CarlKCarlK
commented
4 years ago Greetings,
Thanks for using FaST-LMM!
You found a bug in the FaST-LMM documentation for Windows. (I do the primary development work on Windows, but most users are on Linux.)
Can you use an Anaconda 3.7 environment instead? (For example, with the commands “conda create --name py37b anaconda python=3.7” “activate py37b”). It should work then.
Over the next couple of days, I’ll fix the documentation. Thanks again for finding this problem and for using FaST-LMM.
Yours, Carl
Carl Kadie, Ph.D. FaST-LMM & PySnpTools Team (Microsoft Research, retired) https://fastlmm.github.io/ Join the FaST-LMM user discussion and announcement list via emailmailto:fastlmm-user-join@python.org?subject=Subscribe (or use web sign uphttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.python.org%2Fmailman3%2Flists%2Ffastlmm-user.python.org&data=02%7C01%7C%7C13a5c33d7cd84cad5cdf08d7bba56e20%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637184191498409587&sdata=2CQWjQEwOpQol2rQ1eoyVTgY8WvInV8UH31Wtl68FzY%3D&reserved=0)
From: snowformatics notifications@github.com Sent: Friday, July 24, 2020 4:48 AM To: fastlmm/FaST-LMM FaST-LMM@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [fastlmm/FaST-LMM] Installation problems on Windwos10 (#8)
Dear all,
I am having trouble to install fastlmm on a Windows 10 machine with python36:
ERROR: Command errored out with exit status 1: command: 'D:\Anaconda\envs\gwas36\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\setup.py'"'"'; file='"'"'C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\stefanie\AppData\Local\Temp\pip-record-s1a811oi\install-record.txt' --single-version-externally-managed --compile --install-headers 'D:\Anaconda\envs\gwas36\Include\fastlmm' cwd: C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm Complete output (202 lines): use_cython? False running install running build running build_py creating build creating build\lib.win-amd64-3.6 creating build\lib.win-amd64-3.6\fastlmm copying fastlmminit.py -> build\lib.win-amd64-3.6\fastlmm creating build\lib.win-amd64-3.6\fastlmm\association copying fastlmm/association\epistasis.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\FastLmmSet.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\FastLmmSetLOOC.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\fixed.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\gwas.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\gwas_eval.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\heritability_spatial_correction.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\LeaveOneChromosomeOut.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\LocoGwas.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\lrt.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\meta_analysis.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\PairResult.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\PrecomputeLocoPcs.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\Result.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\score.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp_all_plus_select.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp_linreg.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp_scale.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp_select.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\snp_set.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\testCV.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\varcomp_test.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\windowing_gwas.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association_matchscript.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association_pipelines.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/associationinit.py -> build\lib.win-amd64-3.6\fastlmm/association creating build\lib.win-amd64-3.6\fastlmm\association\altset_list copying fastlmm/association/altset_list\consecutive.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list copying fastlmm/association/altset_list\minmaxsetsize.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list copying fastlmm/association/altset_list\snpandsetnamecollection.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list copying fastlmm/association/altset_list\subset.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list copying fastlmm/association/altset_listinit.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list creating build\lib.win-amd64-3.6\fastlmm\association\tests copying fastlmm/association/tests\Cv.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\Lrt.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\LRT_up.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\Sc.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\testepistasis.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\tests_util.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_gwas.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_heritability_spatial_correction.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp_all_plus_select.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp_linreg.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp_scale.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp_select.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_snp_set.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/testsinit.py -> build\lib.win-amd64-3.6\fastlmm/association/tests creating build\lib.win-amd64-3.6\fastlmm\external copying fastlmm/external\pca.py -> build\lib.win-amd64-3.6\fastlmm/external copying fastlmm/externalinit.py -> build\lib.win-amd64-3.6\fastlmm/external creating build\lib.win-amd64-3.6\fastlmm\external\util copying fastlmm/external/util\math.py -> build\lib.win-amd64-3.6\fastlmm/external/util copying fastlmm/external/utilinit.py -> build\lib.win-amd64-3.6\fastlmm/external/util creating build\lib.win-amd64-3.6\fastlmm\feature_selection copying fastlmm/feature_selection\feature_selection_cv.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\feature_selection_example.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\feature_selection_two_kernel.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\kernel_ridge_cv.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\PerformSelectionDistributable.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\test.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selectioninit.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection creating build\lib.win-amd64-3.6\fastlmm\inference copying fastlmm/inference\ep.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\fastlmm_predictor.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\glmm.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\laplace.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\likelihood.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\linear_regression.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\lmm.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\lmm2k.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\lmm_cov.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inferenceinit.py -> build\lib.win-amd64-3.6\fastlmm/inference creating build\lib.win-amd64-3.6\fastlmm\inference\tests copying fastlmm/inference/tests\test.py -> build\lib.win-amd64-3.6\fastlmm/inference/tests copying fastlmm/inference/tests\test_fastlmm_predictor.py -> build\lib.win-amd64-3.6\fastlmm/inference/tests copying fastlmm/inference/tests\test_linear_regression.py -> build\lib.win-amd64-3.6\fastlmm/inference/tests copying fastlmm/inference/testsinit.py -> build\lib.win-amd64-3.6\fastlmm/inference/tests creating build\lib.win-amd64-3.6\fastlmm\pyplink copying fastlmm/pyplink\plink.py -> build\lib.win-amd64-3.6\fastlmm/pyplink copying fastlmm/pyplink\setup.py -> build\lib.win-amd64-3.6\fastlmm/pyplink copying fastlmm/pyplink\test.py -> build\lib.win-amd64-3.6\fastlmm/pyplink copying fastlmm/pyplink\vcfpy.py -> build\lib.win-amd64-3.6\fastlmm/pyplink copying fastlmm/pyplinkinit.py -> build\lib.win-amd64-3.6\fastlmm/pyplink creating build\lib.win-amd64-3.6\fastlmm\pyplink\altset_list copying fastlmm/pyplink/altset_list\Consecutive.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list copying fastlmm/pyplink/altset_list\MinMaxSetSize.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list copying fastlmm/pyplink/altset_list\SnpAndSetNameCollection.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list copying fastlmm/pyplink/altset_list\Subset.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list copying fastlmm/pyplink/altset_listinit.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list creating build\lib.win-amd64-3.6\fastlmm\pyplink\snpreader copying fastlmm/pyplink/snpreader\Bed.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpreader copying fastlmm/pyplink/snpreader\Dat.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpreader copying fastlmm/pyplink/snpreader\Hdf5.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpreader copying fastlmm/pyplink/snpreaderinit.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpreader creating build\lib.win-amd64-3.6\fastlmm\pyplink\snpset copying fastlmm/pyplink/snpset\AllSnps.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\PositionRange.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\RandomSnpSet.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\SnpIndexList.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\SnpSetAndName.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\SnpsFromFile.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpsetinit.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset creating build\lib.win-amd64-3.6\fastlmm\util copying fastlmm/util\computePC.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\compute_auto_pcs.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\est_h2.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\genphen.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\gensnp.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\mingrid.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\NearBronze.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\pickle_io.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\preprocess.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\run_fastlmmc.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\test.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\util.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\VertexCut.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/utilinit.py -> build\lib.win-amd64-3.6\fastlmm/util creating build\lib.win-amd64-3.6\fastlmm\util\matrix copying fastlmm/util/matrix\bigsvd.py -> build\lib.win-amd64-3.6\fastlmm/util/matrix copying fastlmm/util/matrix\mmultfile.py -> build\lib.win-amd64-3.6\fastlmm/util/matrix copying fastlmm/util/matrixinit.py -> build\lib.win-amd64-3.6\fastlmm/util/matrix creating build\lib.win-amd64-3.6\fastlmm\util\standardizer copying fastlmm/util/standardizer\Beta.py -> build\lib.win-amd64-3.6\fastlmm/util/standardizer copying fastlmm/util/standardizer\Unit.py -> build\lib.win-amd64-3.6\fastlmm/util/standardizer copying fastlmm/util/standardizerinit.py -> build\lib.win-amd64-3.6\fastlmm/util/standardizer creating build\lib.win-amd64-3.6\fastlmm\util\stats copying fastlmm/util/stats\chi2mixture.py -> build\lib.win-amd64-3.6\fastlmm/util/stats copying fastlmm/util/stats\plotp.py -> build\lib.win-amd64-3.6\fastlmm/util/stats copying fastlmm/util/statsinit.py -> build\lib.win-amd64-3.6\fastlmm/util/stats creating build\lib.win-amd64-3.6\fastlmm\util\stats\quadform copying fastlmm/util/stats/quadforminit.py -> build\lib.win-amd64-3.6\fastlmm/util/stats/quadform creating build\lib.win-amd64-3.6\fastlmm\util\stats\quadform\qfc_src copying fastlmm/util/stats/quadform/qfc_srcinit.py -> build\lib.win-amd64-3.6\fastlmm/util/stats/quadform/qfc_src creating build\lib.win-amd64-3.6\fastlmm\association\Fastlmm_autoselect copying fastlmm/association\Fastlmm_autoselect\FastLmmC.exe -> build\lib.win-amd64-3.6\fastlmm/association\Fastlmm_autoselect copying fastlmm/association\Fastlmm_autoselect\libiomp5md.dll -> build\lib.win-amd64-3.6\fastlmm/association\Fastlmm_autoselect copying fastlmm/association\Fastlmm_autoselect\fastlmmc -> build\lib.win-amd64-3.6\fastlmm/association\Fastlmm_autoselect copying fastlmm/association\Fastlmm_autoselect\FastLmmC.Manual.pdf -> build\lib.win-amd64-3.6\fastlmm/association\Fastlmm_autoselect creating build\lib.win-amd64-3.6\fastlmm\feature_selection\examples copying fastlmm/feature_selection\examples\bronze.txt -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\ScanISP.Toydata.config.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\ScanLMM.Toydata.config.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\ScanOSP.Toydata.config.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.5chrom.bed -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.5chrom.bim -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.5chrom.fam -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.bed -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.bim -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.cov -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.dat -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.fam -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.map -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.phe -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.shufflePlus.phe -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.sim -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydataTest.phe -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydataTrain.phe -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples running build_ext building 'fastlmm.util.stats.quadform.qfc_src.wrap_qfc' extension creating build\temp.win-amd64-3.6 creating build\temp.win-amd64-3.6\Release creating build\temp.win-amd64-3.6\Release\fastlmm creating build\temp.win-amd64-3.6\Release\fastlmm\util creating build\temp.win-amd64-3.6\Release\fastlmm\util\stats creating build\temp.win-amd64-3.6\Release\fastlmm\util\stats\quadform creating build\temp.win-amd64-3.6\Release\fastlmm\util\stats\quadform\qfc_src C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -D_WIN32=1 -ID:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include -ID:\Anaconda\envs\gwas36\include -ID:\Anaconda\envs\gwas36\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tpfastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp /Fobuild\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src/wrap_qfc.obj /EHsc wrap_qfc.cpp D:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -D_WIN32=1 -ID:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include -ID:\Anaconda\envs\gwas36\include -ID:\Anaconda\envs\gwas36\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tpfastlmm/util/stats/quadform/qfc_src/QFC.cpp /Fobuild\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src/QFC.obj /EHsc QFC.cpp fastlmm/util/stats/quadform/qfc_src/QFC.cpp(285): warning C4473: "printf": nicht genügend Argumente für Formatzeichenfolge übergeben fastlmm/util/stats/quadform/qfc_src/QFC.cpp(285): note: Platzhalter und deren Parameter erwarten 5 variadic-Argumente, es wurden aber 1 variadic-Argumente bereitgestellt. fastlmm/util/stats/quadform/qfc_src/QFC.cpp(285): note: Das fehlende variadic-Argument "2" ist für die Zeichenfolge "%i" erforderlich. C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\link.exe /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:D:\Anaconda\envs\gwas36\libs /LIBPATH:D:\Anaconda\envs\gwas36\PCbuild\amd64 "/LIBPATH:C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\lib\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.18362.0\ucrt\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.18362.0\um\x64" /EXPORT:PyInit_wrap_qfc build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src/wrap_qfc.obj build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src/QFC.obj /OUT:build\lib.win-amd64-3.6\fastlmm\util\stats\quadform\qfc_src\wrap_qfc.cp36-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src\wrap_qfc.cp36-win_amd64.lib Bibliothek "build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src\wrap_qfc.cp36-win_amd64.lib" und Objekt "build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src\wrap_qfc.cp36-win_amd64.exp" werden erstellt. Code wird generiert. Codegenerierung ist abgeschlossen. building 'fastlmm.util.matrix.cample' extension creating build\temp.win-amd64-3.6\Release\fastlmm\util\matrix C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -D_WIN32=1 -IC:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\external/intel/windows/mkl/include -ID:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include -ID:\Anaconda\envs\gwas36\include -ID:\Anaconda\envs\gwas36\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tpfastlmm/util/matrix/cample.cpp /Fobuild\temp.win-amd64-3.6\Release\fastlmm/util/matrix/cample.obj /DMKL_ILP64 cample.cpp D:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\link.exe /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\external/intel/windows/mkl/lib/intel64 /LIBPATH:C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\external/intel/windows/compiler/lib/intel64 /LIBPATH:D:\Anaconda\envs\gwas36\libs /LIBPATH:D:\Anaconda\envs\gwas36\PCbuild\amd64 "/LIBPATH:C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\lib\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.18362.0\ucrt\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.18362.0\um\x64" mkl_intel_ilp64.lib mkl_core_dll.lib mkl_intel_thread.lib libiomp5md.lib /EXPORT:PyInit_cample build\temp.win-amd64-3.6\Release\fastlmm/util/matrix/cample.obj /OUT:build\lib.win-amd64-3.6\fastlmm\util\matrix\cample.cp36-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.6\Release\fastlmm/util/matrix\cample.cp36-win_amd64.lib LINK : fatal error LNK1181: Eingabedatei "mkl_intel_ilp64.lib" kann nicht geöffnet werden. error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\link.exe' failed with exit status 1181
ERROR: Command errored out with exit status 1: 'D:\Anaconda\envs\gwas36\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\setup.py'"'"'; file='"'"'C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\stefanie\AppData\Local\Temp\pip-record-s1a811oi\install-record.txt' --single-version-externally-managed --compile --install-headers 'D:\Anaconda\envs\gwas36\Include\fastlmm' Check the logs for full command output.
Any ideas how to solve this issue? Thanks
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snowformatics
Dear all,
I am having trouble to install fastlmm on a Windows 10 machine with python36:
ERROR: Command errored out with exit status 1: command: 'D:\Anaconda\envs\gwas36\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\setup.py'"'"'; file='"'"'C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\stefanie\AppData\Local\Temp\pip-record-s1a811oi\install-record.txt' --single-version-externally-managed --compile --install-headers 'D:\Anaconda\envs\gwas36\Include\fastlmm' cwd: C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\ Complete output (202 lines): use_cython? False running install running build running build_py creating build creating build\lib.win-amd64-3.6 creating build\lib.win-amd64-3.6\fastlmm copying fastlmm__init__.py -> build\lib.win-amd64-3.6\fastlmm creating build\lib.win-amd64-3.6\fastlmm\association copying fastlmm/association\epistasis.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\FastLmmSet.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\FastLmmSetLOOC.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\fixed.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\gwas.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\gwas_eval.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\heritability_spatial_correction.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\LeaveOneChromosomeOut.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\LocoGwas.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\lrt.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\meta_analysis.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\PairResult.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\PrecomputeLocoPcs.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\Result.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\score.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp_all_plus_select.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp_linreg.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp_scale.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\single_snp_select.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\snp_set.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\testCV.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\varcomp_test.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association\windowing_gwas.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association_matchscript.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association_pipelines.py -> build\lib.win-amd64-3.6\fastlmm/association copying fastlmm/association__init__.py -> build\lib.win-amd64-3.6\fastlmm/association creating build\lib.win-amd64-3.6\fastlmm\association\altset_list copying fastlmm/association/altset_list\consecutive.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list copying fastlmm/association/altset_list\minmaxsetsize.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list copying fastlmm/association/altset_list\snpandsetnamecollection.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list copying fastlmm/association/altset_list\subset.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list copying fastlmm/association/altset_list__init.py -> build\lib.win-amd64-3.6\fastlmm/association/altset_list creating build\lib.win-amd64-3.6\fastlmm\association\tests copying fastlmm/association/tests\Cv.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\Lrt.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\LRT_up.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\Sc.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\testepistasis.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\tests_util.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_gwas.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_heritability_spatial_correction.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp_all_plus_select.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp_linreg.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp_scale.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_single_snp_select.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests\test_snp_set.py -> build\lib.win-amd64-3.6\fastlmm/association/tests copying fastlmm/association/tests__init.py -> build\lib.win-amd64-3.6\fastlmm/association/tests creating build\lib.win-amd64-3.6\fastlmm\external copying fastlmm/external\pca.py -> build\lib.win-amd64-3.6\fastlmm/external copying fastlmm/external__init.py -> build\lib.win-amd64-3.6\fastlmm/external creating build\lib.win-amd64-3.6\fastlmm\external\util copying fastlmm/external/util\math.py -> build\lib.win-amd64-3.6\fastlmm/external/util copying fastlmm/external/util__init__.py -> build\lib.win-amd64-3.6\fastlmm/external/util creating build\lib.win-amd64-3.6\fastlmm\feature_selection copying fastlmm/feature_selection\feature_selection_cv.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\feature_selection_example.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\feature_selection_two_kernel.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\kernel_ridge_cv.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\PerformSelectionDistributable.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\test.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection copying fastlmm/feature_selection\init.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection creating build\lib.win-amd64-3.6\fastlmm\inference copying fastlmm/inference\ep.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\fastlmm_predictor.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\glmm.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\laplace.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\likelihood.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\linear_regression.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\lmm.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\lmm2k.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\lmm_cov.py -> build\lib.win-amd64-3.6\fastlmm/inference copying fastlmm/inference\init.py -> build\lib.win-amd64-3.6\fastlmm/inference creating build\lib.win-amd64-3.6\fastlmm\inference\tests copying fastlmm/inference/tests\test.py -> build\lib.win-amd64-3.6\fastlmm/inference/tests copying fastlmm/inference/tests\test_fastlmm_predictor.py -> build\lib.win-amd64-3.6\fastlmm/inference/tests copying fastlmm/inference/tests\test_linear_regression.py -> build\lib.win-amd64-3.6\fastlmm/inference/tests copying fastlmm/inference/tests\init.py -> build\lib.win-amd64-3.6\fastlmm/inference/tests creating build\lib.win-amd64-3.6\fastlmm\pyplink copying fastlmm/pyplink\plink.py -> build\lib.win-amd64-3.6\fastlmm/pyplink copying fastlmm/pyplink\setup.py -> build\lib.win-amd64-3.6\fastlmm/pyplink copying fastlmm/pyplink\test.py -> build\lib.win-amd64-3.6\fastlmm/pyplink copying fastlmm/pyplink\vcfpy.py -> build\lib.win-amd64-3.6\fastlmm/pyplink copying fastlmm/pyplink\init.py -> build\lib.win-amd64-3.6\fastlmm/pyplink creating build\lib.win-amd64-3.6\fastlmm\pyplink\altset_list copying fastlmm/pyplink/altset_list\Consecutive.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list copying fastlmm/pyplink/altset_list\MinMaxSetSize.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list copying fastlmm/pyplink/altset_list\SnpAndSetNameCollection.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list copying fastlmm/pyplink/altset_list\Subset.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list copying fastlmm/pyplink/altset_list\init__.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/altset_list creating build\lib.win-amd64-3.6\fastlmm\pyplink\snpreader copying fastlmm/pyplink/snpreader\Bed.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpreader copying fastlmm/pyplink/snpreader\Dat.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpreader copying fastlmm/pyplink/snpreader\Hdf5.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpreader copying fastlmm/pyplink/snpreader\init.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpreader creating build\lib.win-amd64-3.6\fastlmm\pyplink\snpset copying fastlmm/pyplink/snpset\AllSnps.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\PositionRange.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\RandomSnpSet.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\SnpIndexList.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\SnpSetAndName.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\SnpsFromFile.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset copying fastlmm/pyplink/snpset\init__.py -> build\lib.win-amd64-3.6\fastlmm/pyplink/snpset creating build\lib.win-amd64-3.6\fastlmm\util copying fastlmm/util\computePC.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\compute_auto_pcs.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\est_h2.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\genphen.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\gensnp.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\mingrid.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\NearBronze.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\pickle_io.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\preprocess.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\run_fastlmmc.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\test.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\util.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\VertexCut.py -> build\lib.win-amd64-3.6\fastlmm/util copying fastlmm/util\init.py -> build\lib.win-amd64-3.6\fastlmm/util creating build\lib.win-amd64-3.6\fastlmm\util\matrix copying fastlmm/util/matrix\bigsvd.py -> build\lib.win-amd64-3.6\fastlmm/util/matrix copying fastlmm/util/matrix\mmultfile.py -> build\lib.win-amd64-3.6\fastlmm/util/matrix copying fastlmm/util/matrix\init.py -> build\lib.win-amd64-3.6\fastlmm/util/matrix creating build\lib.win-amd64-3.6\fastlmm\util\standardizer copying fastlmm/util/standardizer\Beta.py -> build\lib.win-amd64-3.6\fastlmm/util/standardizer copying fastlmm/util/standardizer\Unit.py -> build\lib.win-amd64-3.6\fastlmm/util/standardizer copying fastlmm/util/standardizer\init.py -> build\lib.win-amd64-3.6\fastlmm/util/standardizer creating build\lib.win-amd64-3.6\fastlmm\util\stats copying fastlmm/util/stats\chi2mixture.py -> build\lib.win-amd64-3.6\fastlmm/util/stats copying fastlmm/util/stats\plotp.py -> build\lib.win-amd64-3.6\fastlmm/util/stats copying fastlmm/util/stats\init.py -> build\lib.win-amd64-3.6\fastlmm/util/stats creating build\lib.win-amd64-3.6\fastlmm\util\stats\quadform copying fastlmm/util/stats/quadform\init.py -> build\lib.win-amd64-3.6\fastlmm/util/stats/quadform creating build\lib.win-amd64-3.6\fastlmm\util\stats\quadform\qfc_src copying fastlmm/util/stats/quadform/qfc_src\init__.py -> build\lib.win-amd64-3.6\fastlmm/util/stats/quadform/qfc_src creating build\lib.win-amd64-3.6\fastlmm\association\Fastlmm_autoselect copying fastlmm/association\Fastlmm_autoselect\FastLmmC.exe -> build\lib.win-amd64-3.6\fastlmm/association\Fastlmm_autoselect copying fastlmm/association\Fastlmm_autoselect\libiomp5md.dll -> build\lib.win-amd64-3.6\fastlmm/association\Fastlmm_autoselect copying fastlmm/association\Fastlmm_autoselect\fastlmmc -> build\lib.win-amd64-3.6\fastlmm/association\Fastlmm_autoselect copying fastlmm/association\Fastlmm_autoselect\FastLmmC.Manual.pdf -> build\lib.win-amd64-3.6\fastlmm/association\Fastlmm_autoselect creating build\lib.win-amd64-3.6\fastlmm\feature_selection\examples copying fastlmm/feature_selection\examples\bronze.txt -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\ScanISP.Toydata.config.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\ScanLMM.Toydata.config.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\ScanOSP.Toydata.config.py -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.5chrom.bed -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.5chrom.bim -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.5chrom.fam -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.bed -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.bim -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.cov -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.dat -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.fam -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.map -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.phe -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.shufflePlus.phe -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydata.sim -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydataTest.phe -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples copying fastlmm/feature_selection\examples\toydataTrain.phe -> build\lib.win-amd64-3.6\fastlmm/feature_selection\examples running build_ext building 'fastlmm.util.stats.quadform.qfc_src.wrap_qfc' extension creating build\temp.win-amd64-3.6 creating build\temp.win-amd64-3.6\Release creating build\temp.win-amd64-3.6\Release\fastlmm creating build\temp.win-amd64-3.6\Release\fastlmm\util creating build\temp.win-amd64-3.6\Release\fastlmm\util\stats creating build\temp.win-amd64-3.6\Release\fastlmm\util\stats\quadform creating build\temp.win-amd64-3.6\Release\fastlmm\util\stats\quadform\qfc_src C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -D_WIN32=1 -ID:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include -ID:\Anaconda\envs\gwas36\include -ID:\Anaconda\envs\gwas36\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tpfastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp /Fobuild\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src/wrap_qfc.obj /EHsc wrap_qfc.cpp D:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust fastlmm/util/stats/quadform/qfc_src/wrap_qfc.cpp(2055): warning C4244: "Argument": Konvertierung von "npy_intp" in "int", möglicher Datenverlust C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -D_WIN32=1 -ID:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include -ID:\Anaconda\envs\gwas36\include -ID:\Anaconda\envs\gwas36\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tpfastlmm/util/stats/quadform/qfc_src/QFC.cpp /Fobuild\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src/QFC.obj /EHsc QFC.cpp fastlmm/util/stats/quadform/qfc_src/QFC.cpp(285): warning C4473: "printf": nicht genügend Argumente für Formatzeichenfolge übergeben fastlmm/util/stats/quadform/qfc_src/QFC.cpp(285): note: Platzhalter und deren Parameter erwarten 5 variadic-Argumente, es wurden aber 1 variadic-Argumente bereitgestellt. fastlmm/util/stats/quadform/qfc_src/QFC.cpp(285): note: Das fehlende variadic-Argument "2" ist für die Zeichenfolge "%i" erforderlich. C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\link.exe /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:D:\Anaconda\envs\gwas36\libs /LIBPATH:D:\Anaconda\envs\gwas36\PCbuild\amd64 "/LIBPATH:C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\lib\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.18362.0\ucrt\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.18362.0\um\x64" /EXPORT:PyInit_wrap_qfc build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src/wrap_qfc.obj build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src/QFC.obj /OUT:build\lib.win-amd64-3.6\fastlmm\util\stats\quadform\qfc_src\wrap_qfc.cp36-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src\wrap_qfc.cp36-win_amd64.lib Bibliothek "build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src\wrap_qfc.cp36-win_amd64.lib" und Objekt "build\temp.win-amd64-3.6\Release\fastlmm/util/stats/quadform/qfc_src\wrap_qfc.cp36-win_amd64.exp" werden erstellt. Code wird generiert. Codegenerierung ist abgeschlossen. building 'fastlmm.util.matrix.cample' extension creating build\temp.win-amd64-3.6\Release\fastlmm\util\matrix C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -D_WIN32=1 -IC:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\external/intel/windows/mkl/include -ID:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include -ID:\Anaconda\envs\gwas36\include -ID:\Anaconda\envs\gwas36\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tpfastlmm/util/matrix/cample.cpp /Fobuild\temp.win-amd64-3.6\Release\fastlmm/util/matrix/cample.obj /DMKL_ILP64 cample.cpp D:\Anaconda\envs\gwas36\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\link.exe /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\external/intel/windows/mkl/lib/intel64 /LIBPATH:C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\external/intel/windows/compiler/lib/intel64 /LIBPATH:D:\Anaconda\envs\gwas36\libs /LIBPATH:D:\Anaconda\envs\gwas36\PCbuild\amd64 "/LIBPATH:C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\lib\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.18362.0\ucrt\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.18362.0\um\x64" mkl_intel_ilp64.lib mkl_core_dll.lib mkl_intel_thread.lib libiomp5md.lib /EXPORT:PyInit_cample build\temp.win-amd64-3.6\Release\fastlmm/util/matrix/cample.obj /OUT:build\lib.win-amd64-3.6\fastlmm\util\matrix\cample.cp36-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.6\Release\fastlmm/util/matrix\cample.cp36-win_amd64.lib LINK : fatal error LNK1181: Eingabedatei "mkl_intel_ilp64.lib" kann nicht geöffnet werden. error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.26.28801\bin\HostX86\x64\link.exe' failed with exit status 1181
ERROR: Command errored out with exit status 1: 'D:\Anaconda\envs\gwas36\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\setup.py'"'"'; file='"'"'C:\Users\stefanie\AppData\Local\Temp\pip-install-zsbm4a7g\fastlmm\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\stefanie\AppData\Local\Temp\pip-record-s1a811oi\install-record.txt' --single-version-externally-managed --compile --install-headers 'D:\Anaconda\envs\gwas36\Include\fastlmm' Check the logs for full command output.
Any ideas how to solve this issue? Thanks