在 R 包中使用 -fPIC 重新编译
Recompile with -fPIC in R package
我试图在 R 中安装 imager 包，但遇到以下错误：
/usr/bin/ld: /usr/local/lib/libfftw3.a(assert.o): relocation R_X86_64_PC32 against symbol `stdout@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: imager.so] Error 1
ERROR: compilation failed for package ‘imager’
* removing ‘/home/tjcooper/R/x86_64-pc-linux-gnu-library/4.0/imager’
Warning in install.packages :
installation of package ‘imager’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpZagOIF/downloaded_packages’
即共享库和静态库之间的一些问题。我不太确定如何解决这个问题 - 有什么想法吗？
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_IL.UTF-8 LC_NUMERIC=C LC_TIME=en_IL.UTF-8 LC_COLLATE=en_IL.UTF-8 LC_MONETARY=en_IL.UTF-8 LC_MESSAGES=en_IL.UTF-8 LC_PAPER=en_IL.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IL.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SummarizedExperiment_1.20.0 Biobase_2.50.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.0 IRanges_2.24.0 S4Vectors_0.28.0
[7] BiocGenerics_0.36.0 MatrixGenerics_1.2.0 matrixStats_0.57.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 GSVA_1.38.0 enrichplot_1.10.0 dynutils_1.0.5 bit64_4.0.5 RColorBrewer_1.1-2 httr_1.4.2 tools_4.0.3
[9] R6_2.5.0 irlba_2.3.3 DBI_1.1.0 colorspace_2.0-0 tidyselect_1.1.0 gridExtra_2.3 proxyC_0.1.5 bit_4.0.4
[17] compiler_4.0.3 graph_1.68.0 scatterpie_0.1.5 DelayedArray_0.16.0 shadowtext_0.0.7 scales_1.1.1 stringr_1.4.0 digest_0.6.27
[25] DOSE_3.16.0 XVector_0.30.0 pkgconfig_2.0.3 rlang_0.4.8 rstudioapi_0.13 RSQLite_2.2.1 farver_2.0.3 generics_0.1.0
[33] BiocParallel_1.24.1 GOSemSim_2.16.1 dplyr_1.0.2 RCurl_1.98-1.2 magrittr_1.5 GO.db_3.12.1 GenomeInfoDbData_1.2.4 Matrix_1.2-18
[41] Rcpp_1.0.5 dyndimred_1.0.3 munsell_0.5.0 viridis_0.5.1 lifecycle_0.2.0 stringi_1.5.3 ggraph_2.0.3 MASS_7.3-53
[49] zlibbioc_1.36.0 plyr_1.8.6 qvalue_2.22.0 grid_4.0.3 blob_1.2.1 ggrepel_0.8.2 DO.db_2.9 crayon_1.3.4
[57] lattice_0.20-41 cowplot_1.1.0 graphlayouts_0.7.1 splines_4.0.3 annotate_1.68.0 pillar_1.4.6 fgsea_1.16.0 igraph_1.2.6
[65] codetools_0.2-16 reshape2_1.4.4 fastmatch_1.1-0 XML_3.99-0.5 glue_1.4.2 downloader_0.4 BiocManager_1.30.10 data.table_1.13.2
[73] remotes_2.2.0 RcppParallel_5.0.2 foreach_1.5.1 tweenr_1.0.1 vctrs_0.3.4 polyclip_1.10-0 gtable_0.3.0 purrr_0.3.4
[81] tidyr_1.1.2 assertthat_0.2.1 ggplot2_3.3.2 ggforce_0.3.2 xfun_0.19 lmds_0.1.0 xtable_1.8-4 tidygraph_1.2.0
[89] viridisLite_0.3.0 tibble_3.0.4 pheatmap_1.0.12 iterators_1.0.13 rvcheck_0.1.8 clusterProfiler_3.18.0 tinytex_0.27 AnnotationDbi_1.52.0
[97] memoise_1.1.0 gam_1.20 ellipsis_0.3.1 GSEABase_1.52.0
这通常意味着您要使用的库，此处 libfftw3 构建方式有误。第一个偏好是作为共享库创建 libfftw3.so。第二个首选是静态库 libftw3.a ，但带有 -fPIC 可重定位代码的编译选项 。此处缺少，正是错误消息所暗示的内容。
一个我的 (Ubuntu) 系统它来对了：
$ file /usr/lib/x86_64-linux-gnu/libfftw3.so
/usr/lib/x86_64-linux-gnu/libfftw3.so: symbolic link to libfftw3.so.3.5.8
$ file /usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.8
/usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.8: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=56a87c8c86308035675bfd1c10d09c29b5450bc7, stripped
$
您需要修复该问题，然后尝试重新安装 imager。
None顺便跟Rcpp有关系
编辑 因为你也在Ubuntu，就这样做：
sudo apt install libfftw3-dev
但还要删除 /usr/local 下面的安装，因为它会影响系统安装。然后重新安装任何使用 fftw3 的东西，包括 imager.
我试图在 R 中安装 imager 包，但遇到以下错误：
/usr/bin/ld: /usr/local/lib/libfftw3.a(assert.o): relocation R_X86_64_PC32 against symbol `stdout@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: imager.so] Error 1
ERROR: compilation failed for package ‘imager’
* removing ‘/home/tjcooper/R/x86_64-pc-linux-gnu-library/4.0/imager’
Warning in install.packages :
installation of package ‘imager’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpZagOIF/downloaded_packages’
即共享库和静态库之间的一些问题。我不太确定如何解决这个问题 - 有什么想法吗？
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_IL.UTF-8 LC_NUMERIC=C LC_TIME=en_IL.UTF-8 LC_COLLATE=en_IL.UTF-8 LC_MONETARY=en_IL.UTF-8 LC_MESSAGES=en_IL.UTF-8 LC_PAPER=en_IL.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IL.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SummarizedExperiment_1.20.0 Biobase_2.50.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.0 IRanges_2.24.0 S4Vectors_0.28.0
[7] BiocGenerics_0.36.0 MatrixGenerics_1.2.0 matrixStats_0.57.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 GSVA_1.38.0 enrichplot_1.10.0 dynutils_1.0.5 bit64_4.0.5 RColorBrewer_1.1-2 httr_1.4.2 tools_4.0.3
[9] R6_2.5.0 irlba_2.3.3 DBI_1.1.0 colorspace_2.0-0 tidyselect_1.1.0 gridExtra_2.3 proxyC_0.1.5 bit_4.0.4
[17] compiler_4.0.3 graph_1.68.0 scatterpie_0.1.5 DelayedArray_0.16.0 shadowtext_0.0.7 scales_1.1.1 stringr_1.4.0 digest_0.6.27
[25] DOSE_3.16.0 XVector_0.30.0 pkgconfig_2.0.3 rlang_0.4.8 rstudioapi_0.13 RSQLite_2.2.1 farver_2.0.3 generics_0.1.0
[33] BiocParallel_1.24.1 GOSemSim_2.16.1 dplyr_1.0.2 RCurl_1.98-1.2 magrittr_1.5 GO.db_3.12.1 GenomeInfoDbData_1.2.4 Matrix_1.2-18
[41] Rcpp_1.0.5 dyndimred_1.0.3 munsell_0.5.0 viridis_0.5.1 lifecycle_0.2.0 stringi_1.5.3 ggraph_2.0.3 MASS_7.3-53
[49] zlibbioc_1.36.0 plyr_1.8.6 qvalue_2.22.0 grid_4.0.3 blob_1.2.1 ggrepel_0.8.2 DO.db_2.9 crayon_1.3.4
[57] lattice_0.20-41 cowplot_1.1.0 graphlayouts_0.7.1 splines_4.0.3 annotate_1.68.0 pillar_1.4.6 fgsea_1.16.0 igraph_1.2.6
[65] codetools_0.2-16 reshape2_1.4.4 fastmatch_1.1-0 XML_3.99-0.5 glue_1.4.2 downloader_0.4 BiocManager_1.30.10 data.table_1.13.2
[73] remotes_2.2.0 RcppParallel_5.0.2 foreach_1.5.1 tweenr_1.0.1 vctrs_0.3.4 polyclip_1.10-0 gtable_0.3.0 purrr_0.3.4
[81] tidyr_1.1.2 assertthat_0.2.1 ggplot2_3.3.2 ggforce_0.3.2 xfun_0.19 lmds_0.1.0 xtable_1.8-4 tidygraph_1.2.0
[89] viridisLite_0.3.0 tibble_3.0.4 pheatmap_1.0.12 iterators_1.0.13 rvcheck_0.1.8 clusterProfiler_3.18.0 tinytex_0.27 AnnotationDbi_1.52.0
[97] memoise_1.1.0 gam_1.20 ellipsis_0.3.1 GSEABase_1.52.0
这通常意味着您要使用的库，此处 libfftw3 构建方式有误。第一个偏好是作为共享库创建 libfftw3.so。第二个首选是静态库 libftw3.a ，但带有 -fPIC 可重定位代码的编译选项 。此处缺少，正是错误消息所暗示的内容。
一个我的 (Ubuntu) 系统它来对了：
$ file /usr/lib/x86_64-linux-gnu/libfftw3.so
/usr/lib/x86_64-linux-gnu/libfftw3.so: symbolic link to libfftw3.so.3.5.8
$ file /usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.8
/usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.8: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=56a87c8c86308035675bfd1c10d09c29b5450bc7, stripped
$
您需要修复该问题，然后尝试重新安装 imager。
None顺便跟Rcpp有关系
编辑 因为你也在Ubuntu，就这样做：
sudo apt install libfftw3-dev
但还要删除 /usr/local 下面的安装，因为它会影响系统安装。然后重新安装任何使用 fftw3 的东西，包括 imager.