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xzhoulab / iDEA

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
GNU General Public License v3.0
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Unable to install Package #9

Closed zamlerd closed 3 years ago

zamlerd commented 4 years ago

Hello,

I was hoping to use your tool to analyze some scSeq datasets I generated-

On the install however I am getting this error-

─ installing source package ‘iDEA’ ... using staged installation libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang: error: unsupported option '-fopenmp' make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘iDEA’ ─ removing ‘/private/var/folders/6n/zbwc61bx7_d3dpjbx4lkn_9ctqxgjh/T/RtmpoSxrNP/Rinst8e635314891/iDEA’

ERROR: package installation failed Error: Failed to install 'iDEA' from GitHub: System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines): E> installing source* package ‘iDEA’ ... E> using staged installation E> libs E> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o E> clang: error: unsupported option '-fopenmp' E> make: ** [RcppExports.o] Error 1 E> ERROR: compilation failed for package ‘iDEA’ E> removing ‘/private/var/folders/6n/zbwc61bx7_d3dpjbx4lkn_9ctqxgjh/T/RtmpoSxrNP/Rinst8e635314891/iDEA’ E> ----------------------------------- E> ERROR: package installation failed In addition: Warning message: replacing previous import ‘vctrs::data_frame’ by ‘tibble::data_frame’ when loading ‘dplyr’

Any idea why? I have already tried re-installing gcc through homebrew

Session info below ─ Session info ─────────────────────────────────────────────────────────────────────────────────── setting value
version R version 3.6.1 (2019-07-05) os macOS Mojave 10.14.6
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Chicago
date 2020-10-13

─ Packages ─────────────────────────────────────────────────────────────────────────────────────── package version date lib source
AnnotationDbi 1.48.0 2019-10-29 [1] Bioconductor
ape 5.4 2020-06-03 [1] CRAN (R 3.6.2) assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) backports 1.1.8 2020-06-17 [1] CRAN (R 3.6.2) Biobase 2.46.0 2019-10-29 [1] Bioconductor
BiocGenerics 0.32.0 2019-10-29 [1] Bioconductor
BiocParallel 1.20.1 2019-12-21 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 3.6.2) bit64 4.0.5 2020-08-30 [1] CRAN (R 3.6.2) blob 1.2.1 2020-01-20 [1] CRAN (R 3.6.0) callr 3.4.3 2020-03-28 [1] CRAN (R 3.6.2) cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0) cluster 2.1.0 2019-06-19 [1] CRAN (R 3.6.1) codetools 0.2-16 2018-12-24 [1] CRAN (R 3.6.1) colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0) cowplot 1.0.0 2019-07-11 [1] CRAN (R 3.6.0) crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) curl 4.3 2019-12-02 [1] CRAN (R 3.6.0) data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.0) DBI 1.1.0 2019-12-15 [1] CRAN (R 3.6.0) desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) devtools 2.3.0 2020-04-10 [1] CRAN (R 3.6.2) digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0) DO.db 2.9 2020-05-05 [1] Bioconductor
DOSE 3.10.2 2019-06-24 [1] Bioconductor
dplyr 1.0.0 2020-05-29 [1] CRAN (R 3.6.2) ellipsis 0.3.1 2020-05-15 [1] CRAN (R 3.6.2) fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0) fastmatch 1.1-0 2017-01-28 [1] CRAN (R 3.6.0) fgsea 1.10.1 2019-08-21 [1] Bioconductor
fitdistrplus 1.1-1 2020-05-19 [1] CRAN (R 3.6.2) fs 1.4.2 2020-06-30 [1] CRAN (R 3.6.2) future 1.18.0 2020-07-09 [1] CRAN (R 3.6.2) future.apply 1.6.0 2020-07-01 [1] CRAN (R 3.6.2) generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.0) ggplot2 3.3.2 2020-06-19 [1] CRAN (R 3.6.2) ggrepel 0.8.2 2020-03-08 [1] CRAN (R 3.6.0) ggridges 0.5.2 2020-01-12 [1] CRAN (R 3.6.0) globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0) glue 1.4.2 2020-08-27 [1] CRAN (R 3.6.2) GO.db 3.8.2 2020-05-05 [1] Bioconductor
GOSemSim 2.10.0 2019-05-02 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) htmltools 0.5.0 2020-06-16 [1] CRAN (R 3.6.2) htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0) httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0) ica 1.0-2 2018-05-24 [1] CRAN (R 3.6.0) igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.0) IRanges 2.20.2 2020-01-13 [1] Bioconductor
irlba 2.3.3 2019-02-05 [1] CRAN (R 3.6.0) jsonlite 1.7.0 2020-06-25 [1] CRAN (R 3.6.2) KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 3.6.2) lattice 0.20-41 2020-04-02 [1] CRAN (R 3.6.2) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0) leiden 0.3.3 2020-02-04 [1] CRAN (R 3.6.0) lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.0) listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0) lmtest 0.9-37 2019-04-30 [1] CRAN (R 3.6.0) magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0) MASS 7.3-51.6 2020-04-26 [1] CRAN (R 3.6.2) Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.0) memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0) munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) nlme 3.1-148 2020-05-24 [1] CRAN (R 3.6.2) patchwork 1.0.1 2020-06-22 [1] CRAN (R 3.6.2) pbapply 1.4-2 2019-08-31 [1] CRAN (R 3.6.0) pillar 1.4.6 2020-07-10 [1] CRAN (R 3.6.2) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 3.6.1) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.0) pkgload 1.1.0 2020-05-29 [1] CRAN (R 3.6.2) plotly 4.9.2.1 2020-04-04 [1] CRAN (R 3.6.2) plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.1) png 0.1-7 2013-12-03 [1] CRAN (R 3.6.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.0) processx 3.4.3 2020-07-05 [1] CRAN (R 3.6.2) ps 1.3.3 2020-05-08 [1] CRAN (R 3.6.2) purrr 0.3.4 2020-04-17 [1] CRAN (R 3.6.2) qvalue 2.16.0 2019-05-02 [1] Bioconductor
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0) RANN 2.6.1 2019-01-08 [1] CRAN (R 3.6.0) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) Rcpp 1.0.5 2020-07-06 [1] CRAN (R 3.6.2) RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 3.6.0) remotes 2.1.1 2020-02-15 [1] CRAN (R 3.6.0) reshape2 1.4.4 2020-04-09 [1] CRAN (R 3.6.2) reticulate 1.16 2020-05-27 [1] CRAN (R 3.6.2) rlang 0.4.7 2020-07-09 [1] CRAN (R 3.6.2) ROCR 1.0-11 2020-05-02 [1] CRAN (R 3.6.2) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0) RSQLite 2.2.0 2020-01-07 [1] CRAN (R 3.6.0) rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.0) rsvd 1.0.3 2020-02-17 [1] CRAN (R 3.6.0) Rtsne 0.15 2018-11-10 [1] CRAN (R 3.6.0) S4Vectors 0.24.4 2020-04-09 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 3.6.2) sctransform 0.2.1 2019-12-17 [1] CRAN (R 3.6.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) Seurat 3.1.5 2020-04-16 [1] CRAN (R 3.6.2) stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0) stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) survival 3.2-3 2020-06-13 [1] CRAN (R 3.6.2) testthat 2.3.2 2020-03-02 [1] CRAN (R 3.6.1) tibble 3.0.3 2020-07-10 [1] CRAN (R 3.6.2) tidyr 1.1.0 2020-05-20 [1] CRAN (R 3.6.2) tidyselect 1.1.0 2020-05-11 [1] CRAN (R 3.6.2) tsne 0.1-3 2016-07-15 [1] CRAN (R 3.6.0) usethis 1.6.1 2020-04-29 [1] CRAN (R 3.6.2) uwot 0.1.8 2020-03-16 [1] CRAN (R 3.6.0) vctrs 0.3.4 2020-08-29 [1] CRAN (R 3.6.2) viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0) withr 2.2.0 2020-04-20 [1] CRAN (R 3.6.2) zoo 1.8-8 2020-05-02 [1] CRAN (R 3.6.2)

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

YingMa0107 commented 4 years ago

Hi @zamlerd

Based on your error, I guess that the installed compiler on your MAC does not support OpenMP. So you have to install the compile which supports the OpenMP. I recommend you to install the compilers such as gcc or clang from homebrew, and after install them, you have to modify variables in your personal makeovers file (~/.R/Makevars). Here is an example of the ~/.R/Makevars files when using gcc as the compiler on the macOS.

VER=-11.0.3 CC=gcc$(VER) CXX=g++$(VER) CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion FLIBS=-L/usr/local/Cellar/gcc/11.0.3/lib/gcc/11

The first line is the gcc version on your computer (type gcc --version on your terminal, you will got the information).And you also have to modify the last line according to your version of gcc.

You can use the homebrew to install it, i.e. brew install gcc

If this does not help, here are also other solutions you can follow: https://github.com/RcppCore/RcppArmadillo/issues/143

Hope it helps!

Best, Ying

zamlerd commented 4 years ago

Hey Ying,

After trying both methods above I am now getting a new error

devtools::install_github('xzhoulab/iDEA') Registered S3 method overwritten by 'cli': method from
print.boxx spatstat Downloading GitHub repo xzhoulab/iDEA@HEAD Error: Failed to install 'iDEA' from GitHub: Could not find tools necessary to compile a package Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

I have devtools installed and can call it

YingMa0107 commented 4 years ago

Hi @zamlerd,

Could you please call the function pkgbuild::check_build_tools(debug = TRUE) to see the output? For example, this is the output of mine:

pkgbuild::check_build_tools(debug = TRUE) Trying to compile a simple C file \Running /usr/lib/R/bin/R CMD SHLIB foo.c gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c foo.c -o foo.o gcc -std=gnu99 -shared -o foo.so foo.o -L/usr/lib/R/lib -lR

Your system is ready to build packages!

Just want to check if you have installed the tools necessary to compile the package.

Thanks!