installing seurat

[smith0493]

I keep trying to install seurat and getting this type of error message. Any suggestions?

library(devtools) install_github("satijalab/seurat") Downloading GitHub repo satijalab/seurat@master from URL https://api.github.com/repos/satijalab/seurat/zipball/master Installing Seurat "C:/Users/smith493/Documents/R/R-3.2.5/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ "C:/Users/smith493/AppData/Local/Temp/Rtmp8yFqXU/devtools11585fd04b12/satijalab-seurat-a08d507" \ --library="C:/Users/smith493/Documents/R/win-library/3.2" --install-tests

• installing source package 'Seurat' ... ** libs

arch - i386 g++ -m32 -std=c++0x -I"C:/Users/smith493/DOCUME~1/R/R-32~1.5/include" -DNDEBUG -I"C:/Users/smith493/Documents/R/win-library/3.2/Rcpp/include" -I"C:/Users/smith493/Documents/R/win-library/3.2/RcppEigen/include" -I"C:/Users/smith493/Documents/R/win-library/3.2/RcppProgress/include" -I"d:/RCompile/r-compiling/local/local323/include" -g -std=c++11 -Wall -pedantic -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o cc1plus.exe: error: unrecognized command line option '-std=c++11' make: [RcppExports.o] Error 1 Warning: running command 'make -f "Makevars" -f "C:/Users/smith493/DOCUME~1/R/R-32~1.5/etc/i386/Makeconf" -f "C:/Users/smith493/DOCUME~1/R/R-32~1.5/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="Seurat.dll" OBJECTS="RcppExports.o data_manipulation.o"' had status 2 ERROR: compilation failed for package 'Seurat'

• removing 'C:/Users/smith493/Documents/R/win-library/3.2/Seurat' Error: Command failed (1)

[andrewwbutler]

You need to have a compiler that supports c++11 and the latest Rtools should come with one that does. Try updating to the latest version of R and Rtools.

[smith0493]

Hi Andrew,

I updated to R 3.3.3 and reloaded the Rtools then tried installing again. After having the install fail maybe ten times (each time because another package was missing) and loading the missing package each time, I might have managed to get Seurat to load some tutorial data.

Thanks.

Karen Smith

On Wed, Apr 19, 2017 at 1:22 PM, Andrew Butler notifications@github.com wrote:

You need to have a compiler that supports c++11 and the latest Rtools should come with one that does. Try updating to the latest version of R and Rtools.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/satijalab/seurat/issues/60#issuecomment-295377426, or mute the thread https://github.com/notifications/unsubscribe-auth/AadPUbMfRMKcCmdtMSjP0IO8tIW8I4DSks5rxlDugaJpZM4NA51V .

[andrewwbutler]

Sorry about the dependency issues. Not sure why on some Windows machines it can't seem to automatically find and download all the right ones. The easiest fix for now is to just install them all "manually" before installing Seurat. Below is the command that should catch all the required ones in case others are having the same issue.

install.packages(c("ROCR", "stringr", "mixtools", "lars", "fastICA", "tsne", "Rtsne", "fpc", "ape", "VGAM", "pbapply", "igraph", "FNN", "caret", "plyr", "dplyr", "RColorBrewer", "MASS", "Matrix", "irlba", "reshape2", "gridExtra", "gplots", "gdata", "ggplot2", "Rcpp", "RcppEigen", "RcppProgress", "tclust", "ranger"), dependencies = T)

[smith0493]

Hi Andrew,

I am trying to do the tutorial for the pmbc's ( which is indicated as an older tutorial) and it appears some of the commands have changed in R 3.3.3. Do you have a link to a tutorial and tutorial data that is for R 3.3.3?

Thank you .

Karen Smith

On Wed, Apr 19, 2017 at 4:03 PM, Andrew Butler notifications@github.com wrote:

Sorry about the dependency issues. Not sure why on some Windows machines it can't seem to automatically find and download all the right ones. The easiest fix for now is to just install them all "manually" before installing Seurat. Below is the command that should catch all the required ones in case others are having the same issue.

install.packages(c("ROCR", "stringr", "mixtools", "lars", "fastICA", "tsne", "Rtsne", "fpc", "ape", "VGAM", "pbapply", "igraph", "FNN", "caret", "plyr", "dplyr", "RColorBrewer", "MASS", "Matrix", "irlba", "reshape2", "gridExtra", "gplots", "gdata", "ggplot2", "Rcpp", "RcppEigen", "RcppProgress", "tclust", "ranger"), dependencies = T)

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[andrewwbutler]

Do you know what version of Seurat you updated from?

[smith0493]

Hi Andrew,

I am a complete newcomer to most of this R stuff. I followed the directions on your lab website and used this line

"install_github("satijalab/seurat")" to get whatever Seurat version this command would install if you used it this week. I also ran the line of code you emailed me yesterday

install.packages(c("ROCR", "stringr", "mixtools", "lars", "fastICA", "tsne", "Rtsne", "fpc", "ape", "VGAM", "pbapply", "igraph", "FNN", "caret", "plyr", "dplyr", "RColorBrewer", "MASS", "Matrix", "irlba", "reshape2", "gridExtra", "gplots", "gdata", "ggplot2", "Rcpp", "RcppEigen", "RcppProgress", "tclust", "ranger"), dependencies = T) Thank you.

Karen

On Thu, Apr 20, 2017 at 1:19 PM, Andrew Butler notifications@github.com wrote:

Do you know what version of Seurat you updated from?

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[andrewwbutler]

The PBMC tutorial on the website corresponds to the latest version of Seurat.

[smith0493]

Hi Andrew,

I have been doing the pbmc tutorial and it looked like things were working ok until I got to the "FindClusters" command. Here is what was being done in R studio

VizPCA(pbmc, 1:2) PCAPlot(pbmc, 1, 2) PCHeatmap(pbmc, pc.use = 1, cells.use = 100, do.balanced = TRUE) Warning messages: 1: In heatmap.2(data.use, Rowv = NA, Colv = NA, trace = "none", col = col.use, : Discrepancy: Rowv is FALSE, while dendrogram is both'. Omitting row dendogram. 2: In heatmap.2(data.use, Rowv = NA, Colv = NA, trace = "none", col = col.use, : Discrepancy: Colv is FALSE, while dendrogram iscolumn'. Omitting column dendogram. PCHeatmap(pbmc, pc.use = 1:12, cells.use = 500, do.balanced = TRUE, label.columns = FALSE, use.full = FALSE) There were 24 warnings (use warnings() to see them) pbmc <- JackStraw(pbmc, num.replicate = 100, do.print = FALSE)

pbmc <- JackStraw(pbmc, num.replicate = 100, do.print = FALSE) JackStrawPlot(pbmc, PCs = 1:12) Warning messages: 1: In prop.test(c(length(which(pAll[, i] <= score.thresh)), floor(nrow(pAll) * : Chi-squared approximation may be incorrect 2: Removed 17462 rows containing missing values (geom_point). PCElbowPlot(pbmc) pbmc <- FindClusters(pbmc, pc.use = 1:10, resolution = 0.6, print.output = 0, save.SNN = T) Error: Registry key 'Software\JavaSoft\Java Runtime Environment'\CurrentVersion' has value '1.8', but '1.7' is required. Error: could not find java.dll Error: Could not find Java SE Runtime Environment. Error in file(file, "rt") : cannot open the connection In addition: Warning messages: 1: running command 'java -jar "C:/Users/smith493/Documents/R/win-library/3.3/Seurat/java/ModularityOptimizer.jar" "C:/Users/smith493/Documents/R/win-library/3.3/edge_17992.txt" "C:/Users/smith493/Documents/R/win-library/3.3/output_17992.txt" 1 0.6 1 100 10 0 0' had status 2 2: In file(file, "rt") : cannot open file 'C:/Users/smith493/Documents/R/win-library/3.3/output_17992.txt': No such file or directory

Is this basically telling me that I am using Java 1.8 and I should be using Java 1.7?

Thank you .

Karen Smith

On Thu, Apr 20, 2017 at 3:14 PM, Andrew Butler notifications@github.com wrote:

The PBMC tutorial http://satijalab.org/seurat/pbmc-tutorial.html on the website corresponds to the latest version of Seurat.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/satijalab/seurat/issues/60#issuecomment-295888643, or mute the thread https://github.com/notifications/unsubscribe-auth/AadPUcwnlqXj45RIcaAvN8r21SV-fjCUks5rx7yIgaJpZM4NA51V .

[smith0493]

Hi Andrew,

I currently have JAva version 8 update 121 (build 1.8.0_121-b13).

Thank you.

Karen Smith

On Wed, May 3, 2017 at 12:00 PM, Karen Smith smith493@umn.edu wrote:

Hi Andrew,

I have been doing the pbmc tutorial and it looked like things were working ok until I got to the "FindClusters" command. Here is what was being done in R studio

VizPCA(pbmc, 1:2) PCAPlot(pbmc, 1, 2) PCHeatmap(pbmc, pc.use = 1, cells.use = 100, do.balanced = TRUE) Warning messages: 1: In heatmap.2(data.use, Rowv = NA, Colv = NA, trace = "none", col = col.use, : Discrepancy: Rowv is FALSE, while dendrogram is both'. Omitting row dendogram. 2: In heatmap.2(data.use, Rowv = NA, Colv = NA, trace = "none", col = col.use, : Discrepancy: Colv is FALSE, while dendrogram iscolumn'. Omitting column dendogram. PCHeatmap(pbmc, pc.use = 1:12, cells.use = 500, do.balanced = TRUE, label.columns = FALSE, use.full = FALSE) There were 24 warnings (use warnings() to see them) pbmc <- JackStraw(pbmc, num.replicate = 100, do.print = FALSE)

pbmc <- JackStraw(pbmc, num.replicate = 100, do.print = FALSE) JackStrawPlot(pbmc, PCs = 1:12) Warning messages: 1: In prop.test(c(length(which(pAll[, i] <= score.thresh)), floor(nrow(pAll) * : Chi-squared approximation may be incorrect 2: Removed 17462 rows containing missing values (geom_point). PCElbowPlot(pbmc) pbmc <- FindClusters(pbmc, pc.use = 1:10, resolution = 0.6, print.output = 0, save.SNN = T) Error: Registry key 'Software\JavaSoft\Java Runtime Environment'\CurrentVersion' has value '1.8', but '1.7' is required. Error: could not find java.dll Error: Could not find Java SE Runtime Environment. Error in file(file, "rt") : cannot open the connection In addition: Warning messages: 1: running command 'java -jar "C:/Users/smith493/Documents/ R/win-library/3.3/Seurat/java/ModularityOptimizer.jar" "C:/Users/smith493/Documents/R/win-library/3.3/edge_17992.txt" "C:/Users/smith493/Documents/R/win-library/3.3/output_17992.txt" 1 0.6 1 100 10 0 0' had status 2 2: In file(file, "rt") : cannot open file 'C:/Users/smith493/Documents/R/win-library/3.3/output_17992.txt': No such file or directory

Is this basically telling me that I am using Java 1.8 and I should be using Java 1.7?

Thank you .

Karen Smith

On Thu, Apr 20, 2017 at 3:14 PM, Andrew Butler notifications@github.com wrote:

The PBMC tutorial http://satijalab.org/seurat/pbmc-tutorial.html on the website corresponds to the latest version of Seurat.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/satijalab/seurat/issues/60#issuecomment-295888643, or mute the thread https://github.com/notifications/unsubscribe-auth/AadPUcwnlqXj45RIcaAvN8r21SV-fjCUks5rx7yIgaJpZM4NA51V .

[andrewwbutler]

Hi Karen,

This seems to be a relatively common problem with java when you upgrade from 7 to 8. Try removing Java entirely and reinstalling Java 8.

Here's a couple of posts where people were having similar trouble and the solutions that worked for them: http://stackoverflow.com/questions/29697543/registry-key-error-java-version-has-value-1-8-but-1-7-is-required http://stackoverflow.com/questions/26324486/properly-installing-java-8-along-with-java-7 http://www.devfish.net/post/2015/07/16/error-java-version-1-7-is-required.aspx