Installing chromVAR

[Funshope]

I've been having problems installing chromVAR. Below is the output that I'm getting. Any idea on how I can install it????

BiocInstaller::biocLite("GreenleafLab/chromVAR") BioCmirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). Installing github package(s) ‘GreenleafLab/chromVAR’ Downloading GitHub repo GreenleafLab/chromVAR@master from URL https://api.github.com/repos/GreenleafLab/chromVAR/zipball/master Installing chromVAR '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file \ --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/s/0_w3y8k54336fm35p1dh6ms40000gn/T/Rtmpvl8fj8/devtools7ce6978bc5/GreenleafLab-chromVAR-7f1d5dc' \ --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' \ --install-tests

• installing source package ‘chromVAR’ ... ** libs clang++ -std=gnu++11 -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++ -std=gnu++11 -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 pwm_similarity.cpp -o pwm_similarity.o clang++ -std=gnu++11 -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 utils.cpp -o utils.o clang++ -std=gnu++11 -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 chromVAR.so RcppExports.o pwm_similarity.o utils.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: *** [chromVAR.so] Error 1 ERROR: compilation failed for package ‘chromVAR’
• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/chromVAR’ Installation failed: Command failed (1)

[AliciaSchep]

I think this might be similar to issue #11, perhaps try out the recommendations Caleb suggested there?

Edit: Are you on a Mac? Can you specify the OS?

[Funshope]

Yes, I'm on MAC.

[Funshope]

Hi Alicia, I'm still struggling to install chromVAR, Below is the error message I'm still getting BiocInstaller::biocLite("GreenleafLab/chromVAR") BioCmirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). Installing github package(s) ‘GreenleafLab/chromVAR’ Downloading GitHub repo GreenleafLab/chromVAR@master from URL https://api.github.com/repos/GreenleafLab/chromVAR/zipball/master Installing chromVAR '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file \ --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/s/0_w3y8k54336fm35p1dh6ms40000gn/T/RtmpT4m9IK/devtoolsc1e40168a60/GreenleafLab-chromVAR-7f1d5dc' \ --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' \ --install-tests

• installing source package ‘chromVAR’ ... ** libs clang++ -std=gnu++11 -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++ -std=gnu++11 -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 pwm_similarity.cpp -o pwm_similarity.o clang++ -std=gnu++11 -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 utils.cpp -o utils.o clang++ -std=gnu++11 -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 chromVAR.so RcppExports.o pwm_similarity.o utils.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 -lquadmath clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [chromVAR.so] Error 1 ERROR: compilation failed for package ‘chromVAR’
• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/chromVAR’ Installation failed: Command failed (1)

[caleblareau]

@Funshope You need the correct version of gfortran installed; see here: http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/

[Funshope]

I have installed gfortran, I'm still finding it difficult to instal ChromVAR. Below is the error message I'm getting The downloaded binary packages are in /var/folders/s_/0_w3y8k54336fm35p1dh6ms40000gn/T//RtmpQ7HviA/downloaded_packages

BiocInstaller::biocLite("GreenleafLab/chromVAR") BioCmirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). Installing github package(s) ‘GreenleafLab/chromVAR’ Downloading GitHub repo GreenleafLab/chromVAR@master from URL https://api.github.com/repos/GreenleafLab/chromVAR/zipball/master Installing chromVAR '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file \ --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/s/0_w3y8k54336fm35p1dh6ms40000gn/T/RtmpQ7HviA/devtools24030afe234/GreenleafLab-chromVAR-7f1d5dc' \ --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' \ --install-tests

• installing source package ‘chromVAR’ ... libs clang++ -std=gnu++11 -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++ -std=gnu++11 -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 pwm_similarity.cpp -o pwm_similarity.o clang++ -std=gnu++11 -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 utils.cpp -o utils.o clang++ -std=gnu++11 -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 chromVAR.so RcppExports.o pwm_similarity.o utils.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-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/chromVAR/libs R ** data * moving datasets to lazyload DB inst tests preparing package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘GO.db’ ERROR: lazy loading failed for package ‘chromVAR’
• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/chromVAR’ Installation failed: Command failed (1)

[caleblareau]

@Funshope you're super close! I think that the Cpp code is compiling now; there's a pesky dependency (GO.db) that doesn't automatically install (https://github.com/GreenleafLab/chromVAR/issues/17 )

Try this in R:

source("https://bioconductor.org/biocLite.R")
biocLite("GO.db")
devtools::install_github("GreenleafLab/chromVAR")

[jaychung10010]

Hi everyone, I've also been having problems compiling chromVar. I'm using Mac OS 10.11 with R3.4.1 (both recently updated). I've tried all previous suggestions but this problem still persists:

Would appreciate any help!

BiocInstaller::biocLite("GreenleafLab/chromVAR")

BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). Installing github package(s) ‘GreenleafLab/chromVAR’ Downloading GitHub repo GreenleafLab/chromVAR@master from URL https://api.github.com/repos/GreenleafLab/chromVAR/zipball/master Installing chromVAR '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ \ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/zk/sr7pyb897114ybyjclrgq_jh0000gp/T/RtmpZWVPp8/devtools2ef62a89a91/GreenleafLab-chromVAR-31c31f9' \ --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' \ --install-tests

• installing source package ‘chromVAR’ ... ** libs 2017-09-29 16:35:34.230 xcodebuild[770:21659] Error loading /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/PrivatePlugIns/iPhoneOS Build System Support.xcplugin/Contents/MacOS/iPhoneOS Build System Support: dlopen(/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/PrivatePlugIns/iPhoneOS Build System Support.xcplugin/Contents/MacOS/iPhoneOS Build System Support, 265): Library not loaded: /System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice Referenced from: /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/PrivateFrameworks/DTDeviceKitBase.framework/Versions/A/DTDeviceKitBase Reason: no suitable image found. Did find: /System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice: GC capability mismatch 2017-09-29 16:35:34.231 xcodebuild[770:21659] WARNING: Failed to load plugin at: /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/PrivatePlugIns/iPhoneOS Build System Support.xcplugin, skipping. Could not load bundle. clang++ -std=gnu++11 -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 2017-09-29 16:35:34.584 xcodebuild[772:21681] Error loading /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/PrivatePlugIns/iPhoneOS Build System Support.xcplugin/Contents/MacOS/iPhoneOS Build System Support: dlopen(/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/PrivatePlugIns/iPhoneOS Build System Support.xcplugin/Contents/MacOS/iPhoneOS Build System Support, 265): Library not loaded: /System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice Referenced from: /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/PrivateFrameworks/DTDeviceKitBase.framework/Versions/A/DTDeviceKitBase Reason: no suitable image found. Did find: /System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice: GC capability mismatch 2017-09-29 16:35:34.585 xcodebuild[772:21681] WARNING: Failed to load plugin at: /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/PrivatePlugIns/iPhoneOS Build System Support.xcplugin, skipping. Could not load bundle. In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34: In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72: In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/functions.h:42: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/sapply.h:26:11: fatal error: 'type_traits' file not found

  include // ::std::result_of

           ^

  1 error generated. make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘chromVAR’

• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/chromVAR’ Installation failed: Command failed (1)

[cajanegra1]

Hi guys, Maybe the problem I experienced was similar to some of the issues people report in this thread, or it might have been a totally different bug, but I'll report it anyhow since it might help other users. It's quite simple. I'm trying to install chromVAR on an Amazon Ubuntu instance. Installation runs like a breeze with R 3.3.0, but it fails with R 3.3.3. Specifically, it gets clogged trying to install TFBSTools. No need to answer to this post since I'm happy to work with R 3.3.0, but just wanted to make you guys aware of this potential compatibility issue.

[yingyonghui]

I think this might be similar to issue #11, perhaps try out the recommendations Caleb suggested there?

Edit: Are you on a Mac? Can you specify the OS?

Hi @AliciaSchep , I'm trying to install chromVar in an Ubuntu 18.04 platform with R 3.6.0, and I encountered the same problem mentioned above. Here is the error output. Any suggestions would be appreciated!

• installing source package ‘chromVAR’ ... using staged installation libs x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/home/luh/.conda/envs/seurat3/lib/R/include" -DNDEBUG -I"/home/luh/.conda/envs/seurat3/lib/R/library/Rcpp/include" -I"/home/luh/.conda/envs/seurat3/lib/R/library/RcppArmadillo/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/luh/.conda/envs/seurat3/include -Wl,-rpath-link,/home/luh/.conda/envs/seurat3/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/luh/.conda/envs/seurat3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/luh/.conda/envs/seurat3=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/home/luh/.conda/envs/seurat3/lib/R/include" -DNDEBUG -I"/home/luh/.conda/envs/seurat3/lib/R/library/Rcpp/include" -I"/home/luh/.conda/envs/seurat3/lib/R/library/RcppArmadillo/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/luh/.conda/envs/seurat3/include -Wl,-rpath-link,/home/luh/.conda/envs/seurat3/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/luh/.conda/envs/seurat3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/luh/.conda/envs/seurat3=/usr/local/src/conda-prefix -c pwm_similarity.cpp -o pwm_similarity.o x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/home/luh/.conda/envs/seurat3/lib/R/include" -DNDEBUG -I"/home/luh/.conda/envs/seurat3/lib/R/library/Rcpp/include" -I"/home/luh/.conda/envs/seurat3/lib/R/library/RcppArmadillo/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/luh/.conda/envs/seurat3/include -Wl,-rpath-link,/home/luh/.conda/envs/seurat3/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/luh/.conda/envs/seurat3/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/luh/.conda/envs/seurat3=/usr/local/src/conda-prefix -c utils.cpp -o utils.o x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -shared -L/home/luh/.conda/envs/seurat3/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/luh/.conda/envs/seurat3/lib -Wl,-rpath-link,/home/luh/.conda/envs/seurat3/lib -L/home/luh/.conda/envs/seurat3/lib -Wl,-rpath-link,/home/luh/.conda/envs/seurat3/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -llapack -lblas -lgfortran -lm -lgomp -lquadmath -lpthread -L/home/luh/.conda/envs/seurat3/lib/R/lib -lR /home/luh/.conda/envs/seurat3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -llapack /home/luh/.conda/envs/seurat3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lblas collect2: error: ld returned 1 exit status make: *** [/home/luh/.conda/envs/seurat3/lib/R/share/make/shlib.mk:6: chromVAR.so] Error 1 ERROR: compilation failed for package ‘chromVAR’
• removing ‘/home/luh/.conda/envs/seurat3/lib/R/library/chromVAR’