Seurat: error installing seurat 3 alpha
Hi,
Thanks for releasing the new Seurat version for testing! I am trying to install it and getting an issue with devtools. I don't know if this is an issue I should ask you or the devtools team. Thanks a lot! -Orr
> devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')
Downloading GitHub repo satijalab/seurat@release/3.0
Installing 7 packages: future, future.apply, ggrepel, globals, listenv, reticulate, rsvd
Error: (converted from warning) unable to access index for repository https://mojaveazure.github.io/loomR/bin/macosx/el-capitan/contrib/3.5:
cannot open URL 'https://mojaveazure.github.io/loomR/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_0.12.19 rstudioapi_0.8 magrittr_1.5 usethis_1.4.0
[5] devtools_2.0.1 pkgload_1.0.2 R6_2.3.0 rlang_0.3.0.1
[9] tools_3.5.1 pkgbuild_1.0.2 sessioninfo_1.1.0 cli_1.0.1
[13] withr_2.1.2 remotes_2.0.2 assertthat_0.2.0 digest_0.6.18
[17] rprojroot_1.3-2 crayon_1.3.4 processx_3.2.0 callr_3.0.0
[21] base64enc_0.1-3 fs_1.2.6 ps_1.2.0 curl_3.2
[25] memoise_1.1.0 glue_1.3.0 compiler_3.5.1 desc_1.2.0
[29] backports_1.1.2 prettyunits_1.0.2
Also for what it's worth, I have loomR already.
> library(loomR)
Loading required package: R6
Loading required package: hdf5r
Loading required package: iterators
Loading required package: itertools
And this command for regular Seurat works
devtools::install_version(package = 'Seurat', version = package_version('2.3.0'))
orrzor
All 31 comments
Hi,
I seem to be having exactly the same issue.
Looking forward to trying out the new Seurat though!
John
> devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')
Downloading GitHub repo satijalab/seurat@release/3.0
These packages have more recent versions available.
Which would you like to update?
1: cli (1.0.0 -> 1.0.1 ) [CRAN]
2: data.table (1.11.4 -> 1.11.8 ) [CRAN]
3: digest (0.6.15 -> 0.6.18 ) [CRAN]
4: dplyr (0.7.6 -> 0.7.7 ) [CRAN]
5: fansi (0.2.3 -> 0.4.0 ) [CRAN]
6: fitdistrplus (1.0-9 -> 1.0-11 ) [CRAN]
7: ggplot2 (3.0.0 -> 3.1.0 ) [CRAN]
8: ggridges (0.5.0 -> 0.5.1 ) [CRAN]
9: htmlwidgets (1.2 -> 1.3 ) [CRAN]
10: later (0.7.3 -> 0.7.5 ) [CRAN]
11: mime (0.5 -> 0.6 ) [CRAN]
12: openssl (1.0.1 -> 1.0.2 ) [CRAN]
13: pkgconfig (2.0.1 -> 2.0.2 ) [CRAN]
14: R.utils (2.6.0 -> 2.7.0 ) [CRAN]
15: R6 (2.2.2 -> 2.3.0 ) [CRAN]
16: Rcpp (0.12.18 -> 0.12.19) [CRAN]
17: Rdpack (0.8-0 -> 0.10-1 ) [CRAN]
18: reticulate (1.9 -> 1.10 ) [CRAN]
19: rlang (0.2.1 -> 0.3.0.1) [CRAN]
20: scales (0.5.0 -> 1.0.0 ) [CRAN]
21: shiny (1.1.0 -> 1.2.0 ) [CRAN]
22: tidyr (0.8.1 -> 0.8.2 ) [CRAN]
23: tidyselect (0.2.4 -> 0.2.5 ) [CRAN]
24: xtable (1.8-2 -> 1.8-3 ) [CRAN]
25: zoo (1.8-3 -> 1.8-4 ) [CRAN]
26: CRAN packages only
27: All
28: None
Enter one or more numbers separated by spaces, or an empty line to cancel
1: 26
cli (1.0.0 -> 1.0.1 ) [CRAN]
data.table (1.11.4 -> 1.11.8 ) [CRAN]
digest (0.6.15 -> 0.6.18 ) [CRAN]
dplyr (0.7.6 -> 0.7.7 ) [CRAN]
fansi (0.2.3 -> 0.4.0 ) [CRAN]
fitdistrplus (1.0-9 -> 1.0-11 ) [CRAN]
future (NA -> 1.10.0 ) [CRAN]
future.apply (NA -> 1.0.1 ) [CRAN]
ggplot2 (3.0.0 -> 3.1.0 ) [CRAN]
ggrepel (NA -> 0.8.0 ) [CRAN]
ggridges (0.5.0 -> 0.5.1 ) [CRAN]
globals (NA -> 0.12.4 ) [CRAN]
htmlwidgets (1.2 -> 1.3 ) [CRAN]
later (0.7.3 -> 0.7.5 ) [CRAN]
listenv (NA -> 0.7.0 ) [CRAN]
lsei (NA -> 1.2-0 ) [CRAN]
mime (0.5 -> 0.6 ) [CRAN]
npsurv (NA -> 0.4-0 ) [CRAN]
openssl (1.0.1 -> 1.0.2 ) [CRAN]
pkgconfig (2.0.1 -> 2.0.2 ) [CRAN]
R.utils (2.6.0 -> 2.7.0 ) [CRAN]
R6 (2.2.2 -> 2.3.0 ) [CRAN]
Rcpp (0.12.18 -> 0.12.19) [CRAN]
Rdpack (0.8-0 -> 0.10-1 ) [CRAN]
reticulate (1.9 -> 1.10 ) [CRAN]
rlang (0.2.1 -> 0.3.0.1) [CRAN]
rsvd (NA -> 0.9 ) [CRAN]
scales (0.5.0 -> 1.0.0 ) [CRAN]
shiny (1.1.0 -> 1.2.0 ) [CRAN]
tidyr (0.8.1 -> 0.8.2 ) [CRAN]
tidyselect (0.2.4 -> 0.2.5 ) [CRAN]
xtable (1.8-2 -> 1.8-3 ) [CRAN]
zoo (1.8-3 -> 1.8-4 ) [CRAN]
Installing 33 packages: cli, data.table, digest, dplyr, fansi, fitdistrplus, future, future.apply, ggplot2, ggrepel, ggridges, globals, htmlwidgets, later, listenv, lsei, mime, npsurv, openssl, pkgconfig, R.utils, R6, Rcpp, Rdpack, reticulate, rlang, rsvd, scales, shiny, tidyr, tidyselect, xtable, zoo
Error: (converted from warning) unable to access index for repository https://mojaveazure.github.io/loomR/bin/macosx/el-capitan/contrib/3.5:
cannot open URL 'https://mojaveazure.github.io/loomR/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_0.12.18 rstudioapi_0.7 magrittr_1.5 usethis_1.4.0 devtools_2.0.1
[6] pkgload_1.0.2 R6_2.2.2 rlang_0.2.1 tools_3.5.1 pkgbuild_1.0.2
[11] sessioninfo_1.1.0 cli_1.0.0 withr_2.1.2 remotes_2.0.2 assertthat_0.2.0
[16] digest_0.6.15 rprojroot_1.3-2 crayon_1.3.4 processx_3.2.0 callr_3.0.0
[21] base64enc_0.1-3 fs_1.2.6 ps_1.2.0 curl_3.2 memoise_1.1.0
[26] glue_1.3.0 compiler_3.5.1 desc_1.2.0 backports_1.1.2 prettyunits_1.0.2
JohnnyNeuro
on 5 Nov 2018
Hi,
it seems like both of you are using Rstudio. Does this error show up if you
try to install Seurat from the terminal (outside of Rstudio)?
On Mon, Nov 5, 2018 at 2:31 AM JohnnyNeuro notifications@github.com wrote:
Hi,
I seem to be having exactly the same issue.
Looking forward to trying out the new Seurat though!
Johndevtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')
Downloading GitHub repo satijalab/seurat@release/3.0
These packages have more recent versions available.
Which would you like to update?
1: cli (1.0.0 -> 1.0.1 ) [CRAN]
2: data.table (1.11.4 -> 1.11.8 ) [CRAN]
3: digest (0.6.15 -> 0.6.18 ) [CRAN]
4: dplyr (0.7.6 -> 0.7.7 ) [CRAN]
5: fansi (0.2.3 -> 0.4.0 ) [CRAN]
6: fitdistrplus (1.0-9 -> 1.0-11 ) [CRAN]
7: ggplot2 (3.0.0 -> 3.1.0 ) [CRAN]
8: ggridges (0.5.0 -> 0.5.1 ) [CRAN]
9: htmlwidgets (1.2 -> 1.3 ) [CRAN]
10: later (0.7.3 -> 0.7.5 ) [CRAN]
11: mime (0.5 -> 0.6 ) [CRAN]
12: openssl (1.0.1 -> 1.0.2 ) [CRAN]
13: pkgconfig (2.0.1 -> 2.0.2 ) [CRAN]
14: R.utils (2.6.0 -> 2.7.0 ) [CRAN]
15: R6 (2.2.2 -> 2.3.0 ) [CRAN]
16: Rcpp (0.12.18 -> 0.12.19) [CRAN]
17: Rdpack (0.8-0 -> 0.10-1 ) [CRAN]
18: reticulate (1.9 -> 1.10 ) [CRAN]
19: rlang (0.2.1 -> 0.3.0.1) [CRAN]
20: scales (0.5.0 -> 1.0.0 ) [CRAN]
21: shiny (1.1.0 -> 1.2.0 ) [CRAN]
22: tidyr (0.8.1 -> 0.8.2 ) [CRAN]
23: tidyselect (0.2.4 -> 0.2.5 ) [CRAN]
24: xtable (1.8-2 -> 1.8-3 ) [CRAN]
25: zoo (1.8-3 -> 1.8-4 ) [CRAN]
26: CRAN packages only
27: All
28: None
Enter one or more numbers separated by spaces, or an empty line to cancel
1: 26
cli (1.0.0 -> 1.0.1 ) [CRAN]
data.table (1.11.4 -> 1.11.8 ) [CRAN]
digest (0.6.15 -> 0.6.18 ) [CRAN]
dplyr (0.7.6 -> 0.7.7 ) [CRAN]
fansi (0.2.3 -> 0.4.0 ) [CRAN]
fitdistrplus (1.0-9 -> 1.0-11 ) [CRAN]
future (NA -> 1.10.0 ) [CRAN]
future.apply (NA -> 1.0.1 ) [CRAN]
ggplot2 (3.0.0 -> 3.1.0 ) [CRAN]
ggrepel (NA -> 0.8.0 ) [CRAN]
ggridges (0.5.0 -> 0.5.1 ) [CRAN]
globals (NA -> 0.12.4 ) [CRAN]
htmlwidgets (1.2 -> 1.3 ) [CRAN]
later (0.7.3 -> 0.7.5 ) [CRAN]
listenv (NA -> 0.7.0 ) [CRAN]
lsei (NA -> 1.2-0 ) [CRAN]
mime (0.5 -> 0.6 ) [CRAN]
npsurv (NA -> 0.4-0 ) [CRAN]
openssl (1.0.1 -> 1.0.2 ) [CRAN]
pkgconfig (2.0.1 -> 2.0.2 ) [CRAN]
R.utils (2.6.0 -> 2.7.0 ) [CRAN]
R6 (2.2.2 -> 2.3.0 ) [CRAN]
Rcpp (0.12.18 -> 0.12.19) [CRAN]
Rdpack (0.8-0 -> 0.10-1 ) [CRAN]
reticulate (1.9 -> 1.10 ) [CRAN]
rlang (0.2.1 -> 0.3.0.1) [CRAN]
rsvd (NA -> 0.9 ) [CRAN]
scales (0.5.0 -> 1.0.0 ) [CRAN]
shiny (1.1.0 -> 1.2.0 ) [CRAN]
tidyr (0.8.1 -> 0.8.2 ) [CRAN]
tidyselect (0.2.4 -> 0.2.5 ) [CRAN]
xtable (1.8-2 -> 1.8-3 ) [CRAN]
zoo (1.8-3 -> 1.8-4 ) [CRAN]
Installing 33 packages: cli, data.table, digest, dplyr, fansi,
fitdistrplus, future, future.apply, ggplot2, ggrepel, ggridges, globals,
htmlwidgets, later, listenv, lsei, mime, npsurv, openssl, pkgconfig,
R.utils, R6, Rcpp, Rdpack, reticulate, rlang, rsvd, scales, shiny, tidyr,
tidyselect, xtable, zooError: (converted from warning) unable to access index for repository
https://mojaveazure.github.io/loomR/bin/macosx/el-capitan/contrib/3.5
https://urldefense.proofpoint.com/v2/url?u=https-3A__mojaveazure.github.io_loomR_bin_macosx_el-2Dcapitan_contrib_3.5&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=e2kPyDtZAzQoyPfLTjZ5kw&m=3-41vRGz0ni3DtkbiVYJMPCSMCJtbTiLKC0Wx9PiHYI&s=5igs3gJX16U-e6khU7GCJ4uN3pypBOA8q3YgIhz4uLM&e=
:
cannot open URL '
https://mojaveazure.github.io/loomR/bin/macosx/el-capitan/contrib/3.5/PACKAGES
https://urldefense.proofpoint.com/v2/url?u=https-3A__mojaveazure.github.io_loomR_bin_macosx_el-2Dcapitan_contrib_3.5_PACKAGES&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=e2kPyDtZAzQoyPfLTjZ5kw&m=3-41vRGz0ni3DtkbiVYJMPCSMCJtbTiLKC0Wx9PiHYI&s=4_k4tWW71W_ybBpWBouOAdtCBNuDJHzj4qpKyY2W79M&e=
'sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dyliblocale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8attached base packages:
[1] stats graphics grDevices utils datasets methods baseloaded via a namespace (and not attached):
[1] Rcpp_0.12.18 rstudioapi_0.7 magrittr_1.5 usethis_1.4.0 devtools_2.0.1
[6] pkgload_1.0.2 R6_2.2.2 rlang_0.2.1 tools_3.5.1 pkgbuild_1.0.2
[11] sessioninfo_1.1.0 cli_1.0.0 withr_2.1.2 remotes_2.0.2 assertthat_0.2.0
[16] digest_0.6.15 rprojroot_1.3-2 crayon_1.3.4 processx_3.2.0 callr_3.0.0
[21] base64enc_0.1-3 fs_1.2.6 ps_1.2.0 curl_3.2 memoise_1.1.0
[26] glue_1.3.0 compiler_3.5.1 desc_1.2.0 backports_1.1.2 prettyunits_1.0.2—
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ChristophH
on 5 Nov 2018
Hi there,
I have the same problem when installing from the Terminal.
Thanks for your help!
ltosti
on 5 Nov 2018
Hi Christoph,
Thanks for your response. I tried it also in R and it did not work. Thank you for helping us with this.
> devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')
Downloading GitHub repo satijalab/seurat@release/3.0
Installing 7 packages: future, future.apply, ggrepel, globals, listenv, reticulate, rsvd
Error: (converted from warning) unable to access index for repository https://mojaveazure.github.io/loomR/bin/macosx/el-capitan/contrib/3.5:
cannot open URL 'https://mojaveazure.github.io/loomR/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_0.12.19 ps_1.2.0 prettyunits_1.0.2 rprojroot_1.3-2
[5] digest_0.6.18 crayon_1.3.4 withr_2.1.2 assertthat_0.2.0
[9] R6_2.3.0 backports_1.1.2 magrittr_1.5 rlang_0.3.0.1
[13] cli_1.0.1 curl_3.2 fs_1.2.6 remotes_2.0.2
[17] callr_3.0.0 desc_1.2.0 devtools_2.0.1 tools_3.5.1
[21] glue_1.3.0 pkgload_1.0.2 compiler_3.5.1 processx_3.2.0
[25] base64enc_0.1-3 pkgbuild_1.0.2 sessioninfo_1.1.0 memoise_1.1.0
[29] usethis_1.4.0
Hi,
We're looking into this but are having trouble consistently reproducing the issue. Do you have your options for warnings set to convert warnings to errors? You can try options("warn"=0) to restore the default warning behavior which might allow the install to complete.
Another alternative to try is to turn off the automatic dependency installation if you already have the required dependencies.
install_github(repo = "satijalab/seurat", ref = "release/3.0", dependencies = FALSE)
andrewwbutler
on 5 Nov 2018
Hi Paul and Andrew,
Thanks so much for your replies. The commit to make loomR not required allowed me to install Seurat3. Thank you so much, and I hope it is not too much work to track down the loomR issue.
Best, Orr
orrzor
on 5 Nov 2018
Hi Orr,
How did you work around the loomR requirement? Did you just turn off the automatic dependency installation like Andrew recommended?
John
JohnnyNeuro
on 5 Nov 2018
Hi @JohnnyNeuro,
We just removed the loomR requirements on that branch for now while we work out the issue. Try reinstalling with install_github(repo = "satijalab/seurat", ref = "release/3.0")
andrewwbutler
on 5 Nov 2018
Thanks Andrew! That fixed it for me too.
John
JohnnyNeuro
on 5 Nov 2018
Having the same loomR issue trying to install release 3.0 today
rspreafico
on 1 Apr 2019
Hi @rspreafico,
I am unable to replicate this issue. Can you make sure that you aren't also trying to install suggested packages as well?
> 'loomR' %in% rownames(x = installed.packages())
[1] FALSE
> devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')
Downloading GitHub repo satijalab/seurat@release/3.0
✔ checking for file ‘/tmp/RtmpVknYha/remotes114633220b51/satijalab-seurat-6d361c0/DESCRIPTION’ ...
─ preparing ‘Seurat’:
✔ 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
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘Seurat_3.0.0.9000.tar.gz’
Installing package into ‘/home/paul/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package ‘Seurat’ ...
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppProgress/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ModularityOptimizer.cpp -o ModularityOptimizer.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppProgress/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RModularityOptimizer.cpp -o RModularityOptimizer.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppProgress/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppProgress/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c data_manipulation.cpp -o data_manipulation.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppProgress/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integration.cpp -o integration.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include" -I"/home/paul/R/x86_64-pc-linux-gnu-library/3.5/RcppProgress/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c snn.cpp -o snn.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Seurat.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o integration.o snn.o -L/usr/lib/R/lib -lR
installing to /home/paul/R/x86_64-pc-linux-gnu-library/3.5/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (Seurat)
mojaveazure
on 1 Apr 2019
Indeed the way I had to work around it is to explicitly tell devtools:install_github not to install suggested packages. This way Seurat installed successfully. For some reason it was pulling suggested packages as well, regardless of whether loomR was not installed (my first attemp) or was installed (manually, it installs nicely).
rspreafico
on 1 Apr 2019
Huh, okay. This seems to be a devtools issue, not a Seurat-specific issue.
mojaveazure
on 1 Apr 2019
I also ran into this. Might be worth mentioning in the docs.
j-andrews7
on 1 Apr 2019
I am getting this error and have not been able to overcome with the suggestions (maybe because I did not understand how to tell devtools explicitly not to install suggested packages (or loomR)?
withr::with_libpaths(new = "C:/data/installs/R-3.5.3/library", devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0'))
Downloading GitHub repo satijalab/seurat@release/3.0
These packages have more recent versions available.
Which would you like to update?
1: assertthat (0.2.0 -> 0.2.1) [CRAN]
2: cli (1.0.1 -> 1.1.0) [CRAN]
3: colorspace (1.4-0 -> 1.4-1) [CRAN]
4: gtable (0.2.0 -> 0.3.0) [CRAN]
5: openssl (1.2.2 -> 1.3 ) [CRAN]
6: rlang (0.3.1 -> 0.3.3) [CRAN]
7: zoo (1.8-4 -> 1.8-5) [CRAN]
8: CRAN packages only
9: All
10: None
Enter one or more numbers separated by spaces, or an empty line to cancel
1: 10
Installing 6 packages: future, future.apply, ggrepel, globals, listenv, rsvd
Error: (converted from warning) unable to access index for repository https://mojaveazure.github.io/loomR/bin/windows/contrib/3.5:
cannot open URL 'https://mojaveazure.github.io/loomR/bin/windows/contrib/3.5/PACKAGES'
In addition: Warning messages:
1: In untar2(tarfile, files, list, exdir) :
skipping pax global extended headers
2: In untar2(tarfile, files, list, exdir) :
skipping pax global extended headers
Also:
'loomR' %in% rownames(x = installed.packages())
[1] FALSE
- Do I need to install loomR separately?
pagarwal14
on 3 Apr 2019
I too am running into this and non of the above methods are helping
AlexChitsazan
on 3 Apr 2019
@pagarwal14 @AlexChitsazan, you should be able to set dependencies = NA or dependencies = c('Depends', 'Imports') in the call to devtools::install_github
mojaveazure
on 3 Apr 2019
@AlexChitsazan @pagarwal14
You do not need loomR.
@mojaveazure's method didn't work for me (though by all means, it should have). I had to set dependencies=False and install the dependencies manually (errors will be thrown telling you which ones are missing):
devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0', dependencies=FALSE)
Hi when I turn off dependencies I'm getting a different error. ```
Error in i.p(...) :
(converted from warning) installation of package ‘../Seurat_3.0.0.9000.tar.gz’
had non-zero exit status
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Is there anything else I can do? thanks!
ahdee
on 4 Apr 2019
nevermind, this was an error because I had to install some of the depenecies manaully. I did this via biocmanager and it finally worked.
ahdee
on 4 Apr 2019
@ahdee
I am having the same issue and I am very new to R. How did you install the dependencies using biocmanager?
kjrgreen1
on 4 Apr 2019
@kjrgreen1 ok assuming you have biocmanager installed. Do this.
BiocManager::install(c('ape', 'fitdistrplus', 'future', 'future.apply', 'ggridges', 'ica', 'igraph', 'irlba', 'lmtest', 'metap', 'pbapply', 'RANN', 'reticulate', 'ROCR', 'rsvd', 'SDMTools', 'tsne', 'RcppProgress'), ask=T )
options("warn"=0)
# some issue iwth loomR
devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0', dependencies=FALSE)
I got the list of dependencies of the error message. This works for me.
ahdee
on 4 Apr 2019
This worked for me, thanks!
AlexChitsazan
on 4 Apr 2019
This worked for me too, thank you!
kjrgreen1
on 4 Apr 2019
Hi @ahdee, many thanks for your example, But I just tried with your method, and it still has the same error.
Downloading GitHub repo satijalab/seurat@release/3.0
√ checking for file 'C:\Users19173\AppData\Local\TempRtmpmQCOferemotes53b867522577\satijalab-seurat-83cfe16/DESCRIPTION'
- preparing 'Seurat': (406ms)
√ checking DESCRIPTION meta-information ... - cleaning src
- checking for LF line-endings in source and make files and shell scripts (474ms)
- checking for empty or unneeded directories
- looking to see if a 'data/datalist' file should be added
- building 'Seurat_3.0.0.9000.tar.gz'
Installing package into �C:/Users/19173/Documents/R/win-library/3.5�
(as �lib� is unspecified)
ERROR: dependencies 'ape', 'igraph', 'irlba', 'lmtest', 'RANN', 'reticulate', 'SDMTools' are not available for package 'Seurat'
- removing 'C:/Users/19173/Documents/R/win-library/3.5/Seurat'
In R CMD INSTALL
installation of package �C:/Users/19173/AppData/Local/Temp/RtmpmQCOfe/file53b81a00cc1/Seurat_3.0.0.9000.tar.gz� had non-zero exit status
And if I manually installed the dependencies again, and it would still occur the error. Do you know what's the issue?
Many thanks
Lesdormis
on 4 Apr 2019
@Lesdormis that is strange. That error is basically suggesting that those packages are not installed. So you installed those packagese succseffully? sometimes you might need restart the Rstudio. Also try to load each of those seperately and do a sessionInfo()
ahdee
on 4 Apr 2019
@ahdee Yep, it works after I restarted the Rstudio. Thanks for your help! Very Appreciated!
Lesdormis
on 4 Apr 2019
Thanks a lot for all the suggestions, installing de packages manually (although after a few rounds of getting a new error and a new uninstalled package) and disabeling the dependencies worked for me as well! Thanks again and thanks for this great package!
Emmavb1988
on 4 Apr 2019
Hi all,
at the end, I was finally able to install Seurat Version 3.0 too and summarized my steps here for other users (thanks a lot to all users from above!!!):
for Seurat Version3 create a new folder on drive "C:" e.g. "SeuratV3" and provide the path (see below)
.libPaths("C:/R-libs2")
.libPaths("C:/R351")
.libPaths("C:/SeuratV3")
Before you start, "Rtools" has to be installed
https://cran.r-project.org/bin/windows/Rtools/
With "sessionInfo()" you can check which R version and packages you have installed (McSt: "I have now R version 3.5.3. installed")
First you have to install "devtools"
install.packages('devtools')
library(devtools)
Second install "BiocManager" to install specific packages (see below)
install.packages('BiocManager')
library(BiocManager)
BiocManager::install(c('ape', 'fitdistrplus', 'future', 'future.apply', 'ggridges', 'ica', 'igraph', 'irlba', 'lmtest', 'metap', 'pbapply', 'RANN', 'reticulate', 'ROCR', 'rsvd', 'SDMTools', 'tsne', 'RcppProgress'), ask=T )
You can try options("warn"=0) to restore the default warning behavior which might allow the install to complete
options("warn"=0)
Now try to install it with depencies = FALSE to turn off the automatic dependency installation if you already have the required dependencies.
devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0', dependencies=FALSE)
You might get this error below
ERROR: dependencies 'cowplot', 'ggrepel', 'plotly', 'png', 'Rtsne', 'RcppEigen' are not available for package 'Seurat'
Now install them with BiocManager manually
BiocManager::install(c('cowplot', 'ggrepel', 'plotly', 'png', 'RcppEigen'), ask=T )
When installing these packages R might ask you if you want to update old packages, yes do it and type "a" for all
BiocManager::install(c('cluster', 'MASS', 'Matrix', 'mgcv', 'survival'), ask=T )
BiocManager::install(c('Rtsne'), ask=T )
Now it should work when you run the same command from before (some users also recommend to restart R), it could take a while so don't worry
Install Seurat Version 3.0
devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0', dependencies=FALSE)
Test it
library(Seurat)
Best regards and have fun,
Michael
McStber
on 5 Apr 2019
I was able to install with the following commands (in case it helps someone)
The following two deps were needed since the actual installation command gave error for them
install.packages("globals", lib="C:/data/installs/R-3.5.3/library")
install.packages("listenv", lib="C:/data/installs/R-3.5.3/library")
Then the command to install Seurat3
withr::with_libpaths(new = "C:/data/installs/R-3.5.3/library", devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0', dependencies = FALSE))
Now can load Seurat3
library(Seurat, lib.loc = "C:/data/installs/R-3.5.3/library")
To use RunUMAP I had to install UMAP separately (through conda..).
But I get the following error at runtime
pancreas.integrated <- RunUMAP(object = pancreas.integrated, reduction = "pca", dims = 1:30)
Error in py_call_impl(callable, dots$args, dots$keywords) :
Evaluation error: Required version of NumPy not available: installation of Numpy >= 1.6 not found.The numpy version that I have is 1.16 and that seems to be the latest for Windows. It was installed when the latest version of conda was installed.
Anyone has experienced this issue?
Thanks,
- Pankaj
pagarwal14
on 5 Apr 2019
🤦♂️
I had all the errors that were in this thread and was like wth is going on here. Then I just did this:
Explanations in #914 on one side and the following run-sequence on one side.
install.packages("Matrix")
install.packages("ggridges")
install.packages("cowplot")
install.packages('devtools')
install.packages('ggrepel')
devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')
Literally, that's all you need to do. Is install ggrepel first.
* building package indices
* testing if installed package can be loaded
- DONE (Seurat)
In R CMD INSTALL
Dragonmasterx87
on 5 Apr 2019
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