abbatidanilo
commented
3 years ago Of course the RcppArmadillo, BH, Rcpp, RcppParallel, matrixStats, RcppHNSW and checkmate packages are correctly installed
Closed abbatidanilo closed 2 years ago
abbatidanilo
commented
3 years ago Of course the RcppArmadillo, BH, Rcpp, RcppParallel, matrixStats, RcppHNSW and checkmate packages are correctly installed
sararselitsky
commented
3 years ago This looks like a C++ error. Mahantesh, do you know what this is?
Also, Stuart, we should add some documentation which describes what is needed for Windows when installing FastPG. It seems like this is a consistent error.
On Mon, Sep 6, 2021 at 12:11 PM abbati @.***> wrote:
Hello, here is what I got when I used BiocManager::install("sararselitsky/FastPG")
BiocManager::install("sararselitsky/FastPG") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories: CRAN: https://cran.stat.unipd.it/ BioCsoft: https://bioconductor.org/packages/3.13/bioc BioCann: https://bioconductor.org/packages/3.13/data/annotation BioCexp: https://bioconductor.org/packages/3.13/data/experiment BioCworkflows: https://bioconductor.org/packages/3.13/workflows
Warning: unable to access index for repository https://cran.stat.unipd.it/src/contrib: cannot open URL 'https://cran.stat.unipd.it/src/contrib/PACKAGES' Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing github package(s) 'sararselitsky/FastPG' Downloading GitHub repo @.*** Skipping 7 packages not available: RcppArmadillo, BH, Rcpp, RcppParallel, matrixStats, RcppHNSW, checkmate √ checking for file 'C:\Users\abbat\AppData\Local\Temp\RtmpIfMFMP\remotes2478179e138e\sararselitsky-FastPG-c57e5d8/DESCRIPTION' ...
preparing 'FastPG': (457ms) √ checking DESCRIPTION meta-information ...
cleaning src
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories Omitted 'LazyData' from DESCRIPTION
building 'FastPG_0.0.7.tar.gz'
installing source package 'FastPG' ... using staged installation libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-411.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-411.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RngStream.cpp -o RngStream.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c buildNextPhase.cpp -o buildNextPhase.o buildNextPhase.cpp:93: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel
buildNextPhase.cpp:119: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:125: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:133: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:145: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:199: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:205: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:243: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:248: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:279: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:283: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:309: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:314: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:339: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:344: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp: In function 'double buildNextLevelGraphOpt(graph, graph, long int, long int, int)': buildNextPhase.cpp:92:9: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ buildNextPhase.cpp💯10: warning: unused variable 'percentange' [-Wunused-variable] long percentange = 80; ^
~~buildNextPhase.cpp:102:12: warning: unused variable 'total' [-Wunused-variable] double total = 0, totItr = 0; ^~~~~ buildNextPhase.cpp:102:23: warning: unused variable 'totItr' [-Wunused-variable] double total = 0, totItr = 0; ^~buildNextPhase.cpp:105:13: warning: unused variable 'NE_in' [-Wunused-variable] long NE_in = Gin->numEdges; ^~~~~ buildNextPhase.cpp: In function 'void buildNextLevelGraph(graph, graph, long int, long int)': buildNextPhase.cpp:262:12: warning: unused variable 'time1' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^~~~~ buildNextPhase.cpp:262:19: warning: unused variable 'time2' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^~~~~ buildNextPhase.cpp:262:26: warning: unused variable 'time3' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^~~~~ buildNextPhase.cpp:262:33: warning: unused variable 'time4' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^~~~~ buildNextPhase.cpp:263:12: warning: unused variable 'total' [-Wunused-variable] double total = 0, totItr = 0; ^~~~~ buildNextPhase.cpp:263:23: warning: unused variable 'totItr' [-Wunused-variable] double total = 0, totItr = 0; ^~buildNextPhase.cpp:264:10: warning: unused variable 'percentange' [-Wunused-variable] long percentange = 80; ^~~buildNextPhase.cpp:267:13: warning: unused variable 'NE_in' [-Wunused-variable] long NE_in = Gin->numEdges; ^~~~~ buildNextPhase.cpp: In function 'long int buildCommunityBasedOnVoltages(graph, long int, long int, long int)': buildNextPhase.cpp:398:13: warning: unused variable 'NE' [-Wunused-variable] long NE = G->numEdges; ^~ buildNextPhase.cpp: In function 'void segregateEdgesBasedOnVoltages(graph, long int)': buildNextPhase.cpp:451:13: warning: unused variable 'NE' [-Wunused-variable] long NE = G->numEdges; ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringDistanceOne.cpp -o coloringDistanceOne.o In file included from coloring.h:5, from coloringDistanceOne.cpp:43: coloringUtils.h:66:1: warning: "/ *" within comment [-Wcomment] /*** Coloring Functions **coloringUtils.h:68:1: warning: "/ " within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/ " within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/ " within comment [-Wcomment] / Vertex base redistribution in vBase.cpp
coloringUtils.h:82:1: warning: "/ " within comment [-Wcomment] / Color base redistribution in cBase.cpp
coloringDistanceOne.cpp:62: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel
coloringDistanceOne.cpp:98: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:107: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for reduction(max: realMaxDegree)
coloringDistanceOne.cpp:137: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:166: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:208: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:248: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel
coloringDistanceOne.cpp:289: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:305: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:316: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:359: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:410: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp: In function 'int algoDistanceOneVertexColoringOpt(graph, int, int, double)': coloringDistanceOne.cpp:60:7: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ coloringDistanceOne.cpp:74:8: warning: unused variable 'NEdge' [-Wunused-variable] long NEdge = G->numEdges; ^~~~~ coloringDistanceOne.cpp: In function 'int algoDistanceOneVertexColoring(graph, int, int, double)': coloringDistanceOne.cpp:247:6: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ coloringDistanceOne.cpp:259:8: warning: unused variable 'NT' [-Wunused-variable] long NT = NVer - NS; ^~ coloringDistanceOne.cpp:260:8: warning: unused variable 'NEdge' [-Wunused-variable] long NEdge = G->numEdges; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringMultiHashMaxMin.cpp -o coloringMultiHashMaxMin.o In file included from coloring.h:5, from coloringMultiHashMaxMin.cpp:43: coloringUtils.h:66:1: warning: "/ *" within comment [-Wcomment] /*** Coloring Functions **
coloringUtils.h:68:1: warning: "/ " within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/ " within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/ " within comment [-Wcomment] / Vertex base redistribution in vBase.cpp
coloringUtils.h:82:1: warning: "/ " within comment [-Wcomment] / Color base redistribution in cBase.cpp
coloringMultiHashMaxMin.cpp:72: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel
coloringMultiHashMaxMin.cpp:112: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringMultiHashMaxMin.cpp:126: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringMultiHashMaxMin.cpp:182: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringMultiHashMaxMin.cpp: In function 'int algoColoringMultiHashMaxMin(graph, int, int, double*, int, int)': coloringMultiHashMaxMin.cpp:202:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] printf("Check - WARNING: Number of conflicts detected after resolution: %d \n\n", myConflicts); ^
~~~~~~~~~~~~~~~~coloringMultiHashMaxMin.cpp:202:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] coloringMultiHashMaxMin.cpp:208:12: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] printf("Number of uncolored vertices : %d \n", unColored); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ coloringMultiHashMaxMin.cpp:208:12: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringUtils.cpp -o coloringUtils.o In file included from coloringUtils.cpp:1: coloringUtils.h:66:1: warning: "/ *" within comment [-Wcomment] /******* Coloring Functions ****** coloringUtils.h:68:1: warning: "/ *" within comment [-Wcomment] /* Basic coloring (unbalanced) in initialColoring.cpp coloringUtils.h:70:1: warning: "/ *" within comment [-Wcomment] /* Basic coloiring (ab-inital) in initialColoringLU.cpp coloringUtils.h:73:1: warning: "/ *" within comment [-Wcomment] /* Vertex base redistribution in vBase.cpp ... too much long I am running R4.1.0 under windows 10 and Rtools40 cheers — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/sararselitsky/FastPG/issues/15>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACQD6T5ST2G2U4FWEPTB4D3UATR4JANCNFSM5DQXVWGQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
sararselitsky
commented
3 years ago Hi Sara,
This is being caused by the C++ compiler since there is no support for OpenMP. Depending on the Operating System, they should be able to fix it easily by using a C++ compiler (GNU, for example) with OpenMP support. I can help if you connect me with the person.
Regards, Mahantesh (he/him)
From: Sara Selitsky @.> Date: Tuesday, September 7, 2021 at 6:17 AM To: sararselitsky/FastPG @.> Cc: sararselitsky/FastPG @.>, Subscribed @.>, "Halappanavar, Mahantesh M" @.>, "Jefferys, Stuart R" @.> Subject: Re: [sararselitsky/FastPG] Cannot install FastPG (#15)
Check twice before you click! This email originated from outside PNNL.
This looks like a C++ error. Mahantesh, do you know what this is?
Also, Stuart, we should add some documentation which describes what is needed for Windows when installing FastPG. It seems like this is a consistent error.
On Mon, Sep 6, 2021 at 12:11 PM abbati @.**@.>> wrote:
Hello, here is what I got when I used BiocManager::install("sararselitsky/FastPG")
BiocManager::install("sararselitsky/FastPG") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories: CRAN: https://cran.stat.unipd.it/https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.stat.unipd.it%2F&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436425454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=af7KEDPX6K8ZaQUheg7I9yopV6%2FL%2F1D4f0cSo45dWWk%3D&reserved=0 BioCsoft: https://bioconductor.org/packages/3.13/biochttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fbioc&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436435411%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=8JAyxU8zCFC2jUBtcgygZPsCl2gQZNWVt65dVQ1e3m0%3D&reserved=0 BioCann: https://bioconductor.org/packages/3.13/data/annotationhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fdata%2Fannotation&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436435411%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=RAOiFmGCcN9ZTCP6P5kkmuZJOanLvI%2B5%2BwtJUFxBuA4%3D&reserved=0 BioCexp: https://bioconductor.org/packages/3.13/data/experimenthttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fdata%2Fexperiment&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436445367%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ha7tQOvdBuvESXhc0dqVz9qUzRDggK56S%2FSaQuHecDU%3D&reserved=0 BioCworkflows: https://bioconductor.org/packages/3.13/workflowshttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fworkflows&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436445367%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6fuCFK1BFszUaLJfCVPPH%2FG8CwhJZfZyzUURE8dePcM%3D&reserved=0
Warning: unable to access index for repository https://cran.stat.unipd.it/src/contribhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.stat.unipd.it%2Fsrc%2Fcontrib&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436445367%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9BRBXhMBwmsO5Krdau%2BrQoTqDRVZuLBsxFYWqd%2FKQkc%3D&reserved=0: cannot open URL 'https://cran.stat.unipd.it/src/contrib/PACKAGEShttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.stat.unipd.it%2Fsrc%2Fcontrib%2FPACKAGES&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436455327%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=khj%2FuQxR6wvPtMdI9lJbi8DMsPf3sDANxfncge0eALI%3D&reserved=0' Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing github package(s) 'sararselitsky/FastPG' Downloading GitHub repo @.*** Skipping 7 packages not available: RcppArmadillo, BH, Rcpp, RcppParallel, matrixStats, RcppHNSW, checkmate √ checking for file 'C:\Users\abbat\AppData\Local\Temp\RtmpIfMFMP\remotes2478179e138e\sararselitsky-FastPG-c57e5d8/DESCRIPTION' ...
preparing 'FastPG': (457ms) √ checking DESCRIPTION meta-information ...
cleaning src
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories Omitted 'LazyData' from DESCRIPTION
building 'FastPG_0.0.7.tar.gz'
installing source package 'FastPG' ... using staged installation libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-411.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-411.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RngStream.cpp -o RngStream.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c buildNextPhase.cpp -o buildNextPhase.o buildNextPhase.cpp:93: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:119: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:125: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:133: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:145: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:199: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:205: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:243: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:248: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:279: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:283: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:309: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:314: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:339: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:344: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp: In function 'double buildNextLevelGraphOpt(graph, graph, long int, long int, int)':
buildNextPhase.cpp:92:9: warning: variable 'nT' set but not used [-Wunused-but-set-variable]
int nT;
^~
buildNextPhase.cpp💯10: warning: unused variable 'percentange' [-Wunused-variable]
long percentange = 80;
^~~
buildNextPhase.cpp:102:12: warning: unused variable 'total' [-Wunused-variable]
double total = 0, totItr = 0;
^~~~~
buildNextPhase.cpp:102:23: warning: unused variable 'totItr' [-Wunused-variable]
double total = 0, totItr = 0;
^~
buildNextPhase.cpp:105:13: warning: unused variable 'NE_in' [-Wunused-variable]
long NE_in = Gin->numEdges;
^~~~~
buildNextPhase.cpp: In function 'void buildNextLevelGraph(graph, graph, long int, long int)':
buildNextPhase.cpp:262:12: warning: unused variable 'time1' [-Wunused-variable]
double time1, time2, time3, time4; //For timing purposes
^~~~~
buildNextPhase.cpp:262:19: warning: unused variable 'time2' [-Wunused-variable]
double time1, time2, time3, time4; //For timing purposes
^~~~~
buildNextPhase.cpp:262:26: warning: unused variable 'time3' [-Wunused-variable]
double time1, time2, time3, time4; //For timing purposes
^~~~~
buildNextPhase.cpp:262:33: warning: unused variable 'time4' [-Wunused-variable]
double time1, time2, time3, time4; //For timing purposes
^~~~~
buildNextPhase.cpp:263:12: warning: unused variable 'total' [-Wunused-variable]
double total = 0, totItr = 0;
^~~~~
buildNextPhase.cpp:263:23: warning: unused variable 'totItr' [-Wunused-variable]
double total = 0, totItr = 0;
^~
buildNextPhase.cpp:264:10: warning: unused variable 'percentange' [-Wunused-variable]
long percentange = 80;
^~~
buildNextPhase.cpp:267:13: warning: unused variable 'NE_in' [-Wunused-variable]
long NE_in = Gin->numEdges;
^~~~~
buildNextPhase.cpp: In function 'long int buildCommunityBasedOnVoltages(graph, long int, long int, long int)':
buildNextPhase.cpp:398:13: warning: unused variable 'NE' [-Wunused-variable]
long NE = G->numEdges;
^~
buildNextPhase.cpp: In function 'void segregateEdgesBasedOnVoltages(graph, long int)':
buildNextPhase.cpp:451:13: warning: unused variable 'NE' [-Wunused-variable]
long NE = G->numEdges;
^~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringDistanceOne.cpp -o coloringDistanceOne.o
In file included from coloring.h:5,
from coloringDistanceOne.cpp:43:
coloringUtils.h:66:1: warning: "/" within comment [-Wcomment]
/** Coloring Functions **
coloringUtils.h:68:1: warning: "/" within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/" within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/" within comment [-Wcomment] / Vertex base redistribution in vBase.cpp
coloringUtils.h:82:1: warning: "/" within comment [-Wcomment] / Color base redistribution in cBase.cpp
coloringDistanceOne.cpp:62: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:98: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:107: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:137: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:166: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:208: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:248: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:289: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:305: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:316: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:359: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:410: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp: In function 'int algoDistanceOneVertexColoringOpt(graph, int, int, double)': coloringDistanceOne.cpp:60:7: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ coloringDistanceOne.cpp:74:8: warning: unused variable 'NEdge' [-Wunused-variable] long NEdge = G->numEdges; ^~~~~ coloringDistanceOne.cpp: In function 'int algoDistanceOneVertexColoring(graph, int, int, double)': coloringDistanceOne.cpp:247:6: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ coloringDistanceOne.cpp:259:8: warning: unused variable 'NT' [-Wunused-variable] long NT = NVer - NS; ^~ coloringDistanceOne.cpp:260:8: warning: unused variable 'NEdge' [-Wunused-variable] long NEdge = G->numEdges; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringMultiHashMaxMin.cpp -o coloringMultiHashMaxMin.o In file included from coloring.h:5, from coloringMultiHashMaxMin.cpp:43: coloringUtils.h:66:1: warning: "/" within comment [-Wcomment] /** Coloring Functions **
coloringUtils.h:68:1: warning: "/" within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/" within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/" within comment [-Wcomment] / Vertex base redistribution in vBase.cpp
coloringUtils.h:82:1: warning: "/" within comment [-Wcomment] / Color base redistribution in cBase.cpp
coloringMultiHashMaxMin.cpp:72: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringMultiHashMaxMin.cpp:112: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringMultiHashMaxMin.cpp:126: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringMultiHashMaxMin.cpp:182: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringMultiHashMaxMin.cpp: In function 'int algoColoringMultiHashMaxMin(graph, int, int, double*, int, int)':
coloringMultiHashMaxMin.cpp:202:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
printf("Check - WARNING: Number of conflicts detected after resolution: %d \n\n", myConflicts);
^~~~~~~~~~~~~~~~~ ~~~
coloringMultiHashMaxMin.cpp:202:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
coloringMultiHashMaxMin.cpp:208:12: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
printf("Number of uncolored vertices : %d \n", unColored);
^~~~~~~~~~ ~~~~~
coloringMultiHashMaxMin.cpp:208:12: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringUtils.cpp -o coloringUtils.o
In file included from coloringUtils.cpp:1:
coloringUtils.h:66:1: warning: "/" within comment [-Wcomment]
/** Coloring Functions **
coloringUtils.h:68:1: warning: "/" within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/" within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/" within comment [-Wcomment] / Vertex base redistribution in vBase.cpp
...
too much long I am running R4.1.0 under windows 10 and Rtools40 cheers
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsararselitsky%2FFastPG%2Fissues%2F15&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436455327%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gidXRyYitwYtRquQ3PJvY2oFl%2FmM7rXxREJwlWO0Bfs%3D&reserved=0, or unsubscribehttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACQD6T5ST2G2U4FWEPTB4D3UATR4JANCNFSM5DQXVWGQ&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436465281%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=7KFwbfmAg8wXtxjoxqp8tknD4h3zH2y4c%2F8RDDgU8Ew%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436465281%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6ERcWEIALOlNnBgZcWTKkUtFoHs26MWTaBtdcWaEUmM%3D&reserved=0 or Androidhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436465281%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=J%2FOpTqlgZ90c2zdyyedM5yV6PWR%2F9qcP98x9EyRy8DQ%3D&reserved=0.
sararselitsky
commented
3 years ago R 4.0+ is now using a different version of RTools on windows to provide the compilers and etc needed by R and packages (https://cran.r-project.org/bin/windows/Rtools/). I think the data.table package indicate it supports OpenMP, but don't have windows available to test on ((https://github.com/Rdatatable/data.table/wiki/Installation).
Stuart.
On Sep 7, 2021, at 10:25 AM, Halappanavar, Mahantesh M @.**@.>> wrote:
Hi Sara,
This is being caused by the C++ compiler since there is no support for OpenMP. Depending on the Operating System, they should be able to fix it easily by using a C++ compiler (GNU, for example) with OpenMP support. I can help if you connect me with the person.
Regards, Mahantesh (he/him)
From: Sara Selitsky @.**@.>> Date: Tuesday, September 7, 2021 at 6:17 AM To: sararselitsky/FastPG @.**@.>> Cc: sararselitsky/FastPG @.**@.>>, Subscribed @.**@.>>, "Halappanavar, Mahantesh M" @.**@.>>, "Jefferys, Stuart R" @.**@.>> Subject: Re: [sararselitsky/FastPG] Cannot install FastPG (#15)
Check twice before you click! This email originated from outside PNNL.
This looks like a C++ error. Mahantesh, do you know what this is?
Also, Stuart, we should add some documentation which describes what is needed for Windows when installing FastPG. It seems like this is a consistent error.
On Mon, Sep 6, 2021 at 12:11 PM abbati @.**@.>> wrote: Hello, here is what I got when I used BiocManager::install("sararselitsky/FastPG") BiocManager::install("sararselitsky/FastPG") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cran.stat.unipd.it/https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.stat.unipd.it%2F&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436425454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=af7KEDPX6K8ZaQUheg7I9yopV6%2FL%2F1D4f0cSo45dWWk%3D&reserved=0 BioCsoft: https://bioconductor.org/packages/3.13/biochttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fbioc&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436435411%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=8JAyxU8zCFC2jUBtcgygZPsCl2gQZNWVt65dVQ1e3m0%3D&reserved=0 BioCann: https://bioconductor.org/packages/3.13/data/annotationhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fdata%2Fannotation&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436435411%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=RAOiFmGCcN9ZTCP6P5kkmuZJOanLvI%2B5%2BwtJUFxBuA4%3D&reserved=0 BioCexp: https://bioconductor.org/packages/3.13/data/experimenthttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fdata%2Fexperiment&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436445367%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ha7tQOvdBuvESXhc0dqVz9qUzRDggK56S%2FSaQuHecDU%3D&reserved=0 BioCworkflows: https://bioconductor.org/packages/3.13/workflowshttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fworkflows&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436445367%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6fuCFK1BFszUaLJfCVPPH%2FG8CwhJZfZyzUURE8dePcM%3D&reserved=0 Warning: unable to access index for repository https://cran.stat.unipd.it/src/contribhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.stat.unipd.it%2Fsrc%2Fcontrib&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436445367%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9BRBXhMBwmsO5Krdau%2BrQoTqDRVZuLBsxFYWqd%2FKQkc%3D&reserved=0: cannot open URL 'https://cran.stat.unipd.it/src/contrib/PACKAGEShttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.stat.unipd.it%2Fsrc%2Fcontrib%2FPACKAGES&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7C19582ca7145140b37fbf08d97201d1c1%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637666174436455327%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=khj%2FuQxR6wvPtMdI9lJbi8DMsPf3sDANxfncge0eALI%3D&reserved=0' Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing github package(s) 'sararselitsky/FastPG' Downloading GitHub repo @.*** Skipping 7 packages not available: RcppArmadillo, BH, Rcpp, RcppParallel, matrixStats, RcppHNSW, checkmate √ checking for file 'C:\Users\abbat\AppData\Local\Temp\RtmpIfMFMP\remotes2478179e138e\sararselitsky-FastPG-c57e5d8/DESCRIPTION' ...
preparing 'FastPG': (457ms) √ checking DESCRIPTION meta-information ...
cleaning src
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories Omitted 'LazyData' from DESCRIPTION
building 'FastPG_0.0.7.tar.gz'
installing source package 'FastPG' ... using staged installation libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-411.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-411.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RngStream.cpp -o RngStream.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c buildNextPhase.cpp -o buildNextPhase.o buildNextPhase.cpp:93: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:119: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:125: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:133: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:145: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:199: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:205: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:243: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:248: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:279: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:283: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:309: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:314: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:339: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp:344: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
buildNextPhase.cpp: In function 'double buildNextLevelGraphOpt(graph, graph, long int, long int, int)':
buildNextPhase.cpp:92:9: warning: variable 'nT' set but not used [-Wunused-but-set-variable]
int nT;
^~
buildNextPhase.cpp💯10: warning: unused variable 'percentange' [-Wunused-variable]
long percentange = 80;
^~~
buildNextPhase.cpp:102:12: warning: unused variable 'total' [-Wunused-variable]
double total = 0, totItr = 0;
^~~~~
buildNextPhase.cpp:102:23: warning: unused variable 'totItr' [-Wunused-variable]
double total = 0, totItr = 0;
^~
buildNextPhase.cpp:105:13: warning: unused variable 'NE_in' [-Wunused-variable]
long NE_in = Gin->numEdges;
^~~~~
buildNextPhase.cpp: In function 'void buildNextLevelGraph(graph, graph, long int, long int)':
buildNextPhase.cpp:262:12: warning: unused variable 'time1' [-Wunused-variable]
double time1, time2, time3, time4; //For timing purposes
^~~~~
buildNextPhase.cpp:262:19: warning: unused variable 'time2' [-Wunused-variable]
double time1, time2, time3, time4; //For timing purposes
^~~~~
buildNextPhase.cpp:262:26: warning: unused variable 'time3' [-Wunused-variable]
double time1, time2, time3, time4; //For timing purposes
^~~~~
buildNextPhase.cpp:262:33: warning: unused variable 'time4' [-Wunused-variable]
double time1, time2, time3, time4; //For timing purposes
^~~~~
buildNextPhase.cpp:263:12: warning: unused variable 'total' [-Wunused-variable]
double total = 0, totItr = 0;
^~~~~
buildNextPhase.cpp:263:23: warning: unused variable 'totItr' [-Wunused-variable]
double total = 0, totItr = 0;
^~
buildNextPhase.cpp:264:10: warning: unused variable 'percentange' [-Wunused-variable]
long percentange = 80;
^~~
buildNextPhase.cpp:267:13: warning: unused variable 'NE_in' [-Wunused-variable]
long NE_in = Gin->numEdges;
^~~~~
buildNextPhase.cpp: In function 'long int buildCommunityBasedOnVoltages(graph, long int, long int, long int)':
buildNextPhase.cpp:398:13: warning: unused variable 'NE' [-Wunused-variable]
long NE = G->numEdges;
^~
buildNextPhase.cpp: In function 'void segregateEdgesBasedOnVoltages(graph, long int)':
buildNextPhase.cpp:451:13: warning: unused variable 'NE' [-Wunused-variable]
long NE = G->numEdges;
^~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringDistanceOne.cpp -o coloringDistanceOne.o
In file included from coloring.h:5,
from coloringDistanceOne.cpp:43:
coloringUtils.h:66:1: warning: "/" within comment [-Wcomment]
/** Coloring Functions **
coloringUtils.h:68:1: warning: "/" within comment [-Wcomment]
/ Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/" within comment [-Wcomment]
/ Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/" within comment [-Wcomment]
/ Vertex base redistribution in vBase.cpp
coloringUtils.h:82:1: warning: "/" within comment [-Wcomment]
/ Color base redistribution in cBase.cpp
coloringDistanceOne.cpp:62: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:98: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:107: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:137: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:166: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:208: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:248: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:289: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:305: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:316: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:359: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp:410: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringDistanceOne.cpp: In function 'int algoDistanceOneVertexColoringOpt(graph, int, int, double)': coloringDistanceOne.cpp:60:7: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ coloringDistanceOne.cpp:74:8: warning: unused variable 'NEdge' [-Wunused-variable] long NEdge = G->numEdges; ^~~~~ coloringDistanceOne.cpp: In function 'int algoDistanceOneVertexColoring(graph, int, int, double)': coloringDistanceOne.cpp:247:6: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ coloringDistanceOne.cpp:259:8: warning: unused variable 'NT' [-Wunused-variable] long NT = NVer - NS; ^~ coloringDistanceOne.cpp:260:8: warning: unused variable 'NEdge' [-Wunused-variable] long NEdge = G->numEdges; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringMultiHashMaxMin.cpp -o coloringMultiHashMaxMin.o In file included from coloring.h:5, from coloringMultiHashMaxMin.cpp:43: coloringUtils.h:66:1: warning: "/" within comment [-Wcomment] /** Coloring Functions ** coloringUtils.h:68:1: warning: "/" within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp coloringUtils.h:70:1: warning: "/" within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp coloringUtils.h:73:1: warning: "/" within comment [-Wcomment] / Vertex base redistribution in vBase.cpp coloringUtils.h:82:1: warning: "/" within comment [-Wcomment] / Color base redistribution in cBase.cpp coloringMultiHashMaxMin.cpp:72: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringMultiHashMaxMin.cpp:112: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringMultiHashMaxMin.cpp:126: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringMultiHashMaxMin.cpp:182: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
coloringMultiHashMaxMin.cpp: In function 'int algoColoringMultiHashMaxMin(graph, int, int, double*, int, int)':
coloringMultiHashMaxMin.cpp:202:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
printf("Check - WARNING: Number of conflicts detected after resolution: %d \n\n", myConflicts);
^~~~~~~~~~~~~~~~~ ~~~
coloringMultiHashMaxMin.cpp:202:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
coloringMultiHashMaxMin.cpp:208:12: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
printf("Number of uncolored vertices : %d \n", unColored);
^~~~~~~~~~ ~~~~~
coloringMultiHashMaxMin.cpp:208:12: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringUtils.cpp -o coloringUtils.o
In file included from coloringUtils.cpp:1:
coloringUtils.h:66:1: warning: "/" within comment [-Wcomment]
/** Coloring Functions **
coloringUtils.h:68:1: warning: "/" within comment [-Wcomment]
/ Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/" within comment [-Wcomment]
/ Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/" within comment [-Wcomment]
/ Vertex base redistribution in vBase.cpp
...
too much long
I am running R4.1.0 under windows 10 and Rtools40
cheers
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jefferys
commented
3 years ago Did you install Rtools as well as R? And link to it on your path? https://cran.r-project.org/bin/windows/Rtools/
Also, some advice from "data.table" may help (https://github.com/Rdatatable/data.table/wiki/Installation):
On Windows, when upgrading any package that uses compiled code, it appears to be important to close all R sessions before upgrading. This releases all locks that Windows holds on dlls. To be really sure, reboot too. Then open a new fresh R session.
abbatidanilo
commented
2 years ago Thank you. I have installed Rtools 4.0 ver.4.0.1.0 64bit Here are some commands from my console:
pkgbuild::has_rtools() [1] TRUE pkgbuild::find_rtools() [1] TRUE pkgbuild::rtools_path() [1] "C:\rtools40/usr/bin" pkgbuild::check_rtools() [1] TRUE make check Error: unexpected symbol in "make check" library("tools") testInstalledBasic("both") running strict specific tests running code in ‘eval-etc.R’ comparing ‘eval-etc.Rout’ to ‘eval-etc.Rout.save’ ... OK running code in ‘simple-true.R’ comparing ‘simple-true.Rout’ to ‘simple-true.Rout.save’ ... OK running code in ‘arith-true.R’ comparing ‘arith-true.Rout’ to ‘arith-true.Rout.save’ ... OK running code in ‘lm-tests.R’ comparing ‘lm-tests.Rout’ to ‘lm-tests.Rout.save’ ... OK running code in ‘ok-errors.R’ comparing ‘ok-errors.Rout’ to ‘ok-errors.Rout.save’ ... OK running code in ‘method-dispatch.R’ comparing ‘method-dispatch.Rout’ to ‘method-dispatch.Rout.save’ ... OK running code in ‘array-subset.R’ running code in ‘p-r-random-tests.R’ comparing ‘p-r-random-tests.Rout’ to ‘p-r-random-tests.Rout.save’ ... OK running code in ‘d-p-q-r-tst-2.R’ running code in ‘any-all.R’ comparing ‘any-all.Rout’ to ‘any-all.Rout.save’ ... OK running code in ‘d-p-q-r-tests.R’ comparing ‘d-p-q-r-tests.Rout’ to ‘d-p-q-r-tests.Rout.save’ ... OK running sloppy specific tests running code in ‘complex.R’ comparing ‘complex.Rout’ to ‘complex.Rout.save’ ... OK running code in ‘print-tests.R’ comparing ‘print-tests.Rout’ to ‘print-tests.Rout.save’ ... OK running code in ‘lapack.R’ comparing ‘lapack.Rout’ to ‘lapack.Rout.save’ ... OK running code in ‘datasets.R’ comparing ‘datasets.Rout’ to ‘datasets.Rout.save’ ... OK running code in ‘datetime.R’ comparing ‘datetime.Rout’ to ‘datetime.Rout.save’ ... OK running code in ‘iec60559.R’ comparing ‘iec60559.Rout’ to ‘iec60559.Rout.save’ ... OK running regression tests running code in ‘reg-tests-1a.R’ running code in ‘reg-tests-1b.R’ running code in ‘reg-tests-1c.R’ running code in ‘reg-tests-2.R’ comparing ‘reg-tests-2.Rout’ to ‘reg-tests-2.Rout.save’ ...7301c7301 < ï..ColA ColB ColC
X...ColA ColB ColC testInstalledPackages(scope = "base", errorsAreFatal = FALSE) Testing examples for package ‘base’ Testing examples for package ‘tools’ comparing ‘tools-Ex.Rout’ to ‘tools-Ex.Rout.save’ ... OK Running specific tests for package ‘tools’ Running ‘QC.R’ Running ‘Rd.R’ Running ‘Rd2HTML.R’ Running ‘S3.R’ Running ‘undoc.R’ Testing examples for package ‘utils’ Running specific tests for package ‘utils’ Running ‘completion.R’ Running ‘download.file.R’ Running ‘Sweave-tst.R’ Running vignettes for package ‘utils’ Running ‘Sweave.Rnw’ Testing examples for package ‘grDevices’ comparing ‘grDevices-Ex.Rout’ to ‘grDevices-Ex.Rout.save’ ... NOTE 3682a3683,3690 List of 3 $ serif: chr [1:4] "Times-Roman" "Times-Bold" "Times-Italic" "Times-BoldItalic" $ sans : chr [1:4] "Helvetica" "Helvetica-Bold" "Helvetica-Oblique" "Helvetica-BoldOblique" $ mono : chr [1:4] "Courier" "Courier-Bold" "Courier-Oblique" "Courier-BoldOblique" $mono [1] "Courier" "Courier-Bold" "Courier-Oblique"
[4] "Courier-BoldOblique"3924,3937d3931 < > windowsFonts() < $serif < [1] "TT Times New Roman" < < $sans < [1] "TT Arial" < < $mono < [1] "TT Courier New" < < > windowsFonts("mono") < $mono < [1] "TT Courier New" < Running specific tests for package ‘grDevices’ Running ‘convertColor-tests.R’ Running ‘ps-tests.R’ comparing ‘ps-tests.Rout’ to ‘ps-tests.Rout.save’ ... OK Running ‘saved-recordPlot.R’ Running ‘xfig-tests.R’ comparing ‘xfig-tests.Rout’ to ‘xfig-tests.Rout.save’ ... OK Testing examples for package ‘graphics’ comparing ‘graphics-Ex.Rout’ to ‘graphics-Ex.Rout.save’ ... OK Testing examples for package ‘stats’ comparing ‘stats-Ex.Rout’ to ‘stats-Ex.Rout.save’ ... OK Running specific tests for package ‘stats’ Running ‘arimaML.R’ Running ‘bandwidth.R’ comparing ‘bandwidth.Rout’ to ‘bandwidth.Rout.save’ ... OK Running ‘cmdscale.R’ Running ‘drop1-polr.R’ Running ‘glm-etc.R’ Running ‘glm.R’ comparing ‘glm.Rout’ to ‘glm.Rout.save’ ... OK Running ‘ig_glm.R’ Running ‘ks-test.R’ comparing ‘ks-test.Rout’ to ‘ks-test.Rout.save’ ... OK Running ‘nafns.R’ Running ‘nlm.R’ Running ‘nls.R’ comparing ‘nls.Rout’ to ‘nls.Rout.save’ ... OK Running ‘NLSstClosest.R’ Running ‘offsets.R’ Running ‘ppr.R’ Running ‘simulate.R’ comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... OK Running ‘smooth.spline.R’ Running ‘table-margins.R’ Running ‘ts-tests.R’ Testing examples for package ‘datasets’ comparing ‘datasets-Ex.Rout’ to ‘datasets-Ex.Rout.save’ ... OK Testing examples for package ‘methods’ Running specific tests for package ‘methods’ Running ‘basicRefClass.R’ Running ‘duplicateClass.R’ Running ‘envRefClass.R’ Running ‘fieldAssignments.R’ Running ‘mixinInitialize.R’ Running ‘namesAndSlots.R’ Running ‘nextWithDots.R’ Running ‘refClassExample.R’ Running ‘S3.R’ Running ‘testConditionalIs.R’ Running ‘testGroupGeneric.R’ Running ‘testIs.R’ Testing examples for package ‘grid’ comparing ‘grid-Ex.Rout’ to ‘grid-Ex.Rout.save’ ... OK Running specific tests for package ‘grid’ Running ‘bugs.R’ Running ‘clippaths.R’ Running ‘coords.R’ Running ‘masks.R’ Running ‘patterns.R’ Running ‘reg.R’ Running ‘testls.R’ comparing ‘testls.Rout’ to ‘testls.Rout.save’ ... OK Running ‘units.R’ Running vignettes for package ‘grid’ Running ‘displaylist.Rnw’ Running ‘frame.Rnw’ Running ‘grid.Rnw’ Running ‘grobs.Rnw’ Running ‘interactive.Rnw’ Running ‘locndimn.Rnw’ Running ‘moveline.Rnw’ Running ‘nonfinite.Rnw’ Running ‘plotexample.Rnw’ Running ‘rotated.Rnw’ Running ‘saveload.Rnw’ Running ‘sharing.Rnw’ Running ‘viewports.Rnw’
Weave Errors
File frame.Rnw: invalid argument type Testing examples for package ‘splines’ comparing ‘splines-Ex.Rout’ to ‘splines-Ex.Rout.save’ ... OK Running specific tests for package ‘splines’ Running ‘sparse-tst.R’ Running ‘spline-tst.R’ Testing examples for package ‘stats4’ comparing ‘stats4-Ex.Rout’ to ‘stats4-Ex.Rout.save’ ... OK Running specific tests for package ‘stats4’ Running ‘confint.R’ Testing examples for package ‘tcltk’ Testing examples for package ‘compiler’ Running specific tests for package ‘compiler’ Running ‘assign.R’ Running ‘basics.R’ Running ‘const.R’ Running ‘curexpr.R’ Running ‘envir.R’ Running ‘jit.R’ Running ‘loop.R’ Running ‘srcref.R’ Running ‘switch.R’ Running ‘vischk.R’ Testing examples for package ‘parallel’ Running specific tests for package ‘parallel’ Running ‘Master.R’ Running ‘RSeed.R’ Running vignettes for package ‘parallel’ Running ‘parallel.Rnw’
testInstalledPackages(scope = "recommended", errorsAreFatal = FALSE) Testing examples for package ‘MASS’ comparing ‘MASS-Ex.Rout’ to ‘MASS-Ex.Rout.save’ ... NOTE 572d571 < Warning: package 'survival' was built under R version 4.1.1 1795d1793 < Warning: package 'survival' was built under R version 4.1.1 2783d2780 < Warning: package 'survival' was built under R version 4.1.1 3037d3033 < Warning: package 'survival' was built under R version 4.1.1 Running specific tests for package ‘MASS’ Running ‘confint.R’ Running ‘cov.mcd.R’ Running ‘fitdistr.R’ comparing ‘fitdistr.Rout’ to ‘fitdistr.Rout.save’ ... OK Running ‘glm.nb.R’ Running ‘hubers.R’ Running ‘lme.R’ Running ‘polr.R’ Running ‘profile.R’ Running ‘regression.R’ comparing ‘regression.Rout’ to ‘regression.Rout.save’ ... OK Running ‘rlm.R’ Running ‘scripts.R’ Testing examples for package ‘lattice’ Running specific tests for package ‘lattice’ Running ‘colorkey-title.R’ Running ‘dates.R’ Running ‘dotplotscoping.R’ Running ‘fontsize.R’ Running ‘levelplot.R’ Running ‘MASSch04.R’ Running ‘scales.R’ Running ‘summary.R’ Running ‘temp.R’ Running ‘test.R’ Running ‘wireframe.R’ Testing examples for package ‘Matrix’ Running vignettes for package ‘Matrix’ Running ‘Comparisons.Rnw’ Running ‘Design-issues.Rnw’ Running ‘Intro2Matrix.Rnw’ Running ‘Introduction.Rnw’ Running ‘sparseModels.Rnw’ Testing examples for package ‘nlme’ Running specific tests for package ‘nlme’ Running ‘anova.gls.R’ Running ‘augPred_lab.R’ Running ‘augPredmissing.R’ Running ‘coef.R’ comparing ‘coef.Rout’ to ‘coef.Rout.save’ ... OK Running ‘contrMat.R’ Running ‘corFactor.R’ Running ‘data.frame.R’ Running ‘deparse.R’ Running ‘deviance.R’ Running ‘fitted.R’ Running ‘getData.R’ Running ‘getVarCov.R’ Running ‘gls.R’ Running ‘gnls-ch8.R’ Running ‘lme.R’ comparing ‘lme.Rout’ to ‘lme.Rout.save’ ... OK Running ‘lmList.R’ Running ‘missing.R’ comparing ‘missing.Rout’ to ‘missing.Rout.save’ ... OK Running ‘nlme-stall.R’ Running ‘nlme.R’ Running ‘nlme2.R’ Running ‘predict.lme.R’ Running ‘sigma-fixed-etc.R’ Running ‘updateLme.R’ Running ‘varConstProp.R’ Running ‘varIdent.R’ Testing examples for package ‘survival’ Running vignettes for package ‘survival’ Running ‘adjcurve.Rnw’ Running ‘approximate.Rnw’ Running ‘compete.Rnw’ Running ‘concordance.Rnw’ Running ‘discrim.Rnw’ Running ‘multi.Rnw’ Running ‘other.Rnw’ Running ‘population.Rnw’ Running ‘splines.Rnw’ Running ‘survival.Rnw’ Running ‘tiedtimes.Rnw’ Running ‘timedep.Rnw’ Running ‘validate.Rnw’
Source Errors
File survival.R: no applicable method for 'layout' applied to an object of class "c('double', 'numeric')"
Weave Errors
File survival.Rnw: chunk 23 (label = curve1) Error in UseMethod("layout") : no applicable method for 'layout' applied to an object of class "c('double', 'numeric')"
Undeclared level(s) .. added in variable: factor_s_duplicated 352c352 < $ factor_s_duplicated : Factor w/ 5 levels "A","A_duplicated_b",..: 1 5 4 NA NA
$ factor_s_duplicated : Factor w/ 4 levels "..","A","A_duplicatedb",..: 2 1 1 NA NA 362c362 < .. ..- attr(, "names")= chr [1:2] "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 ! \" # $ % & ' ( ) + , - . / : ; < = > ? @ [ \ ] ^ ` { | } ~ \200" "abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnop"
.. ..- attr(, "names")= chr [1:2] "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 ! \" # $ % & ' ( ) + , - . / : ; < = > ? @ [ \ ] ^ _ ` { | } ~ ..." "abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnop" 441c441 < Undeclared level(s) ä, ö added in variable: factor_s_duplicated
Undeclared level(s) .. added in variable: factor_s_duplicated 461c461 < $ factor_s_duplicated : Factor w/ 5 levels "A","A_duplicated_b",..: 1 5 4 NA NA
$ factor_s_duplicated : Factor w/ 4 levels "..","A","A_duplicated_b",..: 2 1 1 NA NA 481c481 < Undeclared level(s) ä, ö added in variable: factor_s_duplicated
Undeclared level(s) .. added in variable: factor_s_duplicated 521c521 < Undeclared level(s) ä, ö added in variable: factor_s_duplicated
Undeclared level(s) .. added in variable: factor_s_duplicated 540c540 < Undeclared level(s) ä, ö added in variable: factor_s_duplicated
Undeclared level(s) .. added in variable: factor_s_duplicated 572c572 < Undeclared level(s) ä, ö added in variable: factor_s_duplicated
Undeclared level(s) .. added in variable: factor_s_duplicated 593,595c593,595 < !"§ $%& /() =? '<> #|; ²³~ @`´ ©«» ¤¼× {} abc def ghi jkl mno pqrs < tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !"§ $%& /() =? '<> #|; < ²³~ @`´ ©«» ¤¼× {} abc def ghi j
!".. $%& /() =? '<> #|; ....~ @`.. ...... ...... {} abc def ghi jkl mno pqrs tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !".. $%& /() =? '<> #|; ....~ @
.. ...... ...... {} abc def ghi j 607,610c607,610 < kl mno pqrs tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !"§ $%& /() < =?* '<> #|; ²³~ @´ ©«» ¤¼× {} abc def ghi jkl mno pqrs tuv wxyz ABC < DEF GHI JKL MNO PQRS TUV WXYZ !"§ $%& /() =?* '<> #|; ²³~ @`´ ©«» ¤¼× < {} abc def ghi jklkl mno pqrs tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !".. $%& /() =? '<> #|; ....~ @`.. ...... ...... {} abc def ghi jkl mno pqrs tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !".. $%& /() =? '<> #|; ....~ @
.. ...... ...... {} abc def ghi jkl 631,636c631,637 < !"§ $%& /() =?* '<> #|; ²³~ @´ ©«» ¤¼× {} abc def ghi jkl mno pqrs < tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !"§ $%& /() =? '<> #|; < ²³~ @`´ ©«» ¤¼× {} abc def ghi jkl mno pqrs tuv wxyz ABC DEF GHI JKL < MNO PQRS TUV WXYZ !"§ $%& /() =? '<> #|; ²³~ @´ ©«» ¤¼× {} abc def < ghi jkl mno pqrs tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !"§ $%& < /() =?* '<> #|; ²³~ @´ ©«» ¤¼× {} abc def ghi jkl!".. $%& /() =? '<> #|; ....~ @`.. ...... ...... {} abc def ghi jkl mno pqrs tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !".. $%& /() =? '<> #|; ....~ @
.. ...... ...... {} abc def ghi jkl mno pqrs tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !".. $%& /() =?* '<> #|; ....~ @.. ...... ...... {} abc def ghi jkl mno pqrs tuv wxyz ABC DEF GHI JKL MNO PQRS TUV WXYZ !".. $%& /() =?* '<> #|; ....~ @`.. ...... ...... {} abc def ghi jkl Running ‘stata.R’ comparing ‘stata.Rout’ to ‘stata.Rout.save’ ... OK Running ‘testEmpty.R’ comparing ‘testEmpty.Rout’ to ‘testEmpty.Rout.save’ ... OK Running ‘writeForeignSPSS.R’ comparing ‘writeForeignSPSS.Rout’ to ‘writeForeignSPSS.Rout.save’ ... OK Running ‘xport.R’ comparing ‘xport.Rout’ to ‘xport.Rout.save’ ... OK Testing examples for package ‘KernSmooth’ Running specific tests for package ‘KernSmooth’ Running ‘bkfe.R’ Running ‘locpoly.R’ Testing examples for package ‘rpart’ comparing ‘rpart-Ex.Rout’ to ‘rpart-Ex.Rout.save’ ... NOTE 795d794 < Warning: package 'survival' was built under R version 4.1.1 Running specific tests for package ‘rpart’ Running ‘backticks.R’ comparing ‘backticks.Rout’ to ‘backticks.Rout.save’ ... OK Running ‘cost.R’ comparing ‘cost.Rout’ to ‘cost.Rout.save’ ... files differ in number of lines: 5,6d4 < Warning message: < package 'survival' was built under R version 4.1.1 Running ‘cptest.R’ comparing ‘cptest.Rout’ to ‘cptest.Rout.save’ ... OK Running ‘priors.R’ comparing ‘priors.Rout’ to ‘priors.Rout.save’ ... OK Running ‘rescale.R’ comparing ‘rescale.Rout’ to ‘rescale.Rout.save’ ... files differ in number of lines: 8,9d7 < Warning message: < package 'survival' was built under R version 4.1.1 Running ‘testall.R’ comparing ‘testall.Rout’ to ‘testall.Rout.save’ ... files differ in number of lines: 13,14d12 < Warning message: < package 'survival' was built under R version 4.1.1 Running ‘treble.R’ comparing ‘treble.Rout’ to ‘treble.Rout.save’ ... files differ in number of lines: 13,14d12 < Warning message: < package 'survival' was built under R version 4.1.1 Running ‘treble2.R’ comparing ‘treble2.Rout’ to ‘treble2.Rout.save’ ... OK Running ‘treble3.R’ comparing ‘treble3.Rout’ to ‘treble3.Rout.save’ ... OK Running ‘treble4.R’ comparing ‘treble4.Rout’ to ‘treble4.Rout.save’ ... OK Running ‘usersplits.R’ comparing ‘usersplits.Rout’ to ‘usersplits.Rout.save’ ... OK Running ‘xpred1.R’ comparing ‘xpred1.Rout’ to ‘xpred1.Rout.save’ ... OK Running ‘xpred2.R’ comparing ‘xpred2.Rout’ to ‘xpred2.Rout.save’ ... files differ in number of lines: 9,10d8 < Warning message: < package 'survival' was built under R version 4.1.1 Running vignettes for package ‘rpart’ Running ‘longintro.Rnw’ Running ‘usercode.Rnw’ Testing examples for package ‘class’ Testing examples for package ‘nnet’ Testing examples for package ‘spatial’ comparing ‘spatial-Ex.Rout’ to ‘spatial-Ex.Rout.save’ ... OK Running specific tests for package ‘spatial’ Testing examples for package ‘mgcv’ pkgbuild::check_build_tools() Your system is ready to build packages! pkgbuild::check_compiler() [1] TRUE
abbatidanilo
commented
2 years ago Just tried following your recommendations but it still does not work. The difference is that now I do not see any warning concerning packages not found (see the previous Skipping 7 packages not available: RcppArmadillo, BH, Rcpp, RcppParallel, matrixStats, RcppHNSW, checkmate)
Like before I got a lot of #pragma omp parallel
jefferys
commented
2 years ago Ok. That's one problem resolved. Now lets see if I have guessed a correct Makevars.win file. I can't test this myself; would you mind trying to test it for me? I have pushed a test repository branch, test_win. You can install it with
BiocManager::install("sararselitsky/FastPG@test_win")
abbatidanilo
commented
2 years ago BiocManager::install("sararselitsky/FastPG@test_win") ...
Hello, here is what I got when I used BiocManager::install("sararselitsky/FastPG")
BiocManager::install("sararselitsky/FastPG") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories: CRAN: https://cran.stat.unipd.it/ BioCsoft: https://bioconductor.org/packages/3.13/bioc BioCann: https://bioconductor.org/packages/3.13/data/annotation BioCexp: https://bioconductor.org/packages/3.13/data/experiment BioCworkflows: https://bioconductor.org/packages/3.13/workflows
Warning: unable to access index for repository https://cran.stat.unipd.it/src/contrib: cannot open URL 'https://cran.stat.unipd.it/src/contrib/PACKAGES' Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing github package(s) 'sararselitsky/FastPG' Downloading GitHub repo sararselitsky/FastPG@HEAD Skipping 7 packages not available: RcppArmadillo, BH, Rcpp, RcppParallel, matrixStats, RcppHNSW, checkmate √ checking for file 'C:\Users\abbat\AppData\Local\Temp\RtmpIfMFMP\remotes2478179e138e\sararselitsky-FastPG-c57e5d8/DESCRIPTION' ...
preparing 'FastPG': (457ms) √ checking DESCRIPTION meta-information ...
cleaning src
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories Omitted 'LazyData' from DESCRIPTION
building 'FastPG_0.0.7.tar.gz'
installing source package 'FastPG' ... using staged installation libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RngStream.cpp -o RngStream.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c buildNextPhase.cpp -o buildNextPhase.o buildNextPhase.cpp:93: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel
buildNextPhase.cpp:119: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:125: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:133: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:145: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:199: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:205: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:243: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:248: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:279: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:283: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:309: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:314: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:339: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp:344: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
buildNextPhase.cpp: In function 'double buildNextLevelGraphOpt(graph, graph, long int, long int, int)': buildNextPhase.cpp:92:9: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ buildNextPhase.cpp:100:10: warning: unused variable 'percentange' [-Wunused-variable] long percentange = 80; ^
~~buildNextPhase.cpp:102:12: warning: unused variable 'total' [-Wunused-variable] double total = 0, totItr = 0; ^~~~~ buildNextPhase.cpp:102:23: warning: unused variable 'totItr' [-Wunused-variable] double total = 0, totItr = 0; ^~buildNextPhase.cpp:105:13: warning: unused variable 'NE_in' [-Wunused-variable] long NE_in = Gin->numEdges; ^~~~~ buildNextPhase.cpp: In function 'void buildNextLevelGraph(graph, graph, long int, long int)': buildNextPhase.cpp:262:12: warning: unused variable 'time1' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^~~~~ buildNextPhase.cpp:262:19: warning: unused variable 'time2' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^~~~~ buildNextPhase.cpp:262:26: warning: unused variable 'time3' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^~~~~ buildNextPhase.cpp:262:33: warning: unused variable 'time4' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^~~~~ buildNextPhase.cpp:263:12: warning: unused variable 'total' [-Wunused-variable] double total = 0, totItr = 0; ^~~~~ buildNextPhase.cpp:263:23: warning: unused variable 'totItr' [-Wunused-variable] double total = 0, totItr = 0; ^~buildNextPhase.cpp:264:10: warning: unused variable 'percentange' [-Wunused-variable] long percentange = 80; ^~~buildNextPhase.cpp:267:13: warning: unused variable 'NE_in' [-Wunused-variable] long NE_in = Gin->numEdges; ^~~~~ buildNextPhase.cpp: In function 'long int buildCommunityBasedOnVoltages(graph, long int, long int, long int)': buildNextPhase.cpp:398:13: warning: unused variable 'NE' [-Wunused-variable] long NE = G->numEdges; ^~ buildNextPhase.cpp: In function 'void segregateEdgesBasedOnVoltages(graph, long int)': buildNextPhase.cpp:451:13: warning: unused variable 'NE' [-Wunused-variable] long NE = G->numEdges; ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringDistanceOne.cpp -o coloringDistanceOne.o In file included from coloring.h:5, from coloringDistanceOne.cpp:43: coloringUtils.h:66:1: warning: "/*" within comment [-Wcomment] /*** Coloring Functions **coloringUtils.h:68:1: warning: "/" within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/" within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/" within comment [-Wcomment] / Vertex base redistribution in vBase.cpp
coloringUtils.h:82:1: warning: "/" within comment [-Wcomment] / Color base redistribution in cBase.cpp
coloringDistanceOne.cpp:62: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel
coloringDistanceOne.cpp:98: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:107: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for reduction(max: realMaxDegree)
coloringDistanceOne.cpp:137: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:166: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:208: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:248: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel
coloringDistanceOne.cpp:289: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:305: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:316: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:359: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp:410: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringDistanceOne.cpp: In function 'int algoDistanceOneVertexColoringOpt(graph, int, int, double)': coloringDistanceOne.cpp:60:7: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ coloringDistanceOne.cpp:74:8: warning: unused variable 'NEdge' [-Wunused-variable] long NEdge = G->numEdges; ^~~~~ coloringDistanceOne.cpp: In function 'int algoDistanceOneVertexColoring(graph, int, int, double)': coloringDistanceOne.cpp:247:6: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^~ coloringDistanceOne.cpp:259:8: warning: unused variable 'NT' [-Wunused-variable] long NT = NVer - NS; ^~ coloringDistanceOne.cpp:260:8: warning: unused variable 'NEdge' [-Wunused-variable] long NEdge = G->numEdges; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringMultiHashMaxMin.cpp -o coloringMultiHashMaxMin.o In file included from coloring.h:5, from coloringMultiHashMaxMin.cpp:43: coloringUtils.h:66:1: warning: "/*" within comment [-Wcomment] /*** Coloring Functions **
coloringUtils.h:68:1: warning: "/" within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/" within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/" within comment [-Wcomment] / Vertex base redistribution in vBase.cpp
coloringUtils.h:82:1: warning: "/" within comment [-Wcomment] / Color base redistribution in cBase.cpp
coloringMultiHashMaxMin.cpp:72: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel
coloringMultiHashMaxMin.cpp:112: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringMultiHashMaxMin.cpp:126: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringMultiHashMaxMin.cpp:182: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
pragma omp parallel for
coloringMultiHashMaxMin.cpp: In function 'int algoColoringMultiHashMaxMin(graph, int, int, double, int, int)': coloringMultiHashMaxMin.cpp:202:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] printf("Check - WARNING: Number of conflicts detected after resolution: %d \n\n", myConflicts); ^
~~~~~~~~~~~~~~~~~~~ coloringMultiHashMaxMin.cpp:202:16: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] coloringMultiHashMaxMin.cpp:208:12: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] printf("Number of uncolored vertices : %d \n", unColored); ^~~~~~~~~~~~~~~ coloringMultiHashMaxMin.cpp:208:12: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/R/R-41~1.0/include" -DNDEBUG -I'C:/R/R-4.1.0/library/Rcpp/include' -I'C:/R/R-4.1.0/library/RcppParallel/include' -I'C:/R/R-4.1.0/library/BH/include' -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coloringUtils.cpp -o coloringUtils.o In file included from coloringUtils.cpp:1: coloringUtils.h:66:1: warning: "/" within comment [-Wcomment] /*** Coloring Functions **coloringUtils.h:68:1: warning: "/" within comment [-Wcomment] / Basic coloring (unbalanced) in initialColoring.cpp
coloringUtils.h:70:1: warning: "/" within comment [-Wcomment] / Basic coloiring (ab-inital) in initialColoringLU.cpp
coloringUtils.h:73:1: warning: "/" within comment [-Wcomment] / Vertex base redistribution in vBase.cpp
...
too much long I am running R4.1.0 under windows 10 and Rtools40 cheers