Installation failed

[zhiyuanhu]

I was installing the SC3 from github via Rstudio on my Mac, because I want to use the lastest version used in the scRNA.seq.course. However, the installing did not work.

The installation command and the session info are as followings.

> devtools::install_github("hemberg-lab/SC3")
Downloading GitHub repo hemberg-lab/SC3@master
from URL https://api.github.com/repos/hemberg-lab/SC3/zipball/master
Installing SC3
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/z9/zcddb9jx5bz343w2nfzzc3500000gn/T/RtmpRQrrrD/devtools112e0c43ed85/hemberg-lab-SC3-a8216c5'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests 

* installing *source* package ‘SC3’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cppFunctions.cpp -o cppFunctions.o
clang++ -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 SC3.so RcppExports.o cppFunctions.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [SC3.so] Error 1
ERROR: compilation failed for package ‘SC3’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/SC3’
Installation failed: Command failed (1)

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RUVSeq_1.10.0              EDASeq_2.10.0              ShortRead_1.34.0          
 [4] GenomicAlignments_1.12.1   SummarizedExperiment_1.6.3 DelayedArray_0.2.7        
 [7] matrixStats_0.52.2         Rsamtools_1.28.0           GenomicRanges_1.28.3      
[10] GenomeInfoDb_1.12.1        Biostrings_2.44.1          XVector_0.16.0            
[13] IRanges_2.10.2             S4Vectors_0.14.3           BiocParallel_1.10.1       
[16] edgeR_3.18.1               limma_3.32.2               pheatmap_1.0.8            
[19] scater_1.4.0               ggplot2_2.2.1              Biobase_2.36.2            
[22] BiocGenerics_0.22.0        RColorBrewer_1.1-2         BiocInstaller_1.26.0      

loaded via a namespace (and not attached):
 [1] bitops_1.0-6            devtools_1.13.2         httr_1.2.1              tools_3.4.0            
 [5] R6_2.2.1                vipor_0.4.5             DBI_0.6-1               lazyeval_0.2.0         
 [9] colorspace_1.3-2        withr_1.0.2             gridExtra_2.2.1         curl_2.6               
[13] compiler_3.4.0          git2r_0.18.0            pacman_0.4.6            rtracklayer_1.36.3     
[17] labeling_0.3            scales_0.4.1            genefilter_1.58.1       DESeq_1.28.0           
[21] stringr_1.2.0           digest_0.6.12           R.utils_2.5.0           htmltools_0.3.6        
[25] rlang_0.1.1             RSQLite_1.1-2           shiny_1.0.3             hwriter_1.3.2          
[29] dplyr_0.5.0             R.oo_1.21.0             RCurl_1.95-4.8          magrittr_1.5           
[33] GenomeInfoDbData_0.99.0 Matrix_1.2-10           Rcpp_0.12.11            ggbeeswarm_0.5.3       
[37] munsell_0.4.3           viridis_0.4.0           R.methodsS3_1.7.1       stringi_1.1.5          
[41] MASS_7.3-47             zlibbioc_1.22.0         rhdf5_2.20.0            plyr_1.8.4             
[45] grid_3.4.0              shinydashboard_0.6.0    lattice_0.20-35         splines_3.4.0          
[49] GenomicFeatures_1.28.2  annotate_1.54.0         locfit_1.5-9.1          knitr_1.16             
[53] rjson_0.2.15            geneplotter_1.54.0      reshape2_1.4.2          biomaRt_2.32.0         
[57] XML_3.98-1.7            latticeExtra_0.6-28     data.table_1.10.4       httpuv_1.3.3           
[61] gtable_0.2.0            assertthat_0.2.0        aroma.light_3.6.0       mime_0.5               
[65] xtable_1.8-2            survival_2.41-3         viridisLite_0.2.0       tibble_1.3.3           
[69] AnnotationDbi_1.38.1    beeswarm_0.2.3          memoise_1.1.0           tximport_1.4.0       

[wikiselev]

Hi, you error message says that there is no gfortran library on your system. Could you please install it (https://gcc.gnu.org/wiki/GFortranBinaries) and let me know if the SC3 installation works after that?

[zhiyuanhu]

Thank you! It works.