Comments (15)
bjmt
commented on July 17, 2024
This error has to do with the RcppThread package. It requires a newish c++11 capable compiler, otherwise you get these errors. Try updating it if you can.
Related issues:
from universalmotif.
JianGuoZhou3
commented on July 17, 2024
Hi, it's seems didn't work.
[root@localhost ~]# sudo yum install devtoolset-7-gcc*
已加载插件：fastestmirror, langpacks
Loading mirror speeds from cached hostfile
* base: mirrors.aliyun.com
* centos-sclo-rh: mirrors.nju.edu.cn
* centos-sclo-sclo: mirrors.aliyun.com
* elrepo: hkg.mirror.rackspace.com
* extras: mirrors.aliyun.com
* nux-dextop: mirror.li.nux.ro
* remi-safe: mirrors.tuna.tsinghua.edu.cn
* rpmfusion-free-updates: mirrors.ustc.edu.cn
* rpmfusion-nonfree-updates: mirrors.ustc.edu.cn
* updates: mirrors.aliyun.com
正在解决依赖关系
--> 正在检查事务
---> 软件包 devtoolset-7-gcc.x86_64.0.7.3.1-5.16.el7 将被 安装
--> 正在处理依赖关系 devtoolset-7-binutils >= 2.22.52.0.1，它被软件包 devtoolset-7-gcc-7.3.1-5.16.el7.x86_64 需要
--> 正在处理依赖关系 devtoolset-7-runtime，它被软件包 devtoolset-7-gcc-7.3.1-5.16.el7.x86_64 需要
---> 软件包 devtoolset-7-gcc-c++.x86_64.0.7.3.1-5.16.el7 将被 安装
--> 正在处理依赖关系 devtoolset-7-libstdc++-devel = 7.3.1-5.16.el7，它被软件包 devtoolset-7-gcc-c++-7.3.1-5.16.el7.x86_64 需要
---> 软件包 devtoolset-7-gcc-gdb-plugin.x86_64.0.7.3.1-5.16.el7 将被 安装
---> 软件包 devtoolset-7-gcc-gfortran.x86_64.0.7.3.1-5.16.el7 将被 安装
--> 正在处理依赖关系 devtoolset-7-libquadmath-devel = 7.3.1-5.16.el7，它被软件包 devtoolset-7-gcc-gfortran-7.3.1-5.16.el7.x86_64 需要
--> 正在处理依赖关系 libgfortran4 >= 7.1.1-2，它被软件包 devtoolset-7-gcc-gfortran-7.3.1-5.16.el7.x86_64 需要
---> 软件包 devtoolset-7-gcc-plugin-devel.x86_64.0.7.3.1-5.16.el7 将被 安装
--> 正在检查事务
---> 软件包 devtoolset-7-binutils.x86_64.0.2.28-11.el7 将被 安装
---> 软件包 devtoolset-7-libquadmath-devel.x86_64.0.7.3.1-5.16.el7 将被 安装
---> 软件包 devtoolset-7-libstdc++-devel.x86_64.0.7.3.1-5.16.el7 将被 安装
---> 软件包 devtoolset-7-runtime.x86_64.0.7.1-4.el7 将被 安装
---> 软件包 libgfortran4.x86_64.0.8.3.1-2.1.1.el7 将被 安装
--> 解决依赖关系完成
依赖关系解决
=================================================================================================================
Package 架构 版本 源 大小
=================================================================================================================
正在安装:
devtoolset-7-gcc x86_64 7.3.1-5.16.el7 centos-sclo-rh 29 M
devtoolset-7-gcc-c++ x86_64 7.3.1-5.16.el7 centos-sclo-rh 11 M
devtoolset-7-gcc-gdb-plugin x86_64 7.3.1-5.16.el7 centos-sclo-rh 124 k
devtoolset-7-gcc-gfortran x86_64 7.3.1-5.16.el7 centos-sclo-rh 11 M
devtoolset-7-gcc-plugin-devel x86_64 7.3.1-5.16.el7 centos-sclo-rh 1.3 M
为依赖而安装:
devtoolset-7-binutils x86_64 2.28-11.el7 centos-sclo-rh 5.3 M
devtoolset-7-libquadmath-devel x86_64 7.3.1-5.16.el7 centos-sclo-rh 154 k
devtoolset-7-libstdc++-devel x86_64 7.3.1-5.16.el7 centos-sclo-rh 2.5 M
devtoolset-7-runtime x86_64 7.1-4.el7 centos-sclo-rh 20 k
libgfortran4 x86_64 8.3.1-2.1.1.el7 base 686 k
事务概要
=================================================================================================================
安装 5 软件包 (+5 依赖软件包)
总下载量：62 M
安装大小：175 M
Is this ok [y/d/N]: y
Downloading packages:
警告：/var/cache/yum/x86_64/7/centos-sclo-rh/packages/devtoolset-7-gcc-gdb-plugin-7.3.1-5.16.el7.x86_64.rpm: 头V4 RSA/SHA1 Signature, 密钥 ID f2ee9d55: NOKEY
devtoolset-7-gcc-gdb-plugin-7.3.1-5.16.el7.x86_64.rpm 的公钥尚未安装
(1/10): devtoolset-7-gcc-gdb-plugin-7.3.1-5.16.el7.x86_64.rpm | 124 kB 00:00:00
(2/10): devtoolset-7-gcc-plugin-devel-7.3.1-5.16.el7.x86_64.rpm | 1.3 MB 00:00:00
(3/10): devtoolset-7-libquadmath-devel-7.3.1-5.16.el7.x86_64.rpm | 154 kB 00:00:00
(4/10): devtoolset-7-libstdc++-devel-7.3.1-5.16.el7.x86_64.rpm | 2.5 MB 00:00:00
(5/10): devtoolset-7-runtime-7.1-4.el7.x86_64.rpm | 20 kB 00:00:00
(6/10): libgfortran4-8.3.1-2.1.1.el7.x86_64.rpm | 686 kB 00:00:00
(7/10): devtoolset-7-gcc-7.3.1-5.16.el7.x86_64.rpm | 29 MB 00:00:01
(8/10): devtoolset-7-binutils-2.28-11.el7.x86_64.rpm | 5.3 MB 00:00:06
(9/10): devtoolset-7-gcc-c++-7.3.1-5.16.el7.x86_64.rpm | 11 MB 00:00:06
(10/10): devtoolset-7-gcc-gfortran-7.3.1-5.16.el7.x86_64.rpm | 11 MB 00:00:08
-----------------------------------------------------------------------------------------------------------------
总计 6.9 MB/s | 62 MB 00:00:08
从 file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo 检索密钥
导入 GPG key 0xF2EE9D55:
用户ID : "CentOS SoftwareCollections SIG (https://wiki.centos.org/SpecialInterestGroup/SCLo) <[email protected]>"
指纹 : c4db d535 b1fb ba14 f8ba 64a8 4eb8 4e71 f2ee 9d55
软件包 : centos-release-scl-rh-2-3.el7.centos.noarch (@extras)
来自 : /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo
是否继续？[y/N]：y
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
正在安装 : devtoolset-7-runtime-7.1-4.el7.x86_64 1/10
正在安装 : devtoolset-7-binutils-2.28-11.el7.x86_64 2/10
正在安装 : devtoolset-7-libstdc++-devel-7.3.1-5.16.el7.x86_64 3/10
正在安装 : libgfortran4-8.3.1-2.1.1.el7.x86_64 4/10
正在安装 : devtoolset-7-gcc-7.3.1-5.16.el7.x86_64 5/10
正在安装 : devtoolset-7-libquadmath-devel-7.3.1-5.16.el7.x86_64 6/10
正在安装 : devtoolset-7-gcc-gfortran-7.3.1-5.16.el7.x86_64 7/10
正在安装 : devtoolset-7-gcc-plugin-devel-7.3.1-5.16.el7.x86_64 8/10
正在安装 : devtoolset-7-gcc-gdb-plugin-7.3.1-5.16.el7.x86_64 9/10
正在安装 : devtoolset-7-gcc-c++-7.3.1-5.16.el7.x86_64 10/10
验证中 : devtoolset-7-gcc-gfortran-7.3.1-5.16.el7.x86_64 1/10
验证中 : devtoolset-7-gcc-plugin-devel-7.3.1-5.16.el7.x86_64 2/10
验证中 : devtoolset-7-gcc-gdb-plugin-7.3.1-5.16.el7.x86_64 3/10
验证中 : devtoolset-7-libquadmath-devel-7.3.1-5.16.el7.x86_64 4/10
验证中 : devtoolset-7-gcc-7.3.1-5.16.el7.x86_64 5/10
验证中 : libgfortran4-8.3.1-2.1.1.el7.x86_64 6/10
验证中 : devtoolset-7-binutils-2.28-11.el7.x86_64 7/10
验证中 : devtoolset-7-libstdc++-devel-7.3.1-5.16.el7.x86_64 8/10
验证中 : devtoolset-7-gcc-c++-7.3.1-5.16.el7.x86_64 9/10
验证中 : devtoolset-7-runtime-7.1-4.el7.x86_64 10/10
已安装:
devtoolset-7-gcc.x86_64 0:7.3.1-5.16.el7 devtoolset-7-gcc-c++.x86_64 0:7.3.1-5.16.el7
devtoolset-7-gcc-gdb-plugin.x86_64 0:7.3.1-5.16.el7 devtoolset-7-gcc-gfortran.x86_64 0:7.3.1-5.16.el7
devtoolset-7-gcc-plugin-devel.x86_64 0:7.3.1-5.16.el7
作为依赖被安装:
devtoolset-7-binutils.x86_64 0:2.28-11.el7 devtoolset-7-libquadmath-devel.x86_64 0:7.3.1-5.16.el7
devtoolset-7-libstdc++-devel.x86_64 0:7.3.1-5.16.el7 devtoolset-7-runtime.x86_64 0:7.1-4.el7
libgfortran4.x86_64 0:8.3.1-2.1.1.el7
完毕！
[root@localhost ~]#
[root@localhost ~]#
[root@localhost ~]# scl enable devtoolset-7 bash
[root@localhost ~]# which gcc
/opt/rh/devtoolset-7/root/usr/bin/gcc
[root@localhost ~]# gcc --version
gcc (GCC) 7.3.1 20180303 (Red Hat 7.3.1-5)
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
This seems updated very nicely, and I try to install universalmotif.
BiocManager::install("universalmotif")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'universalmotif' trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/universalmotif_1.8.3.tar.gz' Content type 'application/x-gzip' length 3732415 bytes (3.6 MB) ================================================== downloaded 3.6 MB *
installing *source* package ‘universalmotif’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include -fpic -g -O2 -c add_multifreq.cpp -o add_multifreq.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include -fpic -g -O2 -c compare_motifs.cpp -o compare_motifs.o In file included from /home/zhou/Rlib/RcppThread/include/RcppThread.h:11:0, from compare_motifs.cpp:2: /home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp: In lambda function: /home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:19: error: parameter packs not expanded with ‘...’: f(args...);
^ /home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:19: note: ‘args’ /home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:23: error: expansion pattern ‘args’ contains no argument packs f(args...);
^ In file included from /home/zhou/Rlib/RcppThread/include/RcppThread.h:13:0, from compare_motifs.cpp:2: /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In member function ‘void RcppThread::ThreadPool::push(F&&, Args&& ...)’: /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:31: error: expected ‘,’ before ‘...’ token jobs_.emplace([f, args...] { f(args...); }); ^ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:31: error: expected identifier before ‘...’ token /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:34: error: parameter packs not expanded with ‘...’: jobs_.emplace([f, args...] { f(args...); }); ^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:34: note: ‘args’ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In lambda function: /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:44: error: expansion pattern ‘args’ contains no argument packs jobs_.emplace([f, args...] { f(args...); }); ^ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In member function ‘std::future<decltype (f(args ...))> RcppThread::ThreadPool::pushReturn(F&&, Args&& ...)’: /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:54: error: expected ‘,’ before ‘...’ token auto job = std::make_shared<jobPackage>([&f, args...] { ^ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:54: error: expected identifier before ‘...’ token /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:57: error: parameter packs not expanded with ‘...’: auto job = std::make_shared<jobPackage>([&f, args...] { ^ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:57: note: ‘args’ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In lambda function: /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:147:22: error: expansion pattern ‘args’ contains no argument packs return f(args...);
^ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’: /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9: required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9: required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]’ /home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5: required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13; ptrdiff_t = long int; size_t = long unsigned int]’ compare_motifs.cpp:1426:18: required from here /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’ jobs_.emplace([f, args...] { f(args...); });
^ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’: /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9: required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9: required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]’
/home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5: required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14; ptrdiff_t = long int; size_t = long unsigned int]’ compare_motifs.cpp:1485:18: required from here /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’ /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’: /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9: required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9: required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]’ /home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5: required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15; ptrdiff_t = long int; size_t = long unsigned int]’ compare_motifs.cpp:1859:18: required from here /home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’ make: *** [compare_motifs.o] Error 1 ERROR: compilation failed for package ‘universalmotif’ * removing ‘/home/zhou/Rlib/universalmotif’ The downloaded source packages are in
‘/tmp/RtmpS1nRO3/downloaded_packages’ Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign, KernSmooth, MASS, Matrix, mgcv, nlme, nnet, spatial, survival Old packages: 'e1071', 'shinyWidgets', 'spatstat.utils'
Update all/some/none? [a/s/n]: n Warning message: In install.packages(...) : installation of package ‘universalmotif’ had non-zero exit status
--
> | >
>
from universalmotif.
bjmt
commented on July 17, 2024
Hmm. Not entirely sure. (I don't use CentOS.) Perhaps try installing a newer version still? Are you sure that R itself is using your updated compiler and not the old one?
Apologies for tagging you, but @tnagler do you have any advice?
from universalmotif.
JianGuoZhou3
commented on July 17, 2024
it's fine, thx.
I will check other methods.
Best,
Jian-Guo
from universalmotif.
tnagler
commented on July 17, 2024
Error messages indicate that the compiler does not fully support c++11. Are you sure that BiocManager::install is accessing the new version of g++?
from universalmotif.
JianGuoZhou3
commented on July 17, 2024
accessing
Hi @tnagler I just update the gcc, and re-install the software.
[root@localhost ~]# gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
Copyright © 2015 Free Software Foundation, Inc.
from universalmotif.
JianGuoZhou3
commented on July 17, 2024
[root@localhost ~]# yum install devtoolset-8-gcc devtoolset-8-gcc-c++
已加载插件：fastestmirror, langpacks
Loading mirror speeds from cached hostfile
* base: mirrors.aliyun.com
* centos-sclo-rh: mirrors.nju.edu.cn
* centos-sclo-sclo: mirrors.aliyun.com
* elrepo: hkg.mirror.rackspace.com
* extras: mirrors.aliyun.com
* nux-dextop: mirror.li.nux.ro
* remi-safe: mirrors.tuna.tsinghua.edu.cn
* rpmfusion-free-updates: mirrors.ustc.edu.cn
* rpmfusion-nonfree-updates: mirrors.ustc.edu.cn
* updates: mirrors.aliyun.com
正在解决依赖关系
--> 正在检查事务
---> 软件包 devtoolset-8-gcc.x86_64.0.8.3.1-3.2.el7 将被 安装
--> 正在处理依赖关系 devtoolset-8-binutils >= 2.22.52.0.1，它被软件包 devtoolset-8-gcc-8.3.1-3.2.el7.x86_64 需要
--> 正在处理依赖关系 devtoolset-8-runtime，它被软件包 devtoolset-8-gcc-8.3.1-3.2.el7.x86_64 需要
---> 软件包 devtoolset-8-gcc-c++.x86_64.0.8.3.1-3.2.el7 将被 安装
--> 正在处理依赖关系 devtoolset-8-libstdc++-devel = 8.3.1-3.2.el7，它被软件包 devtoolset-8-gcc-c++-8.3.1-3.2.el7.x86_64 需要
--> 正在检查事务
---> 软件包 devtoolset-8-binutils.x86_64.0.2.30-55.el7.2 将被 安装
---> 软件包 devtoolset-8-libstdc++-devel.x86_64.0.8.3.1-3.2.el7 将被 安装
---> 软件包 devtoolset-8-runtime.x86_64.0.8.1-1.el7 将被 安装
--> 解决依赖关系完成
依赖关系解决
========================================================================================================================================================================================================================
Package 架构 版本 源 大小
========================================================================================================================================================================================================================
正在安装:
devtoolset-8-gcc x86_64 8.3.1-3.2.el7 centos-sclo-rh 30 M
devtoolset-8-gcc-c++ x86_64 8.3.1-3.2.el7 centos-sclo-rh 12 M
为依赖而安装:
devtoolset-8-binutils x86_64 2.30-55.el7.2 centos-sclo-rh 5.5 M
devtoolset-8-libstdc++-devel x86_64 8.3.1-3.2.el7 centos-sclo-rh 2.7 M
devtoolset-8-runtime x86_64 8.1-1.el7 centos-sclo-rh 20 k
事务概要
========================================================================================================================================================================================================================
安装 2 软件包 (+3 依赖软件包)
总下载量：50 M
安装大小：141 M
Is this ok [y/d/N]: y
Downloading packages:
(1/5): devtoolset-8-libstdc++-devel-8.3.1-3.2.el7.x86_64.rpm | 2.7 MB 00:00:00
(2/5): devtoolset-8-gcc-c++-8.3.1-3.2.el7.x86_64.rpm | 12 MB 00:00:00
(3/5): devtoolset-8-binutils-2.30-55.el7.2.x86_64.rpm | 5.5 MB 00:00:01
(4/5): devtoolset-8-runtime-8.1-1.el7.x86_64.rpm | 20 kB 00:00:02
(5/5): devtoolset-8-gcc-8.3.1-3.2.el7.x86_64.rpm | 30 MB 00:00:03
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
总计 14 MB/s | 50 MB 00:00:03
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
正在安装 : devtoolset-8-runtime-8.1-1.el7.x86_64 1/5
正在安装 : devtoolset-8-binutils-2.30-55.el7.2.x86_64 2/5
正在安装 : devtoolset-8-libstdc++-devel-8.3.1-3.2.el7.x86_64 3/5
正在安装 : devtoolset-8-gcc-8.3.1-3.2.el7.x86_64 4/5
正在安装 : devtoolset-8-gcc-c++-8.3.1-3.2.el7.x86_64 5/5
验证中 : devtoolset-8-runtime-8.1-1.el7.x86_64 1/5
验证中 : devtoolset-8-gcc-8.3.1-3.2.el7.x86_64 2/5
验证中 : devtoolset-8-gcc-c++-8.3.1-3.2.el7.x86_64 3/5
验证中 : devtoolset-8-binutils-2.30-55.el7.2.x86_64 4/5
验证中 : devtoolset-8-libstdc++-devel-8.3.1-3.2.el7.x86_64 5/5
已安装:
devtoolset-8-gcc.x86_64 0:8.3.1-3.2.el7 devtoolset-8-gcc-c++.x86_64 0:8.3.1-3.2.el7
作为依赖被安装:
devtoolset-8-binutils.x86_64 0:2.30-55.el7.2 devtoolset-8-libstdc++-devel.x86_64 0:8.3.1-3.2.el7 devtoolset-8-runtime.x86_64 0:8.1-1.el7
完毕！
[root@localhost ~]# scl enable devtoolset-8 -- bash
[root@localhost ~]#
I used the following code to update those.
And re-install,
> BiocManager::install("universalmotif")
BiocManager::install("universalmotif")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'universalmotif'
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/universalmotif_1.8.3.tar.gz'
Content type 'application/x-gzip' length 3732415 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include -fpic -g -O2 -c add_multifreq.cpp -o add_multifreq.o
g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -I'/home/zhou/Rlib/Rcpp/include' -I'/home/zhou/Rlib/RcppThread/include' -I/usr/local/include -fpic -g -O2 -c compare_motifs.cpp -o compare_motifs.o
In file included from /home/zhou/Rlib/RcppThread/include/RcppThread.h:11:0,
from compare_motifs.cpp:2:
/home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp: In lambda function:
/home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:19: error: parameter packs not expanded with ‘...’:
f(args...);
^
/home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:19: note: ‘args’
/home/zhou/Rlib/RcppThread/include/RcppThread/Thread.hpp:42:23: error: expansion pattern ‘args’ contains no argument packs
f(args...);
^
In file included from /home/zhou/Rlib/RcppThread/include/RcppThread.h:13:0,
from compare_motifs.cpp:2:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In member function ‘void RcppThread::ThreadPool::push(F&&, Args&& ...)’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:31: error: expected ‘,’ before ‘...’ token
jobs_.emplace([f, args...] { f(args...); });
^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:31: error: expected identifier before ‘...’ token
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:34: error: parameter packs not expanded with ‘...’:
jobs_.emplace([f, args...] { f(args...); });
^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:34: note: ‘args’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In lambda function:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:44: error: expansion pattern ‘args’ contains no argument packs
jobs_.emplace([f, args...] { f(args...); });
^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In member function ‘std::future<decltype (f(args ...))> RcppThread::ThreadPool::pushReturn(F&&, Args&& ...)’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:54: error: expected ‘,’ before ‘...’ token
auto job = std::make_shared<jobPackage>([&f, args...] {
^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:54: error: expected identifier before ‘...’ token
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:57: error: parameter packs not expanded with ‘...’:
auto job = std::make_shared<jobPackage>([&f, args...] {
^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:146:57: note: ‘args’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In lambda function:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:147:22: error: expansion pattern ‘args’ contains no argument packs
return f(args...);
^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9: required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9: required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13&; ptrdiff_t = long int; size_t = long unsigned int]’
/home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5: required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = compare_motifs_cpp(const List&, const std::vector<int>&, const std::vector<int>&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda13; ptrdiff_t = long int; size_t = long unsigned int]’
compare_motifs.cpp:1426:18: required from here
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’
jobs_.emplace([f, args...] { f(args...); });
^
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9: required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9: required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14&; ptrdiff_t = long int; size_t = long unsigned int]’
/home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5: required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = compare_motifs_all_cpp(const List&, const string&, double, bool, std::vector<std::vector<double> >&, int, bool, double, bool, int, double, const std::vector<double>&, const string&)::__lambda14; ptrdiff_t = long int; size_t = long unsigned int]’
compare_motifs.cpp:1485:18: required from here
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp: In instantiation of ‘struct RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]::__lambda5’:
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:9: required from ‘void RcppThread::ThreadPool::push(F&&, Args&& ...) [with F = RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]::__lambda8&; Args = {const RcppThread::Batch&}]’
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:201:9: required from ‘void RcppThread::ThreadPool::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15&; ptrdiff_t = long int; size_t = long unsigned int]’
/home/zhou/Rlib/RcppThread/include/RcppThread/parallelFor.hpp:48:5: required from ‘void RcppThread::parallelFor(ptrdiff_t, ptrdiff_t, F&&, size_t, size_t) [with F = pval_extractor(const std::vector<int>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const string&, const std::vector<int>&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::basic_string<char> >&, int)::__lambda15; ptrdiff_t = long int; size_t = long unsigned int]’
compare_motifs.cpp:1859:18: required from here
/home/zhou/Rlib/RcppThread/include/RcppThread/ThreadPool.hpp:129:27: error: using invalid field ‘RcppThread::ThreadPool::push(F&&, Args&& ...)::__lambda5::__args’
make: *** [compare_motifs.o] Error 1
ERROR: compilation failed for package ‘universalmotif’
* removing ‘/home/zhou/Rlib/universalmotif’
The downloaded source packages are in
‘/tmp/RtmpS1nRO3/downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, cluster,
codetools, foreign, KernSmooth, MASS, Matrix, mgcv, nlme, nnet, spatial, survival
Old packages: 'e1071', 'shinyWidgets', 'spatstat.sparse', 'spatstat.utils'
Update all/some/none? [a/s/n]:
n
Warning message:
In install.packages(...) :
installation of package ‘universalmotif’ had non-zero exit status
from universalmotif.
tnagler
commented on July 17, 2024
Could you run system("g++ --version") from the R console?
from universalmotif.
JianGuoZhou3
commented on July 17, 2024
> system("g++ --version")
g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
--
> | >
>
from universalmotif.
tnagler
commented on July 17, 2024
so R is not actually using your newly installed version of gcc. I'm not sure how CentOS is setting these things up, you could try running system("CXX = gcc-c++") or system("CXX = devtoolset-8-gcc-c++") or so before calling the BiocManager command.
from universalmotif.
JianGuoZhou3
commented on July 17, 2024
It's seems didn't work.
> system("CXX = gcc-c++")
sh: CXX: command not found
Warning message: In system("CXX = gcc-c++") : error in running command
> system("CXX = devtoolset-8-gcc-c++")
sh: CXX: command not found
Warning message: In system("CXX = devtoolset-8-gcc-c++") : error in running command
--
> | >
>
from universalmotif.
bjmt
commented on July 17, 2024
You could try creating the folder ~/.R, and in it create a file ~/.R/Makevars. Then in the file, write:
CXX=/opt/rh/devtoolset-7/root/usr/bin/g++
CXX11=/opt/rh/devtoolset-7/root/usr/bin/g++
This should force R to use the new gcc you installed.
from universalmotif.
bjmt
commented on July 17, 2024
Sorry I didn't suggest this earlier, I only just now remembered about ~/.R/Makevars. Hopefully this works. And thanks a ton for popping tnagler, my apologies for calling you.
from universalmotif.
JianGuoZhou3
commented on July 17, 2024
It's still didn't work.
from universalmotif.
JianGuoZhou3
commented on July 17, 2024
Hi @tnagler I used the code and worked.
Sys.setenv("PATH"="/opt/rh/devtoolset-8/root/usr/bin:/opt/rh/devtoolset-8/root/usr/bin")
> Sys.which("R")
R
""
> Sys.which("r")
r
""
Restarting R session...
from universalmotif.
Related Issues (18)
- shuffle_sequence truncated HOT 2
- read_meme() yields out that "alphabet type cannot be detected" although "ALPHABET= ACGT" is provided HOT 1
- importing pwd by read_cisbp HOT 3
- Cannot get scan_sequences to report p-values HOT 11
- Improve support for metadata-based manipulations HOT 22
- new view_motifs() function plots in alphabetical order instead of list input order HOT 2
- update_motif on motifs with 1 extrainfo column gives misnamed results
- Error with read_meme HOT 5
- Option to deprotect `motif` column in universalmotif_df HOT 3
- validObject_universalmotif(motifs) fails when strand is "*" HOT 2
- R session aborted / fatal error when running read_homer from a list of motifs HOT 5
- Can't run meme with custom alphabet HOT 7
- How to merge motifs with variable length of gap HOT 7
- Error in convert_motifs for TFBStools-PFMatrixList HOT 10
- `create_motif` makes incorrect motif for amino acid sequences HOT 1
- read_meme fails when alphabet is DNA/RNA/AA-LIKE or custom
- altname is dropped during summarise_motif
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from universalmotif.