Fail to install SeuratV5 on LINUX

[YYYYYWWWYYYYYY]

Hi,I was trying to download seurat v5 using 'remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE)'; and I met the error below:

installing to /tmp/Rtmps1Y5EW/Rinst10f75b43549f/00LOCK-SeuratObject/00new/SeuratObject/libs
** R
Error in parse(outFile) : 
  /tmp/Rtmps1Y5EW/Rbuild10f77f3bac47/SeuratObject/R/assay.R:233:13: unexpected input
232:     expr = Layers(object = object, search = layer),
233:     error = \
                 ^
ERROR: unable to collate and parse R files for package ‘SeuratObject’
* removing ‘/tmp/Rtmps1Y5EW/Rinst10f75b43549f/SeuratObject’
      -----------------------------------
ERROR: package installation failed
STDERR:

Error: Failed to install 'Seurat' from GitHub:
  Failed to install 'SeuratObject' from GitHub:
  Failed to `R CMD build` package, try `build = FALSE`.

My R version is 4.0.5 and rlang is 1.1.0. May I ask how to solve this problem?
Thank you very much!

[saketkc]

Can you update your R to 4.2 or higher and retry?

[AustinHartman]

Hi @YYYYYWWWYYYYYY, I just pushed a fix for this error to SeuratObject which should make installation possible on R versions <4.1.0.

[guisantagui]

Hi, I am having this exact issue. I am on R 4.0.5 and cannot update it since it is the version in my institution's HPC. I am tried both to install Seurat v5 from GitHub, and CRAN's Seurat version with install.packages(). Both gave the same error:
`Error in parse(outFile) :
/tmp/RtmpOWEyqu/R.INSTALL281dd94d24511b/SeuratObject/R/assay5.R:174:13: unexpected input
173: expr = Layers(object = object, search = layer),
174: error =
^
ERROR: unable to collate and parse R files for package ‘SeuratObject’

• removing ‘/mnt/irisgpfs/users/gsantamaria/R/x86_64-pc-linux-gnu-library/4.0/SeuratObject’

The downloaded source packages are in
‘/tmp/RtmpLSa6BA/downloaded_packages’
✔ checking for file ‘/tmp/RtmpLSa6BA/remotes28157f3e49c72e/satijalab-seurat-a4075e7/DESCRIPTION’ (462ms)
─ preparing ‘Seurat’:
✔ checking DESCRIPTION meta-information ... OK
─ cleaning src
─ installing the package to process help pages
-----------------------------------
ERROR: dependency ‘SeuratObject’ is not available for package ‘Seurat’
─ removing ‘/tmp/RtmpEr8o44/Rinst281e2c284fd862/Seurat’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'Seurat' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr:
E> * checking for file ‘/tmp/RtmpLSa6BA/remotes28157f3e49c72e/satijalab-seurat-a4075e7/DESCRIPTION’ ... OK
E> * preparing ‘Seurat’:
E> * checking DESCRIPTION meta-information ... OK
E> * cleaning src
E> * installing the package to process help pages
E> -----------------------------------
E> ERROR: dependency ‘SeuratObject’ is not available for package ‘Seurat’
E> * removing ‘/tmp/RtmpEr8o44/Rinst281e2c284fd862/Seurat’
E> -----------------------------------
E> ERROR: package
In addition: Warning message:
In i.p(...) :
installation of package ‘SeuratObject’ had non-zero exit status`

I have tried to install SeuratObject both from GitHub (mojaveazure/seurat-object) and from CRAN (with install.packages()), and the error persists. Does any of you know how to solve this issue?

[Wenjuan-ZHU]

@guisantagui I had the same issue here and cannot install SeuratObject.

[alexanderchang1]

@guisantagui I have the same issue here.

[helenzhangyc]

@guisantagui I have the same issue here and cannot install SeuratObject. Any help would be appreciated!

[kevinhwong1]

@guisantagui I am also having the same issue (R version 4.0.3 and rlang version 1.1.2). Please let me know if there are any solutions to this without updating R.

Error message:

Error in parse(outFile) :
/private/var/folders/cg/539pdzbj11g5mqx9hyc31qr80000gn/T/RtmpGovcBw/Rbuild892e234dc9e7/SeuratObject/R/assay5.R:174:13: unexpected input
173: expr = Layers(object = object, search = layer),
174: error =
^
ERROR: unable to collate and parse R files for package ‘SeuratObject’
─ removing ‘/private/var/folders/cg/539pdzbj11g5mqx9hyc31qr80000gn/T/RtmpGovcBw/Rinst892e48026ecc/SeuratObject’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'SeuratObject' from GitHub:
! System command 'R' failed

[Andelyu]

I got the same issue here. Can anyone give a hand?

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
ERROR: dependency ‘SeuratObject’ is not available for package ‘SeuratData’

• removing ‘/usr/local/lib/R/site-library/SeuratData’
  Warning messages:
  1: In i.p(...):
  installation of package ‘SeuratObject’ had non-zero exit status.
  2: In i.p(...):
  installation of package ‘/tmp/Rtmp38GKrW/filed5a616079f66/SeuratData_0.2.2.9001.tar.gz’ had non-zero exit status.

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] processx_3.8.1 compiler_4.0.3 R6_2.5.1 rprojroot_2.0.4
[5] cli_3.6.1 prettyunits_1.1.1 tools_4.0.3 withr_2.5.2
[9] curl_5.1.0 crayon_1.5.2 remotes_2.4.2 callr_3.7.3
[13] ps_1.6.0 pkgbuild_1.2.0

[Andelyu]

I successfully install the seuratv5 after I update my R version from v4.0.3 to v4.3.0

[totoroclub123]

Hi, I am experiencing the same issue.
I wonder if anybody can solve the issue WITHOUT updating the R version.

── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpvpE3TC/remotese4157421374/satijalab-seurat-a4075e7/DESCRIPTION’ (707ms)
─ preparing ‘Seurat’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to process help pages
-----------------------------------
ERROR: dependency ‘SeuratObject’ is not available for package ‘Seurat’
─ removing ‘/tmp/RtmpFzLY7C/Rinst75753aaf428b/Seurat’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'Seurat' from GitHub:
! System command 'R' failed
In addition: Warning message:
In i.p(...) :
installation of package ‘SeuratObject’ had non-zero exit status

[jingquanlim]

seurat-object-5.0.1_fixedForR4.1_and_below.tar.gz
Credits to @AustinHartman for pointing out the 'shorthands used' with the "error = (" code. I have manually replaced numerous to "error = function(" and have the files uploaded here for everyone to try it out.