Closed vigneshshanmug closed 1 year ago
jarchana09
commented
2 years ago Hi Vignesh, not a member of Seurat development team, but perhaps this can help. Since you are trying to install 2 packages, you could include them in a vector as:
remotes::install_github(c("satijalab/seurat", "feat/imaging"))
Hope this helps. Thanks.
vigneshshanmug
commented
2 years ago Thanks for your response @jarchana09! That doesn't seem to solve the issue. I am getting the following error with that command -
`Error: Failed to install 'unknown package' from GitHub: HTTP error 404. Not Found
Did you spell the repo owner (feat) and repo name (imaging) correctly?
jarchana09
commented
2 years ago Perhaps, the suggestion by Paul Hoffman (Satija lab) in this link may help: https://github.com/satijalab/seurat/issues/5713#issuecomment-1065210089 Thanks.
vigneshshanmug
commented
2 years ago Thanks @jarchana09! That seems like the same issue as me. But I am still unable to install the newer version of SeuratObject . I am getting a compilation error and I have copied the long error log below. It seems to be an issue with the RcppEigen package which was discussed here #4095 . But reinstalling the RcppEigen package does not seem to solve this problem.
Downloading GitHub repo mojaveazure/seurat-object@feat/imaging
✓ checking for file ‘/private/var/folders/nw/tpbh3cq17d57q0htyz9hp8300000gp/T/Rtmpf95UO8/remotes95178ce3961/mojaveazure-seurat-object-9c405ca/DESCRIPTION’ (968ms) ─ preparing ‘SeuratObject’: ✓ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts (930ms) ─ checking for empty or unneeded directories (739ms) ─ building ‘SeuratObject_4.0.999.9011.tar.gz’
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^18 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I/usr/local/include -fPIC -Wall -g -O2 -c data_manipulation.cpp -o data_manipulation.o In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^In file included from data_manipulation.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
^data_manipulation.cpp:20:20: error: expected expression
[&v](size_t i1, size_t i2) {return v[i1] < v[i2];});
^
data_manipulation.cpp:72:58: warning: use of right-shift operator ('>>') in template argument will require parentheses in C++11 [-Wc++11-compat]
std::vector<Eigen::SparseMatrix<double, Eigen::RowMajor>> mat_vec;
^
data_manipulation.cpp:72:61: error: use of undeclared identifier 'mat_vec'
std::vector<Eigen::SparseMatrix<double, Eigen::RowMajor>> mat_vec;
^
data_manipulation.cpp:72:68: error: expected a type
std::vector<Eigen::SparseMatrix<double, Eigen::RowMajor>> mat_vec;
^
data_manipulation.cpp:72:68: warning: declaration does not declare anything [-Wmissing-declarations]
data_manipulation.cpp:73:3: error: use of undeclared identifier 'mat_vec'
mat_vec.reserve(mat_list.size());
^
data_manipulation.cpp:74:38: error: a space is required between consecutive right angle brackets (use '> >')
std::vector<std::vector
data_manipulation.cpp:76:50: error: a space is required between consecutive right angle brackets (use '> >') std::vector<std::unordered_map<std::string, int>> map_vec; ^~
data_manipulation.cpp:83:5: error: use of undeclared identifier 'mat_vec'; did you mean 'map_vec'? mat_vec.emplace_back(Rcpp::as<Eigen::SparseMatrix<double, Eigen::RowMajor>>(mat_list.at(i))); ^
~~ map_vec data_manipulation.cpp:76:53: note: 'map_vec' declared here std::vector<std::unordered_map<std::string, int>> map_vec; ^ data_manipulation.cpp:83:78: warning: use of right-shift operator ('>>') in template argument will require parentheses in C++11 [-Wc++11-compat] mat_vec.emplace_back(Rcpp::as<Eigen::SparseMatrix<double, Eigen::RowMajor>>(mat_list.at(i))); ^ ( ) data_manipulation.cpp:83:78: error: use of overloaded operator '>>' is ambiguous (with operand types 'Eigen::StorageOptions' and 'Rcpp::Vector<19, PreserveStorage>::Proxy' (aka 'generic_proxy<19, PreserveStorage>')) mat_vec.emplace_back(Rcpp::as<Eigen::SparseMatrix<double, Eigen::RowMajor>>(mat_list.at(i)));data_manipulation.cpp:83:78: note: built-in candidate operator>>(int, int) data_manipulation.cpp:83:78: note: built-in candidate operator>>(int, long) data_manipulation.cpp:83:78: note: built-in candidate operator>>(int, long long) data_manipulation.cpp:83:78: note: built-in candidate operator>>(int, __int128) data_manipulation.cpp:83:78: note: built-in candidate operator>>(int, unsigned int) data_manipulation.cpp:83:78: note: built-in candidate operator>>(int, unsigned long) data_manipulation.cpp:83:78: note: built-in candidate operator>>(int, unsigned long long) data_manipulation.cpp:83:78: note: built-in candidate operator>>(int, unsigned __int128) data_manipulation.cpp:83:97: error: expected a type mat_vec.emplace_back(Rcpp::as<Eigen::SparseMatrix<double, Eigen::RowMajor>>(mat_list.at(i))); ^ data_manipulation.cpp:86:40: error: expected '(' for function-style cast or type construction std::unordered_map<std::string, int> mat_map; ~~~^ data_manipulation.cpp:86:42: error: use of undeclared identifier 'mat_map'; did you mean 'mktemp'? std::unordered_map<std::string, int> mat_map; ^~~~~~~ mktemp /Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk/usr/include/stdlib.h:216:7: note: 'mktemp' declared here char *mktemp(char *); ^ data_manipulation.cpp:83:13: error: no member named 'emplace_back' in 'std::__1::vector<std::__1::unordered_map<std::__1::basic_string<char>, int, std::__1::hash<std::__1::basic_string<char> >, std::__1::equal_to<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, int> > >, std::__1::allocator<std::__1::unordered_map<std::__1::basic_string<char>, int, std::__1::hash<std::__1::basic_string<char> >, std::__1::equal_to<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, int> > > > >'; did you mean '__emplace_back'? mat_vec.emplace_back(Rcpp::as<Eigen::SparseMatrix<double, Eigen::RowMajor>>(mat_list.at(i))); ^~~~~~~~~~~~ __emplace_back /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:702:10: note: '__emplace_back' declared here void __emplace_back(const value_type& __x) { push_back(__x); } ^ data_manipulation.cpp:98:3: error: use of undeclared identifier 'tripletList' tripletList.reserve(num_nZero); ^ data_manipulation.cpp:102:24: error: use of undeclared identifier 'mat_vec'; did you mean 'map_vec'? for(int j = 0; j < mat_vec.size(); j++) { ^~~~~~~ map_vec data_manipulation.cpp:76:53: note: 'map_vec' declared here std::vector<std::unordered_map<std::string, int>> map_vec; ^ data_manipulation.cpp:104:77: error: use of undeclared identifier 'mat_vec'; did you mean 'map_vec'? for(Eigen::SparseMatrix<double, Eigen::RowMajor>::InnerIterator it1(mat_vec[j], map_vec[j][key]); it1; ++it1){ ^~~~~~~ map_vec data_manipulation.cpp:76:53: note: 'map_vec' declared here std::vector<std::unordered_map<std::string, int>> map_vec; ^ data_manipulation.cpp:104:73: error: no matching constructor for initialization of 'Eigen::SparseMatrix<double, Eigen::RowMajor>::InnerIterator' (aka 'Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 1, int> >::InnerIterator') for(Eigen::SparseMatrix<double, Eigen::RowMajor>::InnerIterator it1(mat_vec[j], map_vec[j][key]); it1; ++it1){ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:157:5: note: candidate constructor not viable: no known conversion from 'std::__1::__vector_base<std::__1::unordered_map<std::__1::basic_string<char>, int, std::__1::hash<std::__1::basic_string<char> >, std::__1::equal_to<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, int> > >, std::__1::allocator<std::__1::unordered_map<std::__1::basic_string<char>, int, std::__1::hash<std::__1::basic_string<char> >, std::__1::equal_to<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, int> > > > >::value_type' (aka 'std::__1::unordered_map<std::__1::basic_string<char>, int, std::__1::hash<std::__1::basic_string<char> >, std::__1::equal_to<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, int> > >') to 'const Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 1, int> >' for 1st argument InnerIterator(const SparseCompressedBase& mat, Index outer) ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:210:26: note: candidate template ignored: could not match 'SparseMatrixBase' against 'unordered_map' template<typename T> InnerIterator(const SparseMatrixBase<T>&, Index outer); ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:143:5: note: candidate constructor not viable: requires single argument 'other', but 2 arguments were provided InnerIterator(const InnerIterator& other) ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:175:14: note: candidate constructor not viable: requires single argument 'mat', but 2 arguments were provided explicit InnerIterator(const SparseCompressedBase& mat) ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:181:14: note: candidate constructor not viable: requires single argument 'data', but 2 arguments were provided explicit InnerIterator(const internal::CompressedStorage<Scalar,StorageIndex>& data) ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:139:5: note: candidate constructor not viable: requires 0 arguments, but 2 were provided InnerIterator() ^ data_manipulation.cpp:105:11: error: use of undeclared identifier 'tripletList' tripletList.emplace_back(i, it1.col() + offsets[j], it1.value()); ^ data_manipulation.cpp:111:32: error: use of undeclared identifier 'tripletList' combined_mat.setFromTriplets(tripletList.begin(), tripletList.end()); ^ data_manipulation.cpp:111:53: error: use of undeclared identifier 'tripletList' combined_mat.setFromTriplets(tripletList.begin(), tripletList.end()); ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 21 warnings and 20 errors generated. make: *** [data_manipulation.o] Error 1 ERROR: compilation failed for package ‘SeuratObject’
AustinHartman
commented
1 year ago Closing because the image-based spatial transcriptomics update in Seurat is now available on CRAN.
Hello team,
I am trying to run the new vignette on the analysis of image-based spatial datasets but I am unable to install the correct updated versions of SeuratObject to use the new functions. I am getting an error message (copied below) which states that a different version of SeuratObject (>= 4.0.999.9009) is required and I cannot find this updated version. I would really appreciate your help in resolving this error.
Error message: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘SeuratObject’ 4.0.4 is being loaded, but >= 4.0.999.9009 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘Seurat’
─ removing ‘/private/var/folders/nw/tpbh3cq17d57q0htyz9hp8300000gp/T/RtmpJxomfM/Rinst116e149388475/Seurat’
ERROR: package installation failed
Output of sessionInfo() -
R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] stats graphics grDevices utils datasets methods base
other attached packages: [1] RCTD_1.2.0
loaded via a namespace (and not attached): [1] Seurat_4.1.0 Rtsne_0.15 colorspace_2.0-3
[4] deldir_1.0-6 ellipsis_0.3.2 ggridges_0.5.3
[7] rprojroot_2.0.3 rstudioapi_0.13 spatstat.data_2.1-4
[10] leiden_0.3.9 listenv_0.8.0 farver_2.1.0
[13] remotes_2.4.2 ggrepel_0.9.1 fansi_1.0.3
[16] codetools_0.2-18 splines_4.0.3 doParallel_1.0.16
[19] polyclip_1.10-0 jsonlite_1.8.0 ica_1.0-2
[22] cluster_2.1.2 png_0.1-7 uwot_0.1.11
[25] shiny_1.7.1 sctransform_0.3.3 spatstat.sparse_2.1-0 [28] compiler_4.0.3 httr_1.4.2 assertthat_0.2.1
[31] SeuratObject_4.0.4 Matrix_1.4-0 fastmap_1.1.0
[34] lazyeval_0.2.2 cli_3.2.0 later_1.3.0
[37] htmltools_0.5.2 prettyunits_1.1.1 tools_4.0.3
[40] igraph_1.3.0 gtable_0.3.0 glue_1.6.2
[43] RANN_2.6.1 reshape2_1.4.4 dplyr_1.0.8
[46] Rcpp_1.0.8.3 scattermore_0.8 vctrs_0.4.0
[49] nlme_3.1-155 iterators_1.0.13 lmtest_0.9-40
[52] spatstat.random_2.2-0 stringr_1.4.0 globals_0.14.0
[55] ps_1.6.0 mime_0.12 miniUI_0.1.1.1
[58] lifecycle_1.0.1 irlba_2.3.5 goftest_1.2-3
[61] future_1.24.0 MASS_7.3-55 zoo_1.8-9
[64] scales_1.1.1 spatstat.core_2.4-2 promises_1.2.0.1
[67] spatstat.utils_2.3-0 parallel_4.0.3 RColorBrewer_1.1-3
[70] curl_4.3.2 reticulate_1.24 pbapply_1.5-0
[73] gridExtra_2.3 ggplot2_3.3.5 rpart_4.1.16
[76] stringi_1.7.6 foreach_1.5.1 pkgbuild_1.3.1
[79] rlang_1.0.2 pkgconfig_2.0.3 matrixStats_0.61.0
[82] lattice_0.20-45 ROCR_1.0-11 purrr_0.3.4
[85] tensor_1.5 patchwork_1.1.1 htmlwidgets_1.5.4
[88] cowplot_1.1.1 tidyselect_1.1.2 processx_3.5.2
[91] parallelly_1.31.0 RcppAnnoy_0.0.19 plyr_1.8.7
[94] magrittr_2.0.3 R6_2.5.1 generics_0.1.2
[97] DBI_1.1.2 withr_2.5.0 pillar_1.7.0
[100] mgcv_1.8-38 fitdistrplus_1.1-8 survival_3.2-13
[103] abind_1.4-5 tibble_3.1.6 future.apply_1.8.1
[106] crayon_1.5.1 KernSmooth_2.23-20 utf8_1.2.2
[109] spatstat.geom_2.4-0 plotly_4.10.0 grid_4.0.3
[112] data.table_1.14.2 callr_3.7.0 digest_0.6.29
[115] xtable_1.8-4 tidyr_1.2.0 httpuv_1.6.5
[118] munsell_0.5.0 viridisLite_0.4.0