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xuranw / MuSiC

Multi-subject Single Cell Deconvolution
https://github.com/xuranw/MuSiC
GNU General Public License v3.0
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Error with installation: package ‘TOAST’ 1.8.3 was found, but >= 1.10.1 is required by ‘MuSiC’ #116

Open soueryw opened 1 year ago

soueryw commented 1 year ago

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 commented 9 months ago

Did you ever figure out how to fix this?

colin-leeyc commented 8 months ago

Running into this issue too!

John-Drake commented 7 months ago

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')