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Phoebe
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@b9a43c13
Last seen 3.9 years ago
I seemed to have a problem in installing the package, tried multiple times using the installing method suggested but still had this comment stated "installation of package ‘RforProteomics’ had non-zero exit status"
R version 4.0.1 on mac. Please troubleshoot this, thanks. Much appreciated
# sessionInfo here
> sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 ggplot2_3.3.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 rstudioapi_0.13 magrittr_2.0.1 tidyselect_1.1.0 munsell_0.5.0 colorspace_2.0-0
[7] R6_2.5.0 rlang_0.4.8 fansi_0.4.1 dplyr_1.0.2 tools_4.0.1 grid_4.0.1
[13] broom_0.7.2 gtable_0.3.0 xfun_0.19 tinytex_0.27 cli_2.2.0 withr_2.3.0
[19] ellipsis_0.3.1 assertthat_0.2.1 tibble_3.0.4 lifecycle_0.2.0 crayon_1.3.4 tidyr_1.1.2
[25] BiocManager_1.30.10 purrr_0.3.4 vctrs_0.3.5 glue_1.4.2 compiler_4.0.1 pillar_1.4.7
[31] cellranger_1.1.0 backports_1.2.0 generics_0.1.0 scales_1.1.1 pkgconfig_2.0.3
# installation starts here
> if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
> BiocManager::install("RforProteomics")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.1 (2020-06-06)
Installing package(s) 'RforProteomics'
installing the source package ‘RforProteomics’
trying URL 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/RforProteomics_1.27.1.tar.gz'
Content type 'application/x-gzip' length 8219725 bytes (7.8 MB)
==================================================
downloaded 7.8 MB
dyld: lazy symbol binding failed: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 10289 Done echo 'tools:::.install_packages()'
10290 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
The downloaded source packages are in
‘/private/var/folders/r1/t43yb0ps6c10rjpqstz792l40000gn/T/RtmpT7LvVo/downloaded_packages’
Old packages: 'rmarkdown'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
rmarkdown 2.3 2.5 FALSE
installing the source package ‘rmarkdown’
trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_2.5.tar.gz'
Content type 'application/x-gzip' length 3203415 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
dyld: lazy symbol binding failed: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 10306 Done echo 'tools:::.install_packages()'
10307 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
The downloaded source packages are in
‘/private/var/folders/r1/t43yb0ps6c10rjpqstz792l40000gn/T/RtmpT7LvVo/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘RforProteomics’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘rmarkdown’ had non-zero exit status`
I'll caveat this with the fact that I'm not a Mac user and perhaps there's a simple solution, but it looks to me like you're running Mac OS X Sierra 10.12.6 but R-4.0 is only available for (or at least supported on) for Mac OS X High Sierra 10.13.
You can download R-3.6 for 'legacy OS X systems' from https://cran.r-project.org/bin/macosx/ but maybe it's time to upgrade your version of OS X?