Error with installation: package ‘TOAST’ 1.8.3 was found, but >= 1.10.1 is required by ‘MuSiC’

[soueryw]

Hi, I am having issues in R 4.1 with the installation; specifically errors with TOAST:

See details below:

devtools::install_github('xuranw/MuSiC')
Downloading GitHub repo xuranw/MuSiC@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: rlang (1.1.0 -> 1.1.1) [CRAN]
5: vctrs (0.5.1 -> 0.6.2) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
rlang (1.1.0 -> 1.1.1) [CRAN]
vctrs (0.5.1 -> 0.6.2) [CRAN]
Skipping 3 packages not available: SingleCellExperiment, Biobase, TOAST
Installing 2 packages: rlang, vctrs
Installing packages into ‘/usr3/graduate/soueryw/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rlang_1.1.1.tar.gz'
Content type 'application/x-gzip' length 762533 bytes (744 KB)
downloaded 744 KB

trying URL 'https://cran.rstudio.com/src/contrib/vctrs_0.6.2.tar.gz'
Content type 'application/x-gzip' length 964633 bytes (942 KB)
downloaded 942 KB

ERROR: failed to lock directory ‘/usr3/graduate/soueryw/R/x86_64-pc-linux-gnu-library/4.1’ for modifying
Try removing ‘/usr3/graduate/soueryw/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-rlang’
ERROR: failed to lock directory ‘/usr3/graduate/soueryw/R/x86_64-pc-linux-gnu-library/4.1’ for modifying
Try removing ‘/usr3/graduate/soueryw/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-vctrs’

The downloaded source packages are in
‘/scratch/187841.1.ood/Rtmp8ek7p5/downloaded_packages’
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/scratch/187841.1.ood/Rtmp8ek7p5/remotes586030ae8371/xuranw-MuSiC-0a3e3af/DESCRIPTION’ ...
─ preparing ‘MuSiC’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘MuSiC_1.0.0.tar.gz’
Warning in sprintf(gettext(fmt, domain = domain), ...) :
one argument not used by format 'invalid uid value replaced by that for user 'nobody''
Warning: invalid uid value replaced by that for user 'nobody'
Warning in sprintf(gettext(fmt, domain = domain), ...) :
one argument not used by format 'invalid gid value replaced by that for user 'nobody''
Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/usr3/graduate/soueryw/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)

installing source package ‘MuSiC’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error: package ‘TOAST’ 1.8.3 was found, but >= 1.10.1 is required by ‘MuSiC’
Execution halted
ERROR: lazy loading failed for package ‘MuSiC’
removing ‘/usr3/graduate/soueryw/R/x86_64-pc-linux-gnu-library/4.1/MuSiC’
Warning messages:
1: In i.p(...) : installation of package ‘rlang’ had non-zero exit status
2: In i.p(...) : installation of package ‘vctrs’ had non-zero exit status
3: In i.p(...) :
installation of package ‘/scratch/187841.1.ood/Rtmp8ek7p5/file58607bb9ceae/MuSiC_1.0.0.tar.gz’ had non-zero exit status

[lindsdudley]

Did you ever figure out how to fix this?

[colin-leeyc]

Running into this issue too!

[John-Drake]

Go to https://bioconductor.org/packages/devel/bioc/html/TOAST.html and download the latest source file (Current 1.17).

For instance, wget https://bioconductor.org/packages/devel/bioc/src/contrib/TOAST_1.17.0.tar.gz

Then manually install the package in R.

For instance, install.packages('TOAST_1.17.0.tar.gz', lib='destination_directory')