Error in .doLoadActions(where, attach) : error in load action .__A__.1 for package RcppAnnoy: loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "AnnoyAngular": cannot allocate vector of size 700261.6 Gb

[longrw]

Hi, I have some problems with the error message:

> devtools::install_github(repo="https://github.com/SCA-IRCM/SingleCellSignalR_v1", subdir="SingleCellSignalR")
Downloading GitHub repo SCA-IRCM/SingleCellSignalR_v1@HEAD
✔  checking for file ‘/tmp/pbs.1148590.omics/Rtmph9RXoU/remotes7f8e629b7a96/SCA-IRCM-SingleCellSignalR_v1-feecb30/SingleCellSignalR/DESCRIPTION’ ...
─  preparing ‘SingleCellSignalR’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘SingleCellSignalR_0.0.1.8.tar.gz’

* installing *source* package ‘SingleCellSignalR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in .doLoadActions(where, attach) : 
  error in load action .__A__.1 for package RcppAnnoy: loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "AnnoyAngular": cannot allocate vector of size 700261.6 Gb
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> <Anonymous> -> .doLoadActions
Execution halted
ERROR: lazy loading failed for package ‘SingleCellSignalR’
* removing ‘/pathowh01/disk1/longrw/tmp/.ctdb/.R/4.1.0/library/SingleCellSignalR’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/pbs.1148590.omics/Rtmph9RXoU/file7f8e5c415054/SingleCellSignalR_0.0.1.8.tar.gz’ had non-zero exit status
>

R version 4.1.0 (2021-05-18)

Did anybody have the same question and how did you solve it?

[SCA-IRCM]

Hi,

Try installing from Bioconductor (https://bioconductor.org/packages/release/bioc/html/SingleCellSignalR.html). If the problem persists, let me know.

Thanks for using SingleCellSignalR!

SCA

[longrw]

Thank you for your reply. I tried again, but it threw the same error:

> BiocManager::install('SingleCellSignalR', lib='./tmp/.ctdb/.R/4.1.0/library')
Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.0 (2021-05-18)
Installing package(s) 'SingleCellSignalR'
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/SingleCellSignalR_1.6.0.tar.gz'
Content type 'application/x-gzip' length 4451557 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

* installing *source* package ‘SingleCellSignalR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in .doLoadActions(where, attach) : 
  error in load action .__A__.1 for package RcppAnnoy: loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "AnnoyAngular": cannot allocate vector of size 702421.8 Gb
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> <Anonymous> -> .doLoadActions
Execution halted
ERROR: lazy loading failed for package ‘SingleCellSignalR’
* removing ‘/pathowh01/disk1/longrw/tmp/.ctdb/.R/4.1.0/library/SingleCellSignalR’

The downloaded source packages are in
    ‘/tmp/pbs.1159772.omics/Rtmp6TiOBH/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘SingleCellSignalR’ had non-zero exit status
>

[SCA-IRCM]

Hi,

It seems to come from your setup as you're the only one to have this issue.

Have you tried to install RcppAnnoy alone (install.packages("RcppAnnoy") and relaunch the installation?

Come back to me if the error persists

SCA

[longrw]

Wonderful, it works. Thanks a lot.

** testing if installed package keeps a record of temporary installation path
* DONE (RcppAnnoy)

The downloaded source packages are in
    ‘/tmp/pbs.1160034.omics/RtmpA78vKA/downloaded_packages’
> BiocManager::install('SingleCellSignalR', lib='./tmp/.ctdb/.R/4.1.0/library')
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://mirror-hk.koddos.net/CRAN

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.0 (2021-05-18)
Installing package(s) 'SingleCellSignalR'
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/SingleCellSignalR_1.6.0.tar.gz'
Content type 'application/x-gzip' length 4451557 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

* installing *source* package ‘SingleCellSignalR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SingleCellSignalR)

The downloaded source packages are in
    ‘/tmp/pbs.1160034.omics/RtmpA78vKA/downloaded_packages’
>