dyn.load（dllfile）中的错误-构建链接到Rcpp的软件包的问题

时间：2020-05-02 21:50:31

标签： r rcpp r-package

我的软件包无法在我的机器上或在travis-ci.org上安装。 version on CRAN的唯一更新是我添加了一个小插图。我一直在关注Rcpp - package和R-packages; compiled code的示例。

该错误与这些先前的问题有关，但并非重复。

  1. Q40922814-这里的问题是同时使用C和C ++代码。我只使用C ++代码
  2. Q36952571-我在Mac OS上，因此无法访问ldconfig，尽管可能与我的问题有关。

错误：

从软件包目录：

# 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

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)
}

我的最佳猜测是该错误与Q36952571有关，但我不确定如何解决。任何帮助将不胜感激。

1 个答案:

答案 0 :(得分：3)

我认为，基于一个快速的戳，您的包裹很烂。

安装步骤失败

=LEFT(A1,LEN(A1)-1)*1000000

即，我们错过了您调用的符号** 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)$ ，但您做错了。使用Rcpp及其（出色的）imputeMulti_supDistC，您可以像在此那样不调用compileAttributes()。您调用提供R包装。

您两次犯了这个错误，并解决了这个问题：

.Call()

进行这些简化，运行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)$ 更新两个compileAttributes()文件，然后高兴起来。

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