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

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！！！

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 15.5Matrix 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 3.12.0locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8time zone: Asia/Shanghai
tzcode source: internalattached 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 detailsreplacement 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 MBThe 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 detailsreplacement 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 KBThe 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 detailsreplacement 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 MBThe 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 detailsreplacement 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 directoriesOmitted ‘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！！！！