Seurat: Problems installing from github

[KatieONell]

Since I updated to R version 3.3.1, I've been unable to install Seurat. Below are the error messages when I try to install from Github and with install.packages

Trying to install from Github:

install_github("satijalab/seurat", force=T)
Downloading GitHub repo satijalab/seurat@master
from URL https://api.github.com/repos/satijalab/seurat/zipball/master
Installing Seurat
Downloading GitHub repo StoreyLab/lfa@a1df252
from URL https://api.github.com/repos/StoreyLab/lfa/zipball/a1df252
Installing lfa
‘BiocInstaller’ must be installed for this functionality.
Would you like to install it?

1: Yes
2: No

Selection: 1
Error in loadNamespace(name) : there is no package called ‘BiocInstaller’
In addition: Warning message:
package ‘BiocInstaller’ is not available (for R version 3.3.1)

Trying to install w/ install.packages:

install.packages("seurat")
Warning in install.packages :
package ‘seurat’ is not available (for R version 3.3.1)

[andrewwbutler]

This lfa package is really proving to be a pain for package maintenance. Quick fix for now is to run source("http://bioconductor.org/biocLite.R"). That should get you the BiocInstaller and then you should be able to install Seurat properly from github.

[royfrancis]

> install_github("satijalab/seurat")
Downloading GitHub repo satijalab/seurat@master
from URL https://api.github.com/repos/satijalab/seurat/zipball/master
Installing Seurat
Downloading GitHub repo StoreyLab/lfa@a1df252
from URL https://api.github.com/repos/StoreyLab/lfa/zipball/a1df252
Installing lfa
Error in data.frame(menu_name = aa, URL = repos[new], default = TRUE) : 
  row names contain missing values

I was able to install seurat on windows after an hour of troubleshooting. The dependencies were not installed and they had to be installed separately. But I still unable to install on Ubuntu. I already installed lfa from CRAN and it still gives an error. Would it be possible to have a tar zipped 'release' for linux? I am hoping I can download the package and install locally.

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

[andrewwbutler]

That's an error I haven't seen before. I wasn't able to reproduce it but here's a few things to try. It looks to be something related to devtools so the first thing to try is updating to the most recent version of devtools. Also, make sure you have the BiocInstaller ( source("http://bioconductor.org/biocLite.R") ). If you want to install the package manually, you can always clone the repo. You'll probably run into the same problem though unless you edit the DESCRIPTION file to get rid of the lfa dependency or one of the above suggestions happened to work.

[BrentonPaolella]

Hi Andrew,

I'm trying to install Seurat and still can't get it to work, even with your suggested help. I'm not an R expert, but it would be great if you could provide more detail on the work around to download it directly from git hub, or how to remove the lfa dependency. I apologize in advance if this isn't articulated well. Many thanks!

Here's my code:

install.packages("devtools")
trying URL 'https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.3/devtools_1.12.0.tgz'

Content type 'application/x-gzip' length 415954 bytes (406 KB)

downloaded 406 KB

The downloaded binary packages are in
/var/folders/wn/mwrh20kj6p154xt6xrzt3bnc0000gq/T//Rtmp2Joy5i/downloaded_packages

library(devtools)
source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
install_github("satijalab/seurat")
Downloading GitHub repo satijalab/seurat@master
from URL https://api.github.com/repos/satijalab/seurat/zipball/master
Installing Seurat
Downloading GitHub repo StoreyLab/lfa@a1df252
from URL https://api.github.com/repos/StoreyLab/lfa/zipball/a1df252
Installing lfa
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
'/private/var/folders/wn/mwrh20kj6p154xt6xrzt3bnc0000gq/T/Rtmp2Joy5i/devtoolse44650a53ede/StoreyLab-lfa-a1df252' \
--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

• installing _source_ package ‘lfa’ ...
  * libs
  clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fastmat.c -o fastmat.o
  clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c lfa-init.c -o lfa-init.o
  clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c lfa.c -o lfa.o
  clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c lreg.c -o lreg.o
  clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o lfa.so fastmat.o lfa-init.o lfa.o lreg.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
  ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
  ld: library not found for -lgfortran
  clang: error: linker command failed with exit code 1 (use -v to see invocation)
  make: ** [lfa.so] Error 1
  ERROR: compilation failed for package ‘lfa’
• removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/lfa’
  Error: Command failed (1)

[andrewwbutler]

This is caused by an annoying issue with fortran on macs. Running the code below from the command line and then reinstalling from github should resolve your issue.

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

For a more detailed explanation, see this blog post.

[BrentonPaolella]

awesome! That fixed the problem and I'm walking through the tutorial now. Thanks very much!

[vaughandy]

Hi Andrew,

Really excited to try your package rather than using Fluidigm's Singular. However, I keep getting a weird error at the point of installing Seurat, pasted below. Any ideas ?

• installing _source_ package 'Seurat' ...
  ** R
  ** preparing package for lazy loading
  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  there is no package called 'magrittr'
  Error : package 'reshape2' could not be loaded
  ERROR: lazy loading failed for package 'Seurat'
• removing 'C:/Users/avaughan/Documents/R/win-library/3.3/Seurat'
  Error: Command failed (1)

[andrewwbutler]

This seems to be an issue with installing some of the dependencies. Try running install.packages(c("magrittr", "reshape2")) and then rerun the github install.

[lpbo14]

Hi Andrew,

I've been trying to install the latest Seurat (v 1.3) using R version 3.2 for windows as it's suggested. However, I am obtaining the error message below:

library(devtools)
install_github("satijalab/seurat")
Error in loadNamespace(name) : there is no package called ‘curl’

I tried to download curl package (in all the R versions since 3.2 to 3.3.0) but it still doesn't work.

[andrewwbutler]

What's the message when you try install.packages("curl") ?

[vaughandy]

i actually got this to work, i just had to keep installing the separate
packages it thought it was missing and then the Seurat installer went
though without errors.

On Wed, Aug 24, 2016 at 12:43 PM, Andrew Butler [email protected]
wrote:

What's the message when you try install.packages("curl") ?

—
You are receiving this because you commented.
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PhD, Molecular and Cellular Biology
Postdoctoral Fellow, University of California - San Francisco

[maximilianh]

Here is a new one:

g++ -std=c++0x -I/cluster/home/max/usr/lib64/R/include -DNDEBUG -DR_BUILD -I/usr/local/include -I"/cluster/home/max/usr/src/Rlib/Rcpp/include"   -fpic  -g -O2 -c AAA_check_cpp11.cpp -o AAA_check_cpp11.o
AAA_check_cpp11.cpp:3:2: error: #error Error: ranger requires a real C++11 compiler. You probably have to update gcc.
make: *** [AAA_check_cpp11.o] Error 1
ERROR: compilation failed for package ‘ranger’
* removing ‘/cluster/home/max/usr/src/Rlib/ranger’

I tried this:

export CXX=/opt/rh/devtoolset-3/root/usr/bin/g++
export CXX1X=/opt/rh/devtoolset-3/root/usr/bin/g++

Doesn't fix the error.

Have you had this one before?

[maximilianh]

Nevermind, devtools or ranger seem to ignore CXX, so I just modified my PATH.

[KasperThystrup]

*Edited

Sorry to post another one.
This is from installing Seurat in RStudio on Arch Linux.

Everything seems to go fine (no errors) until this part:

installing to /home/user/R/x86_64-pc-linux-gnu-library/3.4/Seurat/libs
* R
* inst
* tests
* preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/user/R/x86_64-pc-linux-gnu-library/3.4/igraph/libs/igraph.so':
libgfortran.so.3: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘Seurat’

• removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.4/Seurat’
• restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.4/Seurat’
  Installation failed: Command failed (1)

It shows out that reinstalling rstudio would lead to other errors showing up - Couldn't install tclust package. After copying the tclust folder from ~/R/x86_64-pc-linux-gnu-library/3.3/tclust to /3.4, Seurat could suddently be installed...

[IMEx35]

Good day, i have been trying to run seurat on my windows PC but the following error keeps popping up.

compilation terminated.
make: * [RcppExports.o] Error 1
Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-34~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.1/share/make/winshlib.mk" CXX='$(CXX11) $(CXX11STD)' CXXFLAGS='$(CXX11FLAGS)' CXXPICFLAGS='$(CXX11PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX11LDFLAGS)' SHLIB_LD='$(SHLIB_CXX11LD)' SHLIB="Seurat.dll" OBJECTS="RcppExports.o data_manipulation.o"' had status 2
ERROR: compilation failed for package 'Seurat'

• removing '\fs01/users/redirectedfolders/ian.mbano/My Documents/R/win-library/3.4/Seurat'
  Installation failed: Command failed (1)

Is there anyone with useful information on how l can get past this,

Thank you

[hjistb]

@maximilianh
I was running into this problem as well. You said "I just modified my PATH", but how was it exactly modified?
Thank you

[maximilianh]

I added the directory where the updated g++ lives to my PATH. The exact directory depends on your distribution. In my case, I found an updated g++ under /opt/rh/devtoolset-3/

[hjistb]

@maximilianh
Thanks for your help. Really appreciate it.

[ltongyu]

Hi,

My R is version 3.4.1. I kept getting the error as below. Could you help me solve this problem?
Thanks a ton!

install_github("satijalab/seurat")
Downloading GitHub repo satijalab/seurat@master
from URL https://api.github.com/repos/satijalab/seurat/zipball/master
Installing Seurat
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ \
--no-save --no-restore --quiet CMD INSTALL \
'/private/var/folders/wr/gtk247r55sxbyvk8xzy754gw0000gn/T/RtmpqrceqX/devtools99c327ac3928/satijalab-seurat-2385378' \
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' \
--install-tests

• installing source package ‘Seurat’ ...
  Warning in as.POSIXlt.POSIXct(x, tz) :
  unknown timezone 'default/America/Detroit'
  * libs
  clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppProgress/include" -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
  In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:1:
  In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Core:261:
  In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cassert:21:
  In file included from /usr/local/include/assert.h:5:
  /usr/local/include/except.h:15:32: error: typedef redefinition with different types ('struct Except_Frame_T *' vs 'Except_Frame_T')
  typedef struct Except_Frame_T *Except_Frame_T;
  ^
  /usr/local/include/except.h:15:16: note: previous definition is here
  typedef struct Except_Frame_T *Except_Frame_T;
  ^
  /usr/local/include/except.h:17:18: error: field has incomplete type 'Except_Frame_T'
  Except_Frame_T prev;
  ^
  /usr/local/include/except.h:16:8: note: definition of 'Except_Frame_T' is not complete until the closing '}'
  struct Except_Frame_T {
  ^
  2 errors generated.
  make: ** [RcppExports.o] Error 1
  ERROR: compilation failed for package ‘Seurat’
• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Seurat’
  Installation failed: Command failed (1)