dyn.load(dllfile) 中的错误 - 构建链接到 Rcpp 的包时出现问题

Question

我的软件包无法安装在我的机器上或 travis-ci.org 上。CRAN 版本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的示例；编译后的代码。

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该错误与之前的这些问题相关，但不是重复的。

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1. Q40922814——这里的问题是同时使用了 C 和 C++ 代码。我只使用C++代码
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2. Q36952571 - 我使用的是 Mac 操作系统，因此无法访问ldconfig，尽管也许我的问题与之相关。
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错误：

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从包目录：

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# Restarting R session...\n> Rcpp::compileAttributes()\n> devtools::document()     # a similar error using devtools::install()\nUpdating imputeMulti documentation\nLoading imputeMulti\nRe-compiling imputeMulti\n\xe2\x94\x80  installing *source* package \xe2\x80\x98imputeMulti\xe2\x80\x99 ...\n   ** using staged installation\n   ** libs\n   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\n   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\n   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\n   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\n   installing to /private/var/folders/6h/px5b6ds15b72srhkxc42k9drt2vmnc/T/Rtmpa4w8vb/devtools_install_876345d52e22/00LOCK-imputeMulti/00new/imputeMulti/libs\n   ** checking absolute paths in shared objects and dynamic libraries\n\xe2\x94\x80  DONE (imputeMulti)\nError in dyn.load(dllfile) : \n  unable to load shared object \'./imputeMulti/src/imputeMulti.so\':\n  dlopen(./imputeMulti/src/imputeMulti.so, 6): Symbol not found: _imputeMulti_supDistC\n  Referenced from: ./imputeMulti/src/imputeMulti.so\n  Expected in: flat namespace\n in ./imputeMulti/src/imputeMulti.so\n

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和会话信息：

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> sessionInfo()\nR version 3.6.3 (2020-02-29)\nPlatform: x86_64-apple-darwin15.6.0 (64-bit)\nRunning under: macOS Mojave 10.14.6\n\nMatrix products: default\nBLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib\nLAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib\n\nlocale:\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\n\nattached base packages:\n[1] stats     graphics  grDevices utils     datasets  methods   base     \n\nloaded via a namespace (and not attached):\n [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     \n [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    \n[13] rlang_0.4.6       DBI_1.1.0         cli_2.0.2         rstudioapi_0.11   parallel_3.6.3    xfun_0.13        \n[19] withr_2.2.0       stringr_1.4.0     roxygen2_7.1.0    knitr_1.28        xml2_1.3.2        vctrs_0.2.4      \n[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  \n[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\n[37] blob_1.2.1        callr_3.4.3       purrr_0.3.4       magrittr_1.5      backports_1.1.6   ps_1.3.2         \n[43] ellipsis_0.3.0    usethis_1.6.0     assertthat_0.2.1  stringi_1.4.6     crayon_1.3.4  \n\n> devtools::build() # works \n

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代码

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我的包：imputeMulti

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我有以下 C++ 文件src/

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# utilities_rcpp.cpp\n#include <Rcpp.h>\nusing namespace Rcpp;\n\n<two minor functions>\n\n# count_compare.cpp\n#include <Rcpp.h>\nusing namespace Rcpp;\n\n<one minor function>\n

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我也有

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# imputeMulti-package.R\n## usethis namespace: start\n#\' @importFrom Rcpp sourceCpp, evalCpp\n## usethis namespace: end\nNULL\n\n#\' @useDynLib imputeMulti\n\n.onUnload <- function (libpath) {\n  library.dynam.unload(\'imputeMulti\', libpath)\n}\n

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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。

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Answer 1

快速戳了一下，我认为您的包裹已损坏。

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安装步骤失败

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** testing if installed package can be loaded from temporary location\nError: package or namespace load failed for \xe2\x80\x98imputeMulti\xe2\x80\x99 in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object \'/usr/local/lib/R/site-library/00LOCK-imputeMulti/00new/imputeMulti/libs/imputeMulti.so\':\n  /usr/local/lib/R/site-library/00LOCK-imputeMulti/00new/imputeMulti/libs/imputeMulti.so: undefined symbol: imputeMulti_supDistC\nError: loading failed\nExecution halted\nERROR: loading failed\n* removing \xe2\x80\x98/usr/local/lib/R/site-library/imputeMulti\xe2\x80\x99\nWarning message:\nIn install.packages(pkgs = f, lib = lib, repos = if (isMatchingFile(f)) NULL else repos) :\n  installation of package \xe2\x80\x98imputeMulti_0.7.1.tar.gz\xe2\x80\x99 had non-zero exit status\nedd@rob:/tmp/imputeMulti(master)$\n

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也就是说，我们错过了您所说的一个符号imputeMulti_supDistC，而您做错了。使用 Rcpp 及其（很棒），compileAttributes()您无需调用.Call()这里那样您调用提供 R 包装器。

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你犯了两次这个错误，这解决了它：

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edd@rob:/tmp/imputeMulti(master)$ git diff R/int-count_levels.R\ndiff --git a/R/int-count_levels.R b/R/int-count_levels.R\nindex a4ce4cc..9e749cc 100755\n--- a/R/int-count_levels.R\n+++ b/R/int-count_levels.R\n@@ -4,7 +4,8 @@\n # wrapper to supDistC to move error checking outside of C++\n supDist <- function(x,y) {\n   if (length(x) != length(y)) stop("Length of x and y differ.")\n-  .Call(\'imputeMulti_supDistC\', PACKAGE = \'imputeMulti\', x, y)\n+  #.Call(\'imputeMulti_supDistC\', PACKAGE = \'imputeMulti\', x, y)\n+  supDistC(x, y)\n }\n\n # convert a factor-vector to an integer vector, where the integers correspond\n@@ -91,7 +92,8 @@ mx_my_compare <- function(mat_x, mat_y) {\n   mat_y <- do.call("cbind", lapply(mat_y, fact_to_int))\n\n   ## 1. Run code in C\n-  .Call(\'imputeMulti_xy_compare\', PACKAGE = \'imputeMulti\', mat_x, mat_y)\n+  #.Call(\'imputeMulti_xy_compare\', PACKAGE = \'imputeMulti\', mat_x, mat_y)\n+  xy_compare(mat_x, mat_y)\n   # mat_to_mat_compare(mat_x, mat_y, na.rm= TRUE)\n }\n\nedd@rob:/tmp/imputeMulti(master)$ \n

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进行这些简化，运行compileAttributes()以更新这两个RcppExports文件，然后就高兴了。

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