dyn.load(dllfile) 中的错误 -- 构建链接到 Rcpp 的包时出现问题
Error in dyn.load(dllfile) -- problem with building a package linking to Rcpp
我的包无法安装，无论是在我的机器上还是在 travis-ci.org 上。 version on CRAN is that I added a vignette. I have been following the examples of Rcpp - package and R-packages; compiled code.
的唯一更新
该错误与这些先前的问题有关，但不是重复的。
- Q40922814 -- 这里的问题是同时使用了 C 和 C++ 代码。我只使用 C++ 代码
-- 我在 Mac OS，所以无法访问 ldconfig，但也许我的问题是相关的。
错误：
来自包目录：
# Restarting R session...
> Rcpp::compileAttributes()
> devtools::document() # a similar error using devtools::install()
Updating imputeMulti documentation
Loading imputeMulti
Re-compiling imputeMulti
─ installing *source* package ‘imputeMulti’ ...
** using staged installation
** libs
g++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -std=c++0x -c RcppExports.cpp -o RcppExports.o
g++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -std=c++0x -c count_compare.cpp -o count_compare.o
g++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -std=c++0x -c utilities_rcpp.cpp -o utilities_rcpp.o
g++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o imputeMulti.so RcppExports.o count_compare.o utilities_rcpp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /private/var/folders/6h/px5b6ds15b72srhkxc42k9drt2vmnc/T/Rtmpa4w8vb/devtools_install_876345d52e22/00LOCK-imputeMulti/00new/imputeMulti/libs
** checking absolute paths in shared objects and dynamic libraries
─ DONE (imputeMulti)
Error in dyn.load(dllfile) :
unable to load shared object './imputeMulti/src/imputeMulti.so':
dlopen(./imputeMulti/src/imputeMulti.so, 6): Symbol not found: _imputeMulti_supDistC
Referenced from: ./imputeMulti/src/imputeMulti.so
Expected in: flat namespace
in ./imputeMulti/src/imputeMulti.so
和会话信息：
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 compiler_3.6.3 prettyunits_1.1.1 remotes_2.1.1 tools_3.6.3 bit_1.1-15.2
[7] testthat_2.3.2 digest_0.6.25 pkgbuild_1.0.7 pkgload_1.0.2 RSQLite_2.2.0 memoise_1.1.0
[13] rlang_0.4.6 DBI_1.1.0 cli_2.0.2 rstudioapi_0.11 parallel_3.6.3 xfun_0.13
[19] withr_2.2.0 stringr_1.4.0 roxygen2_7.1.0 knitr_1.28 xml2_1.3.2 vctrs_0.2.4
[25] desc_1.2.0 fs_1.4.1 gtools_3.8.2 devtools_2.3.0 bit64_0.9-7 rprojroot_1.3-2
[31] glue_1.4.0 R6_2.4.1 processx_3.4.2 fansi_0.4.1 imputeMulti_0.7.1 sessioninfo_1.1.1
[37] blob_1.2.1 callr_3.4.3 purrr_0.3.4 magrittr_1.5 backports_1.1.6 ps_1.3.2
[43] ellipsis_0.3.0 usethis_1.6.0 assertthat_0.2.1 stringi_1.4.6 crayon_1.3.4
> devtools::build() # works
代码
我的包裹：imputeMulti
我在 src/
中有以下 C++ 文件
# utilities_rcpp.cpp
#include <Rcpp.h>
using namespace Rcpp;
<two minor functions>
# count_compare.cpp
#include <Rcpp.h>
using namespace Rcpp;
<one minor function>
我也有
# imputeMulti-package.R
## usethis namespace: start
#' @importFrom Rcpp sourceCpp, evalCpp
## usethis namespace: end
NULL
#' @useDynLib imputeMulti
.onUnload <- function (libpath) {
library.dynam.unload('imputeMulti', libpath)
}
我最好的猜测是该错误与 Q36952571 有关，但我不确定如何解决。任何帮助将不胜感激。
我快速浏览了一下，认为您的包裹已经破烂了。
安装步骤失败于
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘imputeMulti’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/00LOCK-imputeMulti/00new/imputeMulti/libs/imputeMulti.so':
/usr/local/lib/R/site-library/00LOCK-imputeMulti/00new/imputeMulti/libs/imputeMulti.so: undefined symbol: imputeMulti_supDistC
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/imputeMulti’
Warning message:
In install.packages(pkgs = f, lib = lib, repos = if (isMatchingFile(f)) NULL else repos) :
installation of package ‘imputeMulti_0.7.1.tar.gz’ had non-zero exit status
edd@rob:/tmp/imputeMulti(master)$
即 我们漏掉了一个符号 imputeMulti_supDistC 你称之为，你做错了。使用 Rcpp 及其（很棒的）compileAttributes()，您 而不是 调用 .Call()，就像您在此处所做的那样。您调用提供的 R 包装器。
这个错误你犯了两次，现在改正了：
edd@rob:/tmp/imputeMulti(master)$ git diff R/int-count_levels.R
diff --git a/R/int-count_levels.R b/R/int-count_levels.R
index a4ce4cc..9e749cc 100755
--- a/R/int-count_levels.R
+++ b/R/int-count_levels.R
@@ -4,7 +4,8 @@
# wrapper to supDistC to move error checking outside of C++
supDist <- function(x,y) {
if (length(x) != length(y)) stop("Length of x and y differ.")
- .Call('imputeMulti_supDistC', PACKAGE = 'imputeMulti', x, y)
+ #.Call('imputeMulti_supDistC', PACKAGE = 'imputeMulti', x, y)
+ supDistC(x, y)
}
# convert a factor-vector to an integer vector, where the integers correspond
@@ -91,7 +92,8 @@ mx_my_compare <- function(mat_x, mat_y) {
mat_y <- do.call("cbind", lapply(mat_y, fact_to_int))
## 1. Run code in C
- .Call('imputeMulti_xy_compare', PACKAGE = 'imputeMulti', mat_x, mat_y)
+ #.Call('imputeMulti_xy_compare', PACKAGE = 'imputeMulti', mat_x, mat_y)
+ xy_compare(mat_x, mat_y)
# mat_to_mat_compare(mat_x, mat_y, na.rm= TRUE)
}
edd@rob:/tmp/imputeMulti(master)$
进行这些简化，运行 compileAttributes() 更新两个 RcppExports 文件，祝您愉快。
我的包无法安装，无论是在我的机器上还是在 travis-ci.org 上。 version on CRAN is that I added a vignette. I have been following the examples of Rcpp - package and R-packages; compiled code.
的唯一更新该错误与这些先前的问题有关，但不是重复的。
- Q40922814 -- 这里的问题是同时使用了 C 和 C++ 代码。我只使用 C++ 代码
ldconfig，但也许我的问题是相关的。
错误：
来自包目录：
# Restarting R session...
> Rcpp::compileAttributes()
> devtools::document() # a similar error using devtools::install()
Updating imputeMulti documentation
Loading imputeMulti
Re-compiling imputeMulti
─ installing *source* package ‘imputeMulti’ ...
** using staged installation
** libs
g++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -std=c++0x -c RcppExports.cpp -o RcppExports.o
g++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -std=c++0x -c count_compare.cpp -o count_compare.o
g++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -std=c++0x -c utilities_rcpp.cpp -o utilities_rcpp.o
g++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o imputeMulti.so RcppExports.o count_compare.o utilities_rcpp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /private/var/folders/6h/px5b6ds15b72srhkxc42k9drt2vmnc/T/Rtmpa4w8vb/devtools_install_876345d52e22/00LOCK-imputeMulti/00new/imputeMulti/libs
** checking absolute paths in shared objects and dynamic libraries
─ DONE (imputeMulti)
Error in dyn.load(dllfile) :
unable to load shared object './imputeMulti/src/imputeMulti.so':
dlopen(./imputeMulti/src/imputeMulti.so, 6): Symbol not found: _imputeMulti_supDistC
Referenced from: ./imputeMulti/src/imputeMulti.so
Expected in: flat namespace
in ./imputeMulti/src/imputeMulti.so
和会话信息：
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 compiler_3.6.3 prettyunits_1.1.1 remotes_2.1.1 tools_3.6.3 bit_1.1-15.2
[7] testthat_2.3.2 digest_0.6.25 pkgbuild_1.0.7 pkgload_1.0.2 RSQLite_2.2.0 memoise_1.1.0
[13] rlang_0.4.6 DBI_1.1.0 cli_2.0.2 rstudioapi_0.11 parallel_3.6.3 xfun_0.13
[19] withr_2.2.0 stringr_1.4.0 roxygen2_7.1.0 knitr_1.28 xml2_1.3.2 vctrs_0.2.4
[25] desc_1.2.0 fs_1.4.1 gtools_3.8.2 devtools_2.3.0 bit64_0.9-7 rprojroot_1.3-2
[31] glue_1.4.0 R6_2.4.1 processx_3.4.2 fansi_0.4.1 imputeMulti_0.7.1 sessioninfo_1.1.1
[37] blob_1.2.1 callr_3.4.3 purrr_0.3.4 magrittr_1.5 backports_1.1.6 ps_1.3.2
[43] ellipsis_0.3.0 usethis_1.6.0 assertthat_0.2.1 stringi_1.4.6 crayon_1.3.4
> devtools::build() # works
代码
我的包裹：imputeMulti
我在 src/
# utilities_rcpp.cpp
#include <Rcpp.h>
using namespace Rcpp;
<two minor functions>
# count_compare.cpp
#include <Rcpp.h>
using namespace Rcpp;
<one minor function>
我也有
# imputeMulti-package.R
## usethis namespace: start
#' @importFrom Rcpp sourceCpp, evalCpp
## usethis namespace: end
NULL
#' @useDynLib imputeMulti
.onUnload <- function (libpath) {
library.dynam.unload('imputeMulti', libpath)
}
我最好的猜测是该错误与 Q36952571 有关，但我不确定如何解决。任何帮助将不胜感激。
我快速浏览了一下，认为您的包裹已经破烂了。
安装步骤失败于
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘imputeMulti’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/00LOCK-imputeMulti/00new/imputeMulti/libs/imputeMulti.so':
/usr/local/lib/R/site-library/00LOCK-imputeMulti/00new/imputeMulti/libs/imputeMulti.so: undefined symbol: imputeMulti_supDistC
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/imputeMulti’
Warning message:
In install.packages(pkgs = f, lib = lib, repos = if (isMatchingFile(f)) NULL else repos) :
installation of package ‘imputeMulti_0.7.1.tar.gz’ had non-zero exit status
edd@rob:/tmp/imputeMulti(master)$
即 我们漏掉了一个符号 imputeMulti_supDistC 你称之为，你做错了。使用 Rcpp 及其（很棒的）compileAttributes()，您 而不是 调用 .Call()，就像您在此处所做的那样。您调用提供的 R 包装器。
这个错误你犯了两次，现在改正了：
edd@rob:/tmp/imputeMulti(master)$ git diff R/int-count_levels.R
diff --git a/R/int-count_levels.R b/R/int-count_levels.R
index a4ce4cc..9e749cc 100755
--- a/R/int-count_levels.R
+++ b/R/int-count_levels.R
@@ -4,7 +4,8 @@
# wrapper to supDistC to move error checking outside of C++
supDist <- function(x,y) {
if (length(x) != length(y)) stop("Length of x and y differ.")
- .Call('imputeMulti_supDistC', PACKAGE = 'imputeMulti', x, y)
+ #.Call('imputeMulti_supDistC', PACKAGE = 'imputeMulti', x, y)
+ supDistC(x, y)
}
# convert a factor-vector to an integer vector, where the integers correspond
@@ -91,7 +92,8 @@ mx_my_compare <- function(mat_x, mat_y) {
mat_y <- do.call("cbind", lapply(mat_y, fact_to_int))
## 1. Run code in C
- .Call('imputeMulti_xy_compare', PACKAGE = 'imputeMulti', mat_x, mat_y)
+ #.Call('imputeMulti_xy_compare', PACKAGE = 'imputeMulti', mat_x, mat_y)
+ xy_compare(mat_x, mat_y)
# mat_to_mat_compare(mat_x, mat_y, na.rm= TRUE)
}
edd@rob:/tmp/imputeMulti(master)$
进行这些简化，运行 compileAttributes() 更新两个 RcppExports 文件，祝您愉快。