error installing Monocle3 in R4..4

[sanskritidey]

BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', + 'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment', + 'SummarizedExperiment', 'batchelor', 'HDF5Array', + 'terra', 'ggrastr'), force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14 ucrt) Installing package(s) 'BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', 'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment', 'SummarizedExperiment', 'batchelor', 'HDF5Array', 'terra', 'ggrastr' trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/BiocGenerics_0.50.0.zip' Content type 'application/zip' length 619116 bytes (604 KB) downloaded 604 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/DelayedArray_0.30.1.zip' Content type 'application/zip' length 2394218 bytes (2.3 MB) downloaded 2.3 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/DelayedMatrixStats_1.26.0.zip' Content type 'application/zip' length 736780 bytes (719 KB) downloaded 719 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/limma_3.60.4.zip' Content type 'application/zip' length 3124617 bytes (3.0 MB) downloaded 3.0 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/lme4_1.1-35.5.zip' Content type 'application/zip' length 4556905 bytes (4.3 MB) downloaded 4.3 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/S4Vectors_0.42.1.zip' Content type 'application/zip' length 2390523 bytes (2.3 MB) downloaded 2.3 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/SingleCellExperiment_1.26.0.zip' Content type 'application/zip' length 1975902 bytes (1.9 MB) downloaded 1.9 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/SummarizedExperiment_1.34.0.zip' Content type 'application/zip' length 1993798 bytes (1.9 MB) downloaded 1.9 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/batchelor_1.20.0.zip' Content type 'application/zip' length 1551812 bytes (1.5 MB) downloaded 1.5 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/HDF5Array_1.32.0.zip' Content type 'application/zip' length 11688536 bytes (11.1 MB) downloaded 11.1 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/terra_1.7-78.zip' Content type 'application/zip' length 40335186 bytes (38.5 MB) downloaded 38.5 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/ggrastr_1.0.2.zip' Content type 'application/zip' length 2678484 bytes (2.6 MB) downloaded 2.6 MB package ‘BiocGenerics’ successfully unpacked and MD5 sums checked package ‘DelayedArray’ successfully unpacked and MD5 sums checked package ‘DelayedMatrixStats’ successfully unpacked and MD5 sums checked package ‘limma’ successfully unpacked and MD5 sums checked package ‘lme4’ successfully unpacked and MD5 sums checked package ‘S4Vectors’ successfully unpacked and MD5 sums checked package ‘SingleCellExperiment’ successfully unpacked and MD5 sums checked package ‘SummarizedExperiment’ successfully unpacked and MD5 sums checked package ‘batchelor’ successfully unpacked and MD5 sums checked package ‘HDF5Array’ successfully unpacked and MD5 sums checked package ‘terra’ successfully unpacked and MD5 sums checked package ‘ggrastr’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\UMASHANKAR\AppData\Local\Temp\Rtmp6XTajY\downloaded_packages Old packages: 'MASS', 'nlme', 'survival' Update all/some/none? [a/s/n]: Update all/some/none? [a/s/n]: a trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/MASS_7.3-61.zip' Content type 'application/zip' length 1167407 bytes (1.1 MB) downloaded 1.1 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/nlme_3.1-165.zip' Content type 'application/zip' length 2390023 bytes (2.3 MB) downloaded 2.3 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/survival_3.7-0.zip' Content type 'application/zip' length 7089484 bytes (6.8 MB) downloaded 6.8 MB package ‘MASS’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘MASS’ Warning: restored ‘MASS’ package ‘nlme’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘nlme’ Warning: restored ‘nlme’ package ‘survival’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘survival’ Warning: restored ‘survival’ The downloaded binary packages are in C:\Users\UMASHANKAR\AppData\Local\Temp\Rtmp6XTajY\downloaded_packages Warning messages: 1: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Program Files\R\R-4.4.1\library\00LOCK\MASS\libs\x64\MASS.dll to C:\Program Files\R\R-4.4.1\library\MASS\libs\x64\MASS.dll: Permission denied 2: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Program Files\R\R-4.4.1\library\00LOCK\nlme\libs\x64\nlme.dll to C:\Program Files\R\R-4.4.1\library\nlme\libs\x64\nlme.dll: Permission denied 3: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Program Files\R\R-4.4.1\library\00LOCK\survival\libs\x64\survival.dll to C:\Program Files\R\R-4.4.1\library\survival\libs\x64\survival.dll: Permission denied > devtools::install_github('cole-trapnell-lab/monocle3', force = TRUE) Downloading GitHub repo cole-trapnell-lab/monocle3@HEAD Skipping 29 packages ahead of CRAN: zlibbioc, XVector, SparseArray, S4Arrays, IRanges, S4Vectors, MatrixGenerics, BiocGenerics, GenomeInfoDb, Rhdf5lib, rhdf5filters, DelayedArray, Biobase, sparseMatrixStats, beachmat, DelayedMatrixStats, SummarizedExperiment, GenomicRanges, BiocParallel, SingleCellExperiment, ScaledMatrix, rhdf5, ResidualMatrix, scuttle, BiocSingular, BiocNeighbors, limma, HDF5Array, batchelor Installing 1 packages: GenomeInfoDbData Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES' installing the source package ‘GenomeInfoDbData’ trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz' Content type 'application/gzip' length 12284235 bytes (11.7 MB) downloaded 11.7 MB The downloaded source packages are in ‘C:\Users\UMASHANKAR\AppData\Local\Temp\Rtmp6XTajY\downloaded_packages’ ── R CMD build ────────────────────────────────────────────────────────────── Error: Failed to install 'monocle3' from GitHub: ! System command 'Rcmd.exe' failed In addition: Warning message: In i.p(...) : installation of package ‘GenomeInfoDbData’ had non-zero exit status