Installation of ANTsR fails when linking due to 'too many open files', any hints what may cause this ?
The error occurs with both neuro_install("ANTsR", release = "stable") and neuro_install("ANTsR", release_repo = "github")
Here is the command that causes the error (with some spaces introduced by copying)
removing ‘/home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsR’
Error : Failed to install 'ANTsR' from GitHub:
(konvertiert von Warnung) installation of package ‘/tmp/Rtmpa653vx/file44d73188a5556/ANTsR_0.5.6.1.tar.gz’ had non-zero exit status
Fehler in neuro_install("ANTsR", release_repo = "github") :
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Installation of ANTsR fails when linking due to 'too many open files', any hints what may cause this ? The error occurs with both neuro_install("ANTsR", release = "stable") and neuro_install("ANTsR", release_repo = "github")
Here is the command that causes the error (with some spaces introduced by copying)
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o ANTsR.so AddNoiseToImage.o CreateJacobianDeterminantImage.o FitBSplineObjectToScatteredData.o HistogramMatchImages.o KellyKapowski.o LabelGeometryMeasures.o LabelOverlapMeasures.o SimulateBSplineDisplacementField.o SimulateExponentialDisplacementField.o antsAffineInitializer.o antsMotionCorr.o antsMotionCorrStats.o fastMarchingExtension.o fsl2antsrTransform.o init.o invariantImageSimilarity.o reflectionMatrix.o reorientImage.o sccanX.o sccaner.o timeSeriesSubtraction.o weingartenImageCurvature.o /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkvnl_algo-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmuuid-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKStatistics-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitklbfgs-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOGE-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkhdf5.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIONRRD-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKSmoothing-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmsocketxx-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/ 4.0/ITKR/libs/lib/libITKIOTIFF-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKNrrdIO-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKSpatialObjects-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/l ibITKIOMeta-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOMeshVTK-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKQuadEdgeMesh-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmDICT-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKPolynomials-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkminc2-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKConvolution-5.1.a /home/polzehl/R/ x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOStimulate-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKRegistrationMethodsv4-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkopenjpeg-5.1.a /home/polzehl/R/x86_6 4-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKReview-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOMeshFreeSurfer-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOMeshOBJ-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOMeshBYU-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOPNG-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKznz-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/l ibITKIOMINC-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitktestlib-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKOptimizersv4-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOMeshOFF-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOVTK-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOTransformBase-5.1.a /home/polzehl/R/x8664-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitktiff-5.1.a /home/polzehl/R/x86 64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKKLMRegionGrowing-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOBMP-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKColormap-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu- library/4.0/ITKR/libs/lib/libITKniftiio-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOBruker-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKMarkovRandomFieldsClassifiers-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-l ibrary/4.0/ITKR/libs/lib/libITKBiasCorrection-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIONIFTI-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOMRC-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/lib s/lib/libITKIOBioRad-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmCommon-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkNetlibSlatec-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOM eshBase-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkpng-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkzlib-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOIPL-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKDenoising-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmjpeg16-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOHDF5-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-lib rary/4.0/ITKR/libs/lib/libITKTestKernel-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkMGHIO-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkvcl-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libI TKMesh-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkhdf5_cpp.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitknetlib-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKEXPAT-5.1.a /home/polzehl/R/x 86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKQuadEdgeMeshFiltering-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmcharls-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKRegionGrowing-5.1.a /home/polzehl/R/x8 6_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKVNLInstantiation-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOXML-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOTransformInsightLegacy-5.1.a /home/polzehl/R/x8 6_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKTransformFactory-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKPath-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOLSM-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-li brary/4.0/ITKR/libs/lib/libitkgdcmjpeg12-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkvnl-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKVTK-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libit kdouble-conversion-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmMSFF-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOImageBase-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOJPEG-5 .1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOJPEG2000-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKLabelMap-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmDSED-5.1.a /home/polzehl/ R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOSpatialObjects-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOGIPL-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKMetaIO-5.1.a /home/polzehl/R/x86_64-pc-linux -gnu-library/4.0/ITKR/libs/lib/libITKIOTransformMatlab-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitksys-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKDiffusionTensorImage-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu- library/4.0/ITKR/libs/lib/libITKIOSiemens-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkjpeg-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKTransform-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/l ib/libITKOptimizers-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKImageFeature-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkv3p_netlib-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKComm on-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOTransformHDF5-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKWatersheds-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmMEXD-5.1.a /ho me/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmopenjp2-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOMeshGifti-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmIOD-5.1.a /home/polzehl/R/x86 _64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKDeformableMesh-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKPDEDeformableRegistration-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOGDCM-5.1.a /home/polzehl/R/x86 _64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmjpeg8-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKFastMarching-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKgiftiio-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu- library/4.0/ITKR/libs/lib/libITKFFT-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKImageIntensity-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOCSV-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/l ibs/lib/libl_antsMotionCorrStats.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_antsRegistration.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_LabelClustersUniquely.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ ANTsRCore/libs/lib/libl_ThresholdImage.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_KellyKapowski.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_antsJointFusion.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANT sRCore/libs/lib/libl_LabelGeometryMeasures.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_N4BiasFieldCorrection.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_DenoiseImage.a /home/polzehl/R/x86_64-pc-linux-gnu-librar y/4.0/ANTsRCore/libs/lib/libl_antsAffineInitializer.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_ResampleImage.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_antsMotionCorr.a /home/polzehl/R/x86_64-pc-linux-gnu-lib rary/4.0/ANTsRCore/libs/lib/libl_antsApplyTransforms.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_Atropos.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_SurfaceBasedSmoothing.a /home/polzehl/R/x86_64-pc-linux-gnu-l ibrary/4.0/ANTsRCore/libs/lib/libl_sccan.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_N3BiasFieldCorrection.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libantsUtilities.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4 .0/ANTsRCore/libs/lib/libl_antsApplyTransformsToPoints.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkvnl_algo-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmuuid-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0 /ITKR/libs/lib/libITKStatistics-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitklbfgs-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOGE-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkhdf5. a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIONRRD-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKSmoothing-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libitkgdcmsocketxx-5.1.a /home/polzehl/R/ x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKIOTIFF-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKNrrdIO-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ITKR/libs/lib/libITKSpatialObjects-5.1.a /home/polzehl/R/x86_64-pc-linux-gnu -library/4.0/ITKR/libs/lib/libITKIOMeta-5.1.a 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/home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_LabelGeometryMeasures.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_N4BiasFieldCorrection.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_DenoiseImage.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_antsAffineInitializer.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_ResampleImage.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_antsMotionCorr.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_antsApplyTransforms.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_Atropos.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_SurfaceBasedSmoothing.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_sccan.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_N3BiasFieldCorrection.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libantsUtilities.a /home/polzehl/R/x86_64-pc-linux-gnu-library/4.0/ANTsRCore/libs/lib/libl_antsApplyTransformsToPoints.a -L/usr/local/lib/R/lib -lR /usr/bin/ld: cannot open linker script file /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libm.so: Too many open files collect2: error: ld returned 1 exit status make: *** [/usr/local/lib/R/share/make/shlib.mk:6: ANTsR.so] Fehler 1 ERROR: compilation failed for package ‘ANTsR’
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