documents/Works/Programming/R/libmetis.so(libmetis__FreeRData+0x71)[0x7fd5ef3cf5e1] /home/phoxis/Documents/Works/Programming/R/libmetis.so(libmetis__FreeGraph+0x5a)[0x7fd5ef3cf65a] /home/phoxis/Documents/Works/Programming/R/libmetis.so(libmetis__MlevelRecursiveBisection+0x15c)[0x7fd5ef3d242c] /home/phoxis/Documents/Works/Programming/R/libmetis.so(METIS_PartGraphRecursive+0x166)[0x7fd5ef3d2796] /home/phoxis/Documents/Works/Programming/R/metiswrap.so(metis_wrap+0xc6)[0x7fd5ef184d86] /usr/lib64/R/lib/libR.so[0x376b8b148d] /usr/lib64/R/lib/libR.so(Rf_eval+0x739)[0x376b8e1b09] /usr/lib64/R/lib/libR.so[0x376b8e4790] /usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x376b8e192b] /usr/lib64/R/lib/libR.so[0x376b8e4910] /usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x376b8e192b] /usr/lib64/R/lib/libR.so(Rf_applyClosure+0x322)[0x376b8e5c32] /usr/lib64/R/lib/libR.so(Rf_eval+0x430)[0x376b8e1800] /usr/lib64/R/lib/libR.so[0x376b8e4790] /usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x376b8e192b] /usr/lib64/R/lib/libR.so[0x376b8e4910] /usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x376b8e192b] /usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x376b8e192b] /usr/lib64/R/lib/libR.so[0x376b8e4910] /usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x376b8e192b] /usr/lib64/R/lib/libR.so[0x376b8e65ec] /usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x376b8e192b]/usr/lib64/R/lib/libR.so[0x376b8e4910]/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x376b8e192b]/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x322)[0x376b8e5c32]/usr/lib64/R/lib/libR.so(Rf_eval+0x430)[0x376b8e1800]/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x1e3)[0x376b9178b3]/usr/lib64/R/lib/libR.so[0x376b917b40]/usr/lib64/R/lib/libR.so(run_Rmainloop+0x50)[0x376b918060]/usr/lib64/R/bin/exec/R(main+0x1b)[0x40076b]/lib64/libc.so.6(__libc_start_main+0xed)[0x313a42169d]/usr/lib64/R/bin/exec/R[0x40079d]=======Memory map:========00400000-00401000 r-xp 0000000008:011051073/usr/lib64/R/bin/exec/R 00600000-00601000 r--p 0000000008:011051073/usr/lib64/R/bin/exec/R 00601000-00603000 rw-p 0000100008:011051073/usr/lib64/R/bin/exec/R 022f8000-03928000 rw-p 0000000000:000[heap]313a000000-313a022000 r-xp 0000000008:01786460/lib64/ld-2.14.90.so313a221000-313a222000 r--p 0002100008:01786460/lib64/ld-2.14.90.so313a222000-313a223000 rw-p 0002200008:01786460/lib64/ld-2.14.90.so313a223000-313a224000 rw-p 0000000000:000313a400000-313a5ad000 r-xp 0000000008:01786461/lib64/libc-2.14.90.so313a5ad000-313a7ad000---p 001ad00008:01786461/lib64/libc-2.14.90.so313a7ad000-313a7b1000 r--p 001ad00008:01786461/lib64/libc-2.14.90.so313a7b1000-313a7b3000 rw-p 001b100008:01786461/lib64/libc-2.14.90.so313a7b3000-313a7b8000 rw-p 0000000000:000313a800000-313a883000 r-xp 0000000008:01788752/lib64/libm-2.14.90.so313a883000-313aa82000---p 0008300008:01788752/lib64/libm-2.14.90.so313aa82000-313aa83000 r--p 0008200008:01788752/lib64/libm-2.14.90.so313aa83000-313aa84000 rw-p 0008300008:01788752/lib64/libm-2.14.90.so313ac00000-313ac17000 r-xp 0000000008:01786462/lib64/libpthread-2.14.90.so313ac17000-313ae16000---p 0001700008:01786462/lib64/libpthread-2.14.90.so313ae16000-313ae17000 r--p 0001600008:01786462/lib64/libpthread-2.14.90.so313ae17000-313ae18000 rw-p 0001700008:01786462/lib64/libpthread-2.14.90.so313ae18000-313ae1c000 rw-p 0000000000:000313b000000-313b002000 r-xp 0000000008:01786502/lib64/libdl-2.14.90.so313b002000-313b202000---p 0000200008:01786502/lib64/libdl-2.14.90.so313b202000-313b203000 r--p 0000200008:01786502/lib64/libdl-2.14.90.so313b203000-313b204000 rw-p 0000300008:01786502/lib64/libdl-2.14.90.so313b400000-313b407000 r-xp 0000000008:01786463/lib64/librt-2.14.90.so313b407000-313b606000---p 0000700008:01786463/lib64/librt-2.14.90.so313b606000-313b607000 r--p 0000600008:01786463/lib64/librt-2.14.90.so313b607000-313b608000 rw-p 0000700008:01786463/lib64/librt-2.14.90.so313b800000-313b815000 r-xp 0000000008:01788765/lib64/libgcc_s-4.6.3-20120306.so.1313b815000-313ba14000---p 0001500008:01788765/lib64/libgcc_s-4.6.3-20120306.so.1313ba14000-313ba15000 rw-p 0001400008:01788765/lib64/libgcc_s-4.6.3-20120306.so.1313bc00000-313bc17000 r-xp 0000000008:01786474/lib64/libz.so.1.2.5313bc17000-313be16000---p 0001700008:01786474/lib64/libz.so.1.2.5313be16000-313be17000 rw-p 0001600008:01786474/lib64/libz.so.1.2.5313ec00000-313ece8000 r-xp 0000000008:01150116/usr/lib64/libstdc++.so.6.0.16313ece8000-313eee8000---p 000e800008:01150116/usr/lib64/libstdc++.so.6.0.16313eee8000-313eef0000 r--p 000e800008:01150116/usr/lib64/libstdc++.so.6.0.16313eef0000-313eef2000 rw-p 000f000008:01150116/usr/lib64/libstdc++.so.6.0.16313eef2000-313ef07000 rw-p 0000000000:0003140400000-314043c000 r-xp 0000000008:01786583/lib64/libreadline.so.6.2314043c000-314063b000---p 0003c00008:01786583/lib64/libreadline.so.6.2314063b000-3140643000 rw-p 0003b00008:01786583/lib64/libreadline.so.6.23140643000-3140644000 rw-p 0000000000:0003145000000-314500f000 r-xp 0000000008:01788834/lib64/libbz2.so.1.0.6314500f000-314520e000---p 0000f00008:01788834/lib64/libbz2.so.1.0.6314520e000-3145210000 rw-p 0000e00008:01788834/lib64/libbz2.so.1.0.63148c00000-3148c23000 r-xp 0000000008:01815621/lib64/libtinfo.so.5.93148c23000-3148e22000---p 0002300008:01815621/lib64/libtinfo.so.5.93148e22000-3148e26000 r--p 0002200008:01815621/lib64/libtinfo.so.5.93148e26000-3148e27000 rw-p 0002600008:01815621/lib64/libtinfo.so.5.93149200000-3149338000 r-xp 0000000008:01177515/usr/lib64/libicuuc.so.46.03149338000-3149538000---p 0013800008:01177515/usr/lib64/libicuuc.so.46.03149538000-3149547000 r--p 0013800008:01177515/usr/lib64/libicuuc.so.46.03149547000-3149548000 rw-p 0014700008:01177515/usr/lib64/libicuuc.so.46.03149548000-314954c000 rw-p 0000000000:000314b600000-314b7b1000 r-xp 0000000008:01148922/usr/lib64/libicui18n.so.46.0314b7b1000-314b9b1000---p 001b100008:01148922/usr/lib64/libicui18n.so.46.0314b9b1000-314b9bc000 r--p 001b100008:01148922/usr/lib64/libicui18n.so.46.0314b9bc000-314b9be000 rw-p 001bc00008:01148922/usr/lib64/libicui18n.so.46.0314da00000-314e873000 r-xp 0000000008:01137354/usr/lib64/libicudata.so.46.0314e873000-314ea72000---p 00e7300008:01137354/usr/lib64/libicudata.so.46.0314ea72000-314ea73000 r--p 00e7200008:01137354/usr/lib64/libicudata.so.46.0314ea73000-314ea74000 rw-p 00e7300008:01137354/usr/lib64/libicudata.so.46.03158200000-315820d000 r-xp 0000000008:01165367/usr/lib64/libgomp.so.1.0.0315820d000-315840c000---p 0000d00008:01165367/usr/lib64/libgomp.so.1.0.0315840c000-315840d000 rw-p 0000c00008:01165367/usr/lib64/libgomp.so.1.0.0315d600000-315d63c000 r-xp 0000000008:01788840/lib64/libpcre.so.0.0.1315d63c000-315d83b000---p 0003c00008:01788840/lib64/libpcre.so.0.0.1315d83b000-315d83c000 r--p 0003b00008:01788840/lib64/libpcre.so.0.0.1315d83c000-315d83d000 rw-p 0003c00008:01788840/lib64/libpcre.so.0.0.1376b400000-376b42b000 r-xp 0000000008:011062362/usr/lib64/R/lib/libRblas.so 376b42b000-376b62a000---p 0002b00008:011062362/usr/lib64/R/lib/libRblas.so 376b62a000-376b62b000 r--p 0002a00008:011062362/usr/lib64/R/lib/libRblas.so 376b62b000-376b62c000 rw-p 0002b00008:011062362/usr/lib64/R/lib/libRblas.so 376b800000-376baa7000 r-xp 0000000008:011062365/usr/lib64/R/lib/libR.so 376baa7000-376bca7000---p 002a700008:011062365/usr/lib64/R/lib/libR.so 376bca7000-376bcad000 r--p 002a700008:011062365/usr/lib64/R/lib/libR.so 376bcad000-376bcbd000 rw-p 002ad00008:011062365/usr/lib64/R/lib/libR.so 376bcbd000-376bdac000 rw-p 0000000000:000376be00000-376bf78000 r-xp 0000000008:011062364/usr/lib64/R/lib/libRlapack.so 376bf78000-376c178000---p 0017800008:011062364/usr/lib64/R/lib/libRlapack.so 376c178000-376c179000 r--p 0017800008:011062364/usr/lib64/R/lib/libRlapack.so 376c179000-376c17a000 rw-p 0017900008:011062364/usr/lib64/R/lib/libRlapack.so 376c200000-376c235000 r-xp 0000000008:01136624/usr/lib64/libquadmath.so.0.0.0376c235000-376c434000---p 0003500008:01136624/usr/lib64/libquadmath.so.0.0.0376c434000-376c435000 rw-p 0003400008:01136624/usr/lib64/libquadmath.so.0.0.0376c600000-376c714000 r-xp 0000000008:01138203/usr/lib64/libgfortran.so.3.0.0376c714000-376c913000---p 0011400008:01138203/usr/lib64/libgfortran.so.3.0.0376c913000-376c915000 rw-p 0011300008:01138203/usr/lib64/libgfortran.so.3.0.0376c915000-376c916000 rw-p 0000000000:0007fd5ef184000-7fd5ef185000 r-xp 0000000008:037609099/home/phoxis/Documents/Works/Programming/R/metiswrap.so 7fd5ef185000-7fd5ef385000---p 0000100008:037609099/home/phoxis/Documents/Works/Programming/R/metiswrap.so 7fd5ef385000-7fd5ef386000 r--p 0000100008:037609099/home/phoxis/Documents/Works/Programming/R/metiswrap.so 7fd5ef386000-7fd5ef387000 rw-p 0000200008:037609099/home/phoxis/Documents/Works/Programming/R/metiswrap.so 7fd5ef387000-7fd5ef3ea000 r-xp 0000000008:037610359/home/phoxis/Documents/Works/Programming/R/libmetis.so 7fd5ef3ea000-7fd5ef5e9000---p 0006300008:037610359/home/phoxis/Documents/Works/Programming/R/libmetis.so 7fd5ef5e9000-7fd5ef5eb000 rw-p 0006200008:037610359/home/phoxis/Documents/Works/Programming/R/libmetis.so 7fd5ef5eb000-7fd5ef5f9000 r-xp 0000000008:037740125/home/phoxis/R/x86_64-redhat-linux-gnu-library/2.15/RANN/libs/RANN.so 7fd5ef5f9000-7fd5ef7f9000---p 0000e00008:037740125/home/phoxis/R/x86_64-redhat-linux-gnu-library/2.15/RANN/libs/RANN.so 7fd5ef7f9000-7fd5ef7fa000 r--p 0000e00008:037740125/home/phoxis/R/x86_64-redhat-linux-gnu-library/2.15/RANN/libs/RANN.so 7fd5ef7fa000-7fd5ef7fb000 rw-p 0000f00008:037740125/home/phoxis/R/x86_64-redhat-linux-gnu-library/2.15/RANN/libs/RANN.so 7fd5ef7fb000-7fd5ef869000 r-xp 0000000008:011203642/usr/lib64/R/library/stats/libs/stats.so 7fd5ef869000-7fd5efa68000---p 0006e00008:011203642/usr/lib64/R/library/stats/libs/stats.so 7fd5efa68000-7fd5efa6a000 r--p 0006d00008:011203642/usr/lib64/R/library/stats/libs/stats.so 7fd5efa6a000-7fd5efa6c000 rw-p 0006f00008:011203642/usr/lib64/R/library/stats/libs/stats.so 7fd5efa6c000-7fd5efbda000 rw-p 0000000000:0007fd5efbda000-7fd5efbfd000 r-xp 0000000008:011077695/usr/lib64/R/library/grDevices/libs/grDevices.so 7fd5efbfd000-7fd5efdfc000---p 0002300008:011077695/usr/lib64/R/library/grDevices/libs/grDevices.so 7fd5efdfc000-7fd5efdfd000 r--p 0002200008:011077695/usr/lib64/R/library/grDevices/libs/grDevices.so 7fd5efdfd000-7fd5efdfe000 rw-p 0002300008:011077695/usr/lib64/R/library/grDevices/libs/grDevices.so 7fd5eff2e000-7fd5f0165000 rw-p 0000000000:0007fd5f0165000-7fd5f016c000 r-xp 0000000008:011078260/usr/lib64/R/library/methods/libs/methods.so 7fd5f016c000-7fd5f036b000---p 0000700008:011078260/usr/lib64/R/library/methods/libs/methods.so 7fd5f036b000-7fd5f036c000 r--p 0000600008:011078260/usr/lib64/R/library/methods/libs/methods.so 7fd5f036c000-7fd5f036d000 rw-p 0000700008:011078260/usr/lib64/R/library/methods/libs/methods.so 7fd5f036d000-7fd5f0402000 rw-p 0000000000:0007fd5f0402000-7fd5f040e000 r-xp 0000000008:01789196/lib64/libnss_files-2.14.90.so7fd5f040e000-7fd5f060d000---p 0000c00008:01789196/lib64/libnss_files-2.14.90.so7fd5f060d000-7fd5f060e000 r--p 0000b00008:01789196/lib64/libnss_files-2.14.90.so7fd5f060e000-7fd5f060f000 rw-p 0000c00008:01789196/lib64/libnss_files-2.14.90.so7fd5f0640000-7fd5f06f1000 rw-p 0000000000:0007fd5f06f3000-7fd5f089c000 rw-p 0000000000:0007fd5f089c000-7fd5f6cbf000 r--p 0000000008:01157303/usr/lib/locale/locale-archive 7fd5f6cbf000-7fd5f6cc9000 rw-p 0000000000:0007fd5f6ccc000-7fd5f6cf3000 rw-p 0000000000:0007fd5f6cf3000-7fd5f6cfa000 r--s 0000000008:01139093/usr/lib64/gconv/gconv-modules.cache 7fd5f6cfa000-7fd5f6cfc000 rw-p 0000000000:0007fff473da000-7fff47403000 rw-p 0000000000:000[stack]7fff474a2000-7fff474a3000 r-xp 0000000000:000[vdso] ffffffffff600000-ffffffffff601000 r-xp 0000000000:000[vsyscall]*** caught segfault *** address (nil), cause 'memory not mapped'
错误应该是由于R语言 版本冲突导致。
启动sparkr时报错为
*** caught segfault *** address 0xffffffffd058abf8, cause 'memory not mapped'
类似解决思路如下：
2015年5月30日 上午2:51 1 楼
缘梦缘
Participant
在mac系统中运行“ GEOquery”包的getGEO ()函数时出现如下提示。但是相同的函数在windows系统运行没有问题。查看一些网页，类似的问题似乎比较多，说可能更新R版本就可以解决，但是我更新完之后，还是有此提示，非常希望能得到大家的指点，非常感谢，^_^
> library(GEOquery)
> data1 <- getGEO(“GSE9844”)
*** caught segfault ***
address 0x18, cause ‘memory not mapped’
Traceback:
1: .Call(“R_getCURLOptionEnum”, PACKAGE = “RCurl”)
2: getCurlOptionsConstants()
3: mapCurlOptNames(names(.els), asNames = TRUE)
4: curlOptions(URL = url, writefunction = writeFun, …, .opts = .opts)
5: getURL(url)
6: getDirListing(sprintf(gdsurl, stub, GEO))
7: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL)
8: getGEO(“GSE9844”)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 2
Save workspace image? [y/n/c]: c
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)
locale:
[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GEOquery_2.35.4 Biobase_2.29.1 BiocGenerics_0.15.1
loaded via a namespace (and not attached):
[1] RCurl_1.95-4.6 bitops_1.0-6 XML_3.98-1.1
2015年5月30日 上午3:44 2 楼
enthumelon
Participant
你的RCurl能运行不？更新下Rcurl可能可以解决。
2015年5月30日 上午9:42 3 楼
缘梦缘
Participant
回复 2 楼 的 enthumelon：
非常感谢，不过没怎么用过RCurl，不知道怎么检验才算运行正常，从网上查了一些RCurl的帮助，尝试运行curl_easy_init函数的例子，但是似乎好像运行不了，这是不是就提示RCurl不能正常运行。尝试更新RCurl包之后再次运行curl_easy_init函数的例子，任然运行不了，请指点。
> library(“RCurl”)
载入需要的程辑包：bitops
> CURL *curl = curl_easy_init();
错误: 没有”curl_easy_init”这个函数
> if(curl) {
+ CURLcode res;
错误: unexpected symbol in:
“if(curl) {
CURLcode res”
> curl_easy_setopt(curl, CURLOPT_URL, “http://example.com”);
错误: 没有”curl_easy_setopt”这个函数
> res = curl_easy_perform(curl);
错误: 没有”curl_easy_perform”这个函数
> curl_easy_cleanup(curl);
错误: 没有”curl_easy_cleanup”这个函数
> }
错误: 意外的’}’ in “}”
2015年5月30日 下午10:53 4 楼
缘梦缘
Participant
问题已经解决，虽然不确定具体是什么原因照成的，但是考虑是在更新R for MAC版本时（由R-3.1.3-snowleopard.pkg更新至R-3.2.0.pkg版本），由于没有完全卸载旧版本，而是安装新版本的时候直接覆盖旧版本。考虑两个版本之间可能存在一些不兼容，直接覆盖就会导致某些程序包无法正常运行。
因此，在mac系统中更新R版本时，建议：一定要完全卸载旧版本，而不要直接采用覆盖的形式安装新的R版本。
完全卸载R时需注意，不是简单从应用程序中卸载，需要同时找到R的Home路径，然后删除该路径下所有内容。
查找R的Home路径的方法，使用函数Sys.getenv(“R_HOME”)。
需要对遇到相同问题的战友有帮助，^_^
解决办法为卸载全部r语言 的rpm包 然后重新安装
#显示全部r版本的rpm已安装包
rpm -qa | grep 3.3.3*
然后逐个卸载
rpm -e libRmath-devel
rpm -e libRmath
rpm -e R-java-devel
rpm -e R-java
rpm -e R-core-devel
rpm -e R-devel
#此处也可尝试 yum remove R
然后再重新用yum install R 进行安装
最后还可以查找R相关的路径 whereis R 将相关路径删除 例如 rm -rf /usr/include/R
问题完美解决
