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R包安装报错解决案例系列｜R包使用及ARM架构解决data.table安装错误问题

2025-05-28 分类：服务器百科 阅读(16) 评论(0)

有不少同学是Mac系统的，分析过程中会发现部分R包总是安装不成功，这是因为部分R包基于windowsx86架构编译的，最常见的就是含 C/C++/Fortran 的包，对于初学者都是建议linux和win去做，Windows 通常直接安装预编译好的二进制包。mac这种半开源的封闭性系统会很折腾，除非重新编译嘿嘿嘿，能把人折磨麻了！！！！！

绝大部分都是因为Apple不支持openmp等这类，需要到多线程加速运行的R包，必翻车。没办法，喜欢 Mac OS 得折腾！！！

文章目录

    • data.table报错的出现
      • 情况1 源代码编译
      • 情况2 内置C++加速的并行OpenMP
      • 情况3 退而求其次
      • 情况4 安装中间R包
    • 还有什么R包安装疑难杂症！！留言！！！
    • 我也不信邪了，得折腾！！！！

data.table报错的出现

这个问题非常常见，这里举例两个这几天多人问到的，TCGAbiolinks和maftools都需要的一个依赖包 data.table

Error: package or namespace load failed for ‘data.table’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-data.table/00new/data.table/libs/data_table.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.4–arm64/Resources/library/00LOCK–data.table/00new/data.table/libs/data_table.so, 0x0006): symbol not found in flat namespace '___kmpc_dispatch_deinit'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.4–arm64/Resources/library/data.table’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.4–arm64/Resources/library/data.table’

The downloaded source packages are in
‘/private/var/folders/r1/fyhb81050xd7jv1g6r1783dr0000gn/T/RtmptW7Nf8/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘data.table’ had non–zero exit status

我的Mac版本是macOS Sequoia 15.5，这是测试电脑的R环境：

> sessionInfo()
R version 4.4.3 (2025–02–28)
Platform: aarch64–apple–darwin20
Running under: macOS Sequoia 15.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4–arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF–8/en_US.UTF–8/en_US.UTF–8/C/en_US.UTF–8/en_US.UTF–8

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] ggplot2_3.5.2 TCGAbiolinks_2.34.1 maftools_2.22.0 BiocParallel_1.40.2 data.table_1.17.2 tibble_3.2.1 stringr_1.5.1
[8] dplyr_1.1.4

loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 farver_2.1.2 blob_1.2.4 R.utils_2.13.0 filelock_1.0.3
[6] Biostrings_2.74.1 fastmap_1.2.0 BiocFileCache_2.14.0 promises_1.3.2 XML_3.99–0.18
[11] digest_0.6.37 lifecycle_1.0.4 processx_3.8.6 survival_3.8–3 KEGGREST_1.46.0
[16] RSQLite_2.3.11 magrittr_2.0.3 compiler_4.4.3 rlang_1.1.6 progress_1.2.3
[21] tools_4.4.3 knitr_1.50 prettyunits_1.2.0 S4Arrays_1.6.0 bit_4.6.0
[26] curl_6.2.3 DelayedArray_0.32.0 plyr_1.8.9 xml2_1.3.8 RColorBrewer_1.1–3
[31] websocket_1.4.4 abind_1.4–8 purrr_1.0.4 withr_3.0.2 R.oo_1.27.1
[36] BiocGenerics_0.52.0 grid_4.4.3 stats4_4.4.3 scales_1.4.0 biomaRt_2.62.1
[41] SummarizedExperiment_1.36.0 cli_3.6.5 crayon_1.5.3 generics_0.1.4 remotes_2.5.0
[46] rstudioapi_0.17.1 httr_1.4.7 tzdb_0.5.0 chromote_0.5.1 DBI_1.2.3
[51] DNAcopy_1.80.0 cachem_1.1.0 zlibbioc_1.52.0 splines_4.4.3 rvest_1.0.4
[56] parallel_4.4.3 AnnotationDbi_1.68.0 TCGAbiolinksGUI.data_1.26.0 BiocManager_1.30.25 XVector_0.46.0
[61] matrixStats_1.5.0 vctrs_0.6.5 Matrix_1.7–3 jsonlite_2.0.0 IRanges_2.40.1
[66] hms_1.1.3 S4Vectors_0.44.0 bit64_4.6.0–1 tidyr_1.3.1 glue_1.8.0
[71] ps_1.9.1 codetools_0.2–20 stringi_1.8.7 gtable_0.3.6 later_1.4.2
[76] GenomeInfoDb_1.42.3 GenomicRanges_1.58.0 UCSC.utils_1.2.0 pillar_1.10.2 rappdirs_0.3.3
[81] GenomeInfoDbData_1.2.13 R6_2.6.1 dbplyr_2.5.0 httr2_1.1.2 vroom_1.6.5
[86] evaluate_1.0.3 lattice_0.22–7 Biobase_2.66.0 readr_2.1.5 R.methodsS3_1.8.2
[91] png_0.1–8 memoise_2.0.1 Rcpp_1.0.14 SparseArray_1.6.2 xfun_0.52
[96] downloader_0.4.1 MatrixGenerics_1.18.1 pkgconfig_2.0.3

为什么会这样，猜测

  • data.table 包用到了 OpenMP 并行支持（C/C++层面），系统在编译时找不到特定的 OpenMP 符号（如 ___kmpc_dispatch_deinit）
  • 在 macOS 上 R 是通过 Homebrew、M1 架构下的 clang 编译，OpenMP 配置不完整

不同人会有不同情况的，真的，有的提前独立安装好依赖包后直接重启一下R环境又醒了，有的却要重新编译。不同情况大家借鉴一下，绕不开的，都是libomp、libxm12、openssl这些系统库，或者像gfortran，或者环境变量，或者一些中间R包没安装成功。。。出现情况都谷歌一下，老外的论坛里很多踩过的坑比我们都早个1-2年，兴许都有解决方案

情况1 源代码编译

这是直接去源代码编译的， https://stackoverflow.com/questions/65251887/clang-7-error-linker-command-failed-with-exit-code-1-for-macos-big-sur/65334247?answertab=modifieddesc#tab-top

如果还失败了考虑是不是这种情况，重新安装gfortran，https://stackoverflow.com/questions/65860439/installing-data-table-on-macos

情况2 内置C++加速的并行OpenMP

针对于部分机器学习的R包会出现，例如xgboost、lightgbm这类强依赖的，在 macOS 系统中，默认编译器不支持 OpenMP，需额外安装 libomp 并配置编译参数，常成为某些 R 包在 Apple M 系列芯片上安装失败的根源。

https://mac.r-project.org/openmp/

还有一个网址，作者的教程也很详细

https://investcookies.ru/post/datatable_m1/data_table_arm/

情况3 退而求其次

本质上还是因为这些R包采用的多线程，但是很多时候没有考虑到M芯片的使用环境，怎么办呢？换，换成像基于 dplyr 这种单线程的包，或者换 win/linux 吧。

情况4 安装中间R包

恭喜你，最简单的一种方式，去看那个报错，看具体是什么原因，有r包没装成功，独立去下载安装包，本地安装！！

> BiocManager::install("maftools",force=T)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022–10–31)
Installing package(s) 'maftools'
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/contrib/4.2/maftools_2.14.0.tgz'
Content type 'application/x-gzip' length 11567249 bytes (11.0 MB)
==================================================
downloaded 11.0 MB

The downloaded binary packages are in
/var/folders/bx/n5y8wbvx6td4rk2q0ht795lm0000gn/T//Rtmp8t6yAm/downloaded_packages

> library("maftools")
Error: package or namespace load failed for ‘maftools’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so, 0x0006): Symbol not found: (__gfortran_os_error_at)
Referenced from: '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so'
Expected in: '/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib'
> BiocManager::install("DNAcopy",force=T)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022–10–31)
Installing package(s) 'DNAcopy'
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/contrib/4.2/DNAcopy_1.72.1.tgz'
Content type 'application/x-gzip' length 510684 bytes (498 KB)
==================================================
downloaded 498 KB

The downloaded binary packages are in
/var/folders/bx/n5y8wbvx6td4rk2q0ht795lm0000gn/T//Rtmp8t6yAm/downloaded_packages

> BiocManager::install("maftools",force=T)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022–10–31)
Installing package(s) 'maftools'
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/contrib/4.2/maftools_2.14.0.tgz'
Content type 'application/x-gzip' length 11567249 bytes (11.0 MB)
==================================================
downloaded 11.0 MB

The downloaded binary packages are in
/var/folders/bx/n5y8wbvx6td4rk2q0ht795lm0000gn/T//Rtmp8t6yAm/downloaded_packages

> library("maftools")
Error: package or namespace load failed for ‘maftools’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so, 0x0006): Symbol not found: (__gfortran_os_error_at)
Referenced from: '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so'
Expected in: '/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib'

> BiocManager::install("PoisonAlien/maftools",force=T)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022–10–31)
Installing github package(s) 'PoisonAlien/maftools'
Downloading GitHub repo PoisonAlien/maftools@HEAD
✔ checking for file ‘/private/var/folders/bx/n5y8wbvx6td4rk2q0ht795lm0000gn/T/Rtmp8t6yAm/remotes109d7f7f267f/PoisonAlien–maftools–1c64bf9/DESCRIPTION’ …
─ preparing ‘maftools’:
✔ checking DESCRIPTION meta–information …
─ cleaning src
─ checking for LF line–endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘maftools_2.12.05.tar.gz’

* installing *source* package ‘maftools’ …
** using staged installation
** libs
clang –mmacosx–version–min=10.13 –I"/Library/Frameworks/R.framework/Resources/include" –DNDEBUG –D_FILE_OFFSET_BITS=64 –I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' –I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' –I/usr/local/include –fPIC –Wall –g –O2 –c ntcounts.c –o ntcounts.o
clang –mmacosx–version–min=10.13 –I"/Library/Frameworks/R.framework/Resources/include" –DNDEBUG –D_FILE_OFFSET_BITS=64 –I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' –I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' –I/usr/local/include –fPIC –Wall –g –O2 –c snpcounts.c –o snpcounts.o
snpcounts.c:56:26: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [–Wincompatible–pointer–types–discards–qualifiers]
int nloci = countlines(bedfile);
^~~~~~~
snpcounts.c:13:22: note: passing argument to parameter 'filename' here
int countlines(char *filename){
^
snpcounts.c:56:7: warning: unused variable 'nloci' [–Wunused–variable]
int nloci = countlines(bedfile);
^
2 warnings generated.
clang –mmacosx–version–min=10.13 –I"/Library/Frameworks/R.framework/Resources/include" –DNDEBUG –D_FILE_OFFSET_BITS=64 –I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' –I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' –I/usr/local/include –fPIC –Wall –g –O2 –c somaticfreq.c –o somaticfreq.o
clang –mmacosx–version–min=10.13 –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 maftools.so ntcounts.o snpcounts.o somaticfreq.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/usrlib/libhts.a –lcurl –F/Library/Frameworks/R.framework/.. –framework R –Wl,–framework –Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK–maftools/00new/maftools/libs
** R
** inst
** byte–compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, …) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so, 0x0006): Symbol not found: (__gfortran_os_error_at)
Referenced from: '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so'
Expected in: '/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib'
Calls: <Anonymous> … namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘maftools’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/maftools’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/maftools’
Warning message:
In i.p(…) :
installation of package ‘/var/folders/bx/n5y8wbvx6td4rk2q0ht795lm0000gn/T//Rtmp8t6yAm/file109d18ef3832/maftools_2.12.05.tar.gz’ had non–zero exit status

这种情况，都删了，然后在官网下载压缩包本地安装一下R包即可

BiocManager::install("DNAcopy", type = "source")

还有什么R包安装疑难杂症！！留言！！！

我也不信邪了，得折腾！！！！

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