error in install #16

JianGuoZhou3 · 2021-03-15T18:01:57Z

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 Warning message: In install.packages(...) :   installation of package ‘universalmotif’ had non-zero exit status
--

The text was updated successfully, but these errors were encountered:

bjmt · 2021-03-16T10:01:47Z

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:

#3
tnagler/RcppThread#13

JianGuoZhou3 · 2021-03-16T13:01:11Z

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) <security@centos.org>"
 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
--
 
> | >
>

bjmt · 2021-03-16T13:14:15Z

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?

JianGuoZhou3 · 2021-03-16T13:15:44Z

it's fine, thx.
I will check other methods.
Best,
Jian-Guo

tnagler · 2021-03-16T14:03:59Z

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++?

JianGuoZhou3 · 2021-03-16T16:17:01Z

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.

JianGuoZhou3 · 2021-03-16T16:24:21Z

[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

tnagler · 2021-03-16T16:27:19Z

Could you run system("g++ --version") from the R console?

JianGuoZhou3 · 2021-03-16T16:33:16Z


> 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.
--
 
> | >
>

tnagler · 2021-03-16T16:39:10Z

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.

JianGuoZhou3 · 2021-03-16T16:43:50Z

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
--
 
> | >
>

bjmt · 2021-03-16T16:50:11Z

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.

bjmt · 2021-03-16T16:52:58Z

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.

JianGuoZhou3 · 2021-03-16T17:14:22Z

It's still didn't work.

JianGuoZhou3 · 2021-03-18T07:22:39Z

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...

JianGuoZhou3 closed this as completed Mar 18, 2021

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error in install #16

error in install #16

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