WGCNA
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Jerry Cholo ▴ 190
@jerry-cholo-6218
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Hello, When I ran this line: > sft=pickSoftThreshold(datExprFemale,powerVector=powers) I got this error: Error in { : task 1 failed - ""corFast" not available for .C() for package "WGCNA"" May someone let me know how I could fix it? Thanks, Jerry [[alternative HTML version deleted]]
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@peter-langfelder-4469
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This is a common error that happens because you run a parallel computation from R studio. Please read the Runtime Errors section of WGCNA FAQ at http://labs.genetics.ucla.edu/horvath/htdocs/Coexpression Network/Rpackages/WGCNA/faq.html. The upshot is that you should skip the enableWGCNAThreads() call, or perhaps call disableWGCNAThreads() when running an R session in RStudio. HTH, Peter On Sat, Feb 15, 2014 at 5:24 PM, Jerry Cholo <jerrycholo at="" gmail.com=""> wrote: > Hello, > > When I ran this line: >> sft=pickSoftThreshold(datExprFemale,powerVector=powers) > > I got this error: > > Error in { : > task 1 failed - ""corFast" not available for .C() for package "WGCNA"" > > May someone let me know how I could fix it? > > Thanks, > Jerry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On 2/16/2014 12:41 AM, Peter Langfelder wrote: > This is a common error that happens because you run a parallel > computation from R studio. Please read the Runtime Errors section of > WGCNA FAQ at http://labs.genetics.ucla.edu/horvath/htdocs/Coexpressi onNetwork/Rpackages/WGCNA/faq.html. > > The upshot is that you should skip the enableWGCNAThreads() call, or > perhaps call disableWGCNAThreads() when running an R session in > RStudio. I wonder what the real underlying problem is for this non-Bioconductor package? This works for me, from ?corFast library(WGCNA) allowWGCNAThreads() set.seed(10) nrow = 100 ncol = 500 data = matrix(rnorm(nrow*ncol), nrow, ncol) trace(.C) x = cor(data, data) sessionInfo() with RStudio 0.98.501 > x = cor(data, data) trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx = as.integer(ncol(x)), y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), nThreads = as.integer(nThreads), verbose = as.integer(verbose), indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = "WGCNA") > > sessionInfo() R Under development (unstable) (2014-02-14 r65008) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines grid stats graphics grDevices utils [7] datasets methods base other attached packages: [1] WGCNA_1.34 Hmisc_3.14-0 Formula_1.1-1 [4] survival_2.37-7 lattice_0.20-24 flashClust_1.01-2 [7] dynamicTreeCut_1.60-1 loaded via a namespace (and not attached): [1] cluster_1.14.4 codetools_0.2-8 doParallel_1.0.6 [4] foreach_1.4.1 impute_1.37.0 iterators_1.0.6 [7] latticeExtra_0.6-26 matrixStats_0.8.14 parallel_3.1.0 [10] R.methodsS3_1.6.1 RColorBrewer_1.0-5 reshape_0.8.4 [13] tools_3.1.0 Likewise for > x = pickSoftThreshold(data) trace: .C("checkAvailableMemoryForR", size = as.double(size), PACKAGE = "WGCNA") trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx = as.integer(ncol(x)), y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), nThreads = as.integer(nThreads), verbose = as.integer(verbose), indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = "WGCNA") trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx = as.integer(ncol(x)), y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), nThreads = as.integer(nThreads), verbose = as.integer(verbose), indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = "WGCNA") Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. 1 1 0.173 -11.00 0.98400 4.02e+01 4.02e+01 4.45e+01 2 2 0.326 -8.45 0.95700 5.04e+00 5.04e+00 6.12e+00 3 3 0.241 -4.30 0.95300 8.01e-01 8.02e-01 1.05e+00 4 4 0.348 -4.04 0.95000 1.49e-01 1.49e-01 2.25e-01 5 5 0.513 -3.74 0.90400 3.15e-02 3.09e-02 5.77e-02 6 6 0.697 -3.72 0.92600 7.32e-03 6.99e-03 1.70e-02 7 7 0.811 -3.26 0.93300 1.85e-03 1.70e-03 5.55e-03 8 8 0.893 -2.92 0.95700 4.99e-04 4.32e-04 1.97e-03 9 9 0.923 -2.67 0.94400 1.43e-04 1.15e-04 7.35e-04 10 10 0.958 -2.38 0.96500 4.34e-05 3.15e-05 2.85e-04 11 12 0.910 -2.07 0.88600 4.50e-06 2.59e-06 4.55e-05 12 14 0.325 -3.02 0.21800 5.31e-07 2.29e-07 7.58e-06 13 16 0.219 -3.01 0.00942 6.88e-08 2.06e-08 1.29e-06 14 18 0.206 -3.06 0.03550 9.53e-09 1.93e-09 2.29e-07 15 20 0.227 -2.97 0.02620 1.39e-09 1.85e-10 4.11e-08 Also I don't see where the error message is coming from (who is printing "task 1 failed - " ?) I have a vague recollection that the x[["Version"]] (which comes from getAnywhere("print.sessionInfo")) has to do with multiple installed versions of a package, but again it would be good to get to the bottom of this problem. Martin > > HTH, > > Peter > > On Sat, Feb 15, 2014 at 5:24 PM, Jerry Cholo <jerrycholo at="" gmail.com=""> wrote: >> Hello, >> >> When I ran this line: >>> sft=pickSoftThreshold(datExprFemale,powerVector=powers) >> >> I got this error: >> >> Error in { : >> task 1 failed - ""corFast" not available for .C() for package "WGCNA"" >> >> May someone let me know how I could fix it? >> >> Thanks, >> Jerry >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
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As far as I know, RStudio has problems with parallel calculations that fork R processes (such as those called by parallel or foreach/doParallel on machines where fork is available). The WGCNA function pickSoftThreshold uses this parallelization. The correlation functions use multithreading from within C code, which does not fork the entire R session. That's why corFast etc in WGCNA work fine but pickSoftThreshold does not. Hope this clears up any lingering confusion. Also see inline below On Sun, Feb 16, 2014 at 12:26 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > > > Also I don't see where the error message is coming from (who is printing > "task 1 failed - " ?) I believe this is printed by foreach/doParallel but here I could be wrong. HTH, Peter > > I have a vague recollection that the x[["Version"]] (which comes from > getAnywhere("print.sessionInfo")) has to do with multiple installed versions > of a package, but again it would be good to get to the bottom of this > problem. > > Martin
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On 02/16/2014 06:14 PM, Peter Langfelder wrote: > As far as I know, RStudio has problems with parallel calculations that > fork R processes (such as those called by parallel or > foreach/doParallel on machines where fork is available). The WGCNA > function pickSoftThreshold uses this parallelization. The correlation > functions use multithreading from within C code, which does not fork > the entire R session. That's why corFast etc in WGCNA work fine but > pickSoftThreshold does not. but from my original mail pickSoftThreshold 'worked for me' under Rstudio on Windows (output below, again); maybe I didn't invoke it in a way that would trigger the error, so a reproducible illustration would help (me). Also on Windows (platform of the original post) the parallel package doesn't fork, e.g., from ?mcfork These are low-level functions, not available on Windows, and not exported from the namespace. or ?mclapply It relies on forking and hence is not available on Windows unless 'mc.cores = 1'. Do you mean something less literally forking, like spawning a new process? Maybe from http://stackoverflow.com/questions/20704235 the solution is as simple as adding .packages="WGCNA" to your foreach calls? > x = pickSoftThreshold(data) trace: .C("checkAvailableMemoryForR", size = as.double(size), PACKAGE = "WGCNA") trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx = as.integer(ncol(x)), y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), nThreads = as.integer(nThreads), verbose = as.integer(verbose), indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = "WGCNA") trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx = as.integer(ncol(x)), y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), nThreads = as.integer(nThreads), verbose = as.integer(verbose), indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = "WGCNA") Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. 1 1 0.173 -11.00 0.98400 4.02e+01 4.02e+01 4.45e+01 2 2 0.326 -8.45 0.95700 5.04e+00 5.04e+00 6.12e+00 3 3 0.241 -4.30 0.95300 8.01e-01 8.02e-01 1.05e+00 4 4 0.348 -4.04 0.95000 1.49e-01 1.49e-01 2.25e-01 5 5 0.513 -3.74 0.90400 3.15e-02 3.09e-02 5.77e-02 6 6 0.697 -3.72 0.92600 7.32e-03 6.99e-03 1.70e-02 7 7 0.811 -3.26 0.93300 1.85e-03 1.70e-03 5.55e-03 8 8 0.893 -2.92 0.95700 4.99e-04 4.32e-04 1.97e-03 9 9 0.923 -2.67 0.94400 1.43e-04 1.15e-04 7.35e-04 10 10 0.958 -2.38 0.96500 4.34e-05 3.15e-05 2.85e-04 11 12 0.910 -2.07 0.88600 4.50e-06 2.59e-06 4.55e-05 12 14 0.325 -3.02 0.21800 5.31e-07 2.29e-07 7.58e-06 13 16 0.219 -3.01 0.00942 6.88e-08 2.06e-08 1.29e-06 14 18 0.206 -3.06 0.03550 9.53e-09 1.93e-09 2.29e-07 15 20 0.227 -2.97 0.02620 1.39e-09 1.85e-10 4.11e-08 > > Hope this clears up any lingering confusion. > > Also see inline below > > On Sun, Feb 16, 2014 at 12:26 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > >> >> >> Also I don't see where the error message is coming from (who is printing >> "task 1 failed - " ?) > > > I believe this is printed by foreach/doParallel but here I could be wrong. > > > > HTH, > > Peter > >> >> I have a vague recollection that the x[["Version"]] (which comes from >> getAnywhere("print.sessionInfo")) has to do with multiple installed versions >> of a package, but again it would be good to get to the bottom of this >> problem. >> >> Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hi Martin, if you simply run pickSoftThreshold without calling enableWGCNAThreads before, the function is run in a single-worker mode. To reproduce the error, you have to call enableWGCNAThreads with an argument of 2 or more. For a reproducible example, you can run the first two sections of WGCNA Tutorial I at http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpack ages/WGCNA/Tutorials/index.html. Sorry, I don't have a quick simulated example ready but could cook one up. I am actually not sure whether this problem also occurs on Windows, since the cluster parallelization is very different from the forking on linux. I am only aware of it through bug reports of WGCNA users (who usually email me directly). Peter On Sun, Feb 16, 2014 at 6:30 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > > but from my original mail pickSoftThreshold 'worked for me' under Rstudio on > Windows (output below, again); maybe I didn't invoke it in a way that would > trigger the error, so a reproducible illustration would help (me). Also on > Windows (platform of the original post) the parallel package doesn't fork, > e.g., from ?mcfork > > These are low-level functions, not available on Windows, and not > exported from the namespace. > > or ?mclapply > > It relies on forking and hence is not available on Windows unless > 'mc.cores = 1'. > > Do you mean something less literally forking, like spawning a new process? > Maybe from > > http://stackoverflow.com/questions/20704235 > > the solution is as simple as adding .packages="WGCNA" to your foreach calls? > > >> x = pickSoftThreshold(data) > trace: .C("checkAvailableMemoryForR", size = as.double(size), PACKAGE = > "WGCNA") > trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx = > as.integer(ncol(x)), > y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), > cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), > res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), > nThreads = as.integer(nThreads), verbose = as.integer(verbose), > indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = > "WGCNA") > trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx = > as.integer(ncol(x)), > y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), > cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), > res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), > nThreads = as.integer(nThreads), verbose = as.integer(verbose), > indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = > "WGCNA") > Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. > 1 1 0.173 -11.00 0.98400 4.02e+01 4.02e+01 4.45e+01 > 2 2 0.326 -8.45 0.95700 5.04e+00 5.04e+00 6.12e+00 > 3 3 0.241 -4.30 0.95300 8.01e-01 8.02e-01 1.05e+00 > 4 4 0.348 -4.04 0.95000 1.49e-01 1.49e-01 2.25e-01 > 5 5 0.513 -3.74 0.90400 3.15e-02 3.09e-02 5.77e-02 > 6 6 0.697 -3.72 0.92600 7.32e-03 6.99e-03 1.70e-02 > 7 7 0.811 -3.26 0.93300 1.85e-03 1.70e-03 5.55e-03 > 8 8 0.893 -2.92 0.95700 4.99e-04 4.32e-04 1.97e-03 > 9 9 0.923 -2.67 0.94400 1.43e-04 1.15e-04 7.35e-04 > 10 10 0.958 -2.38 0.96500 4.34e-05 3.15e-05 2.85e-04 > 11 12 0.910 -2.07 0.88600 4.50e-06 2.59e-06 4.55e-05 > 12 14 0.325 -3.02 0.21800 5.31e-07 2.29e-07 7.58e-06 > 13 16 0.219 -3.01 0.00942 6.88e-08 2.06e-08 1.29e-06 > 14 18 0.206 -3.06 0.03550 9.53e-09 1.93e-09 2.29e-07 > 15 20 0.227 -2.97 0.02620 1.39e-09 1.85e-10 4.11e-08 > > > > >> >> Hope this clears up any lingering confusion. >> >> Also see inline below >> >> On Sun, Feb 16, 2014 at 12:26 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> >> wrote: >> >>> >>> >>> Also I don't see where the error message is coming from (who is printing >>> "task 1 failed - " ?) >> >> >> >> I believe this is printed by foreach/doParallel but here I could be wrong. >> >> >> >> HTH, >> >> Peter >> >>> >>> I have a vague recollection that the x[["Version"]] (which comes from >>> getAnywhere("print.sessionInfo")) has to do with multiple installed >>> versions >>> of a package, but again it would be good to get to the bottom of this >>> problem. >>> >>> Martin > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793
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Thank you Peter. Adding "disableWGCNAThreads() " in RStudio really solved the problem of ""corFast_call" not available for .Call() for package "WGCNA"""

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Tim Triche ★ 4.2k
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This appears to be an issue with a C function not being able to call corFast. Please post your sessionInfo() when reporting issues like this as it will make it MUCH easier for library authors to support. best, --t Statistics is the grammar of science. Karl Pearson <http: en.wikipedia.org="" wiki="" the_grammar_of_science=""> On Sat, Feb 15, 2014 at 5:24 PM, Jerry Cholo <jerrycholo@gmail.com> wrote: > Hello, > > When I ran this line: > > sft=pickSoftThreshold(datExprFemale,powerVector=powers) > > I got this error: > > Error in { : > task 1 failed - ""corFast" not available for .C() for package "WGCNA"" > > May someone let me know how I could fix it? > > Thanks, > Jerry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Tim Triche ★ 4.2k
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I'm going to guess that, based on your sessionInfo() alone, your R install is hosed: > Error in x[["Version"]] : subscript out of bounds In addition: Warning message: In FUN(c("codetools", "compiler", "doParallel", "foreach", "impute", : DESCRIPTION file of package 'impute' is missing or broken That's not good. You might need to reinstall (at least) the 'impute' package and possibly several others. Statistics is the grammar of science. Karl Pearson <http: en.wikipedia.org="" wiki="" the_grammar_of_science=""> On Sat, Feb 15, 2014 at 5:45 PM, Jerry Cholo <jerrycholo@gmail.com> wrote: > Here you go: > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > attached base packages: > [1] parallel splines grid stats graphics grDevices utils > datasets methods > [10] base > other attached packages: > [1] nlme_3.1-113 igraph_0.7.0 GEOquery_2.28.0 > Biobase_2.22.0 > [5] BiocGenerics_0.8.0 cluster_1.14.4 BiocInstaller_1.12.0 > WGCNA_1.34 > [9] Hmisc_3.14-0 Formula_1.1-1 survival_2.37-7 > lattice_0.20-24 > [13] flashClust_1.01-2 dynamicTreeCut_1.60-1 > loaded via a namespace (and not attached): > Error in x[["Version"]] : subscript out of bounds > In addition: Warning message: > In FUN(c("codetools", "compiler", "doParallel", "foreach", "impute", : > DESCRIPTION file of package 'impute' is missing or broken > > Thanks, > Jerry > > > On Sat, Feb 15, 2014 at 5:31 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > >> This appears to be an issue with a C function not being able to call >> corFast. Please post your >> >> sessionInfo() >> >> when reporting issues like this as it will make it MUCH easier for >> library authors to support. >> >> best, >> >> --t >> >> >> >> Statistics is the grammar of science. >> Karl Pearson <http: en.wikipedia.org="" wiki="" the_grammar_of_science=""> >> >> >> On Sat, Feb 15, 2014 at 5:24 PM, Jerry Cholo <jerrycholo@gmail.com>wrote: >> >>> Hello, >>> >>> When I ran this line: >>> > sft=pickSoftThreshold(datExprFemale,powerVector=powers) >>> >>> I got this error: >>> >>> Error in { : >>> task 1 failed - ""corFast" not available for .C() for package "WGCNA"" >>> >>> May someone let me know how I could fix it? >>> >>> Thanks, >>> Jerry >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]
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My guess is that this some kind of RStudio or other third party R GUI quirk. But if I'm wrong, please correct me. Best, Peter On Sat, Feb 15, 2014 at 5:55 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > I'm going to guess that, based on your sessionInfo() alone, your R install > is hosed: > >> Error in x[["Version"]] : subscript out of bounds > In addition: Warning message: > In FUN(c("codetools", "compiler", "doParallel", "foreach", "impute", : > DESCRIPTION file of package 'impute' is missing or broken > > > That's not good. You might need to reinstall (at least) the 'impute' > package and possibly several others. > > > Statistics is the grammar of science. > Karl Pearson <http: en.wikipedia.org="" wiki="" the_grammar_of_science=""> > > > On Sat, Feb 15, 2014 at 5:45 PM, Jerry Cholo <jerrycholo at="" gmail.com=""> wrote: > >> Here you go: >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 >> [3] LC_MONETARY=English_United States.1252 >> LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> attached base packages: >> [1] parallel splines grid stats graphics grDevices utils >> datasets methods >> [10] base >> other attached packages: >> [1] nlme_3.1-113 igraph_0.7.0 GEOquery_2.28.0 >> Biobase_2.22.0 >> [5] BiocGenerics_0.8.0 cluster_1.14.4 BiocInstaller_1.12.0 >> WGCNA_1.34 >> [9] Hmisc_3.14-0 Formula_1.1-1 survival_2.37-7 >> lattice_0.20-24 >> [13] flashClust_1.01-2 dynamicTreeCut_1.60-1 >> loaded via a namespace (and not attached): >> Error in x[["Version"]] : subscript out of bounds >> In addition: Warning message: >> In FUN(c("codetools", "compiler", "doParallel", "foreach", "impute", : >> DESCRIPTION file of package 'impute' is missing or broken >> >> Thanks, >> Jerry >> >> >> On Sat, Feb 15, 2014 at 5:31 PM, Tim Triche, Jr. <tim.triche at="" gmail.com="">wrote: >> >>> This appears to be an issue with a C function not being able to call >>> corFast. Please post your >>> >>> sessionInfo() >>> >>> when reporting issues like this as it will make it MUCH easier for >>> library authors to support. >>> >>> best, >>> >>> --t >>> >>> >>> >>> Statistics is the grammar of science. >>> Karl Pearson <http: en.wikipedia.org="" wiki="" the_grammar_of_science=""> >>> >>> >>> On Sat, Feb 15, 2014 at 5:24 PM, Jerry Cholo <jerrycholo at="" gmail.com="">wrote: >>> >>>> Hello, >>>> >>>> When I ran this line: >>>> > sft=pickSoftThreshold(datExprFemale,powerVector=powers) >>>> >>>> I got this error: >>>> >>>> Error in { : >>>> task 1 failed - ""corFast" not available for .C() for package "WGCNA"" >>>> >>>> May someone let me know how I could fix it? >>>> >>>> Thanks, >>>> Jerry >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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