Entering edit mode
Hi everybody, I didn't use the waterfall function from GenVisR for several months and while re-using it now the mainDropMut option did not work anymore (no error messages were displayed). If set to 'TRUE' the legend still displays all mutation types (but I do want to discard the unused ones). As a first step I wanted to update to the most recent version, so I had to install R 4.2.0 in order to obtain Bioconductor 3.16. While both installations worked well, the installation of GenVisR does not work now. As stated in the output below, there seems to be an error while trying to access the associated packages.
I'm using an M1 chip and had some problems when I first installed RStudio at the end of last year, however it worked out after an updated version was released. I also tried to use it on my Windows 10 computer, but the mainDropMut option does not work either. I'd be grateful for some help.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenVisR")
Bioconductor version 3.16 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)
Installing package(s) 'GenVisR'
also installing the dependencies ‘GenomicAlignments’, ‘DelayedArray’, ‘Biobase’, ‘S4Vectors’, ‘KEGGREST’, ‘XVector’, ‘BiocIO’, ‘rtracklayer’, ‘zlibbioc’, ‘BiocParallel’, ‘Rhtslib’, ‘SummarizedExperiment’, ‘AnnotationDbi’, ‘biomaRt’, ‘Biostrings’, ‘GenomicFeatures’, ‘GenomicRanges’, ‘IRanges’, ‘Rsamtools’, ‘BSgenome’, ‘GenomeInfoDb’, ‘VariantAnnotation’
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Packages which are only available in source form, and may need
compilation of C/C++/Fortran: ‘GenomicAlignments’ ‘DelayedArray’
‘Biobase’ ‘S4Vectors’ ‘XVector’ ‘rtracklayer’ ‘zlibbioc’
‘BiocParallel’ ‘Rhtslib’ ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’
‘Rsamtools’ ‘VariantAnnotation’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source packages ‘GenomicAlignments’, ‘DelayedArray’, ‘Biobase’, ‘S4Vectors’, ‘KEGGREST’, ‘XVector’, ‘BiocIO’, ‘rtracklayer’, ‘zlibbioc’, ‘BiocParallel’, ‘Rhtslib’, ‘SummarizedExperiment’, ‘AnnotationDbi’, ‘biomaRt’, ‘Biostrings’, ‘GenomicFeatures’, ‘GenomicRanges’, ‘IRanges’, ‘Rsamtools’, ‘BSgenome’, ‘GenomeInfoDb’, ‘VariantAnnotation’, ‘GenVisR’
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/GenomicAlignments_1.33.0.tar.gz'
Content type 'application/x-gzip' length 2220015 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/DelayedArray_0.23.0.tar.gz'
Content type 'application/x-gzip' length 642838 bytes (627 KB)
==================================================
downloaded 627 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Biobase_2.57.1.tar.gz'
Content type 'application/x-gzip' length 1550877 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/S4Vectors_0.35.0.tar.gz'
Content type 'application/x-gzip' length 618625 bytes (604 KB)
==================================================
downloaded 604 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/KEGGREST_1.37.0.tar.gz'
Content type 'application/x-gzip' length 25780 bytes (25 KB)
==================================================
downloaded 25 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/XVector_0.37.0.tar.gz'
Content type 'application/x-gzip' length 67772 bytes (66 KB)
==================================================
downloaded 66 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/BiocIO_1.7.1.tar.gz'
Content type 'application/x-gzip' length 229258 bytes (223 KB)
==================================================
downloaded 223 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/rtracklayer_1.57.0.tar.gz'
Content type 'application/x-gzip' length 4017644 bytes (3.8 MB)
==================================================
downloaded 3.8 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/zlibbioc_1.43.0.tar.gz'
Content type 'application/x-gzip' length 214244 bytes (209 KB)
==================================================
downloaded 209 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/BiocParallel_1.31.6.tar.gz'
Content type 'application/x-gzip' length 896449 bytes (875 KB)
==================================================
downloaded 875 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Rhtslib_1.99.5.tar.gz'
Content type 'application/x-gzip' length 4581330 bytes (4.4 MB)
==================================================
downloaded 4.4 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/SummarizedExperiment_1.27.1.tar.gz'
Content type 'application/x-gzip' length 1525091 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/AnnotationDbi_1.59.1.tar.gz'
Content type 'application/x-gzip' length 4329390 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/biomaRt_2.53.2.tar.gz'
Content type 'application/x-gzip' length 668119 bytes (652 KB)
==================================================
downloaded 652 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Biostrings_2.65.0.tar.gz'
Content type 'application/x-gzip' length 12424141 bytes (11.8 MB)
==================================================
downloaded 11.8 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/GenomicFeatures_1.49.5.tar.gz'
Content type 'application/x-gzip' length 1183660 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/GenomicRanges_1.49.0.tar.gz'
Content type 'application/x-gzip' length 1121418 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/IRanges_2.31.0.tar.gz'
Content type 'application/x-gzip' length 455718 bytes (445 KB)
==================================================
downloaded 445 KB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Rsamtools_2.13.3.tar.gz'
Content type 'application/x-gzip' length 2870299 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/BSgenome_1.65.1.tar.gz'
Content type 'application/x-gzip' length 5904805 bytes (5.6 MB)
==================================================
downloaded 5.6 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/GenomeInfoDb_1.33.3.tar.gz'
Content type 'application/x-gzip' length 3453431 bytes (3.3 MB)
==================================================
downloaded 3.3 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/VariantAnnotation_1.43.2.tar.gz'
Content type 'application/x-gzip' length 1726698 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/GenVisR_1.29.0.tar.gz'
Content type 'application/x-gzip' length 9364670 bytes (8.9 MB)
==================================================
downloaded 8.9 MB
configure: creating ./config.status
config.status: creating src/Makevars
checking for gcc... gcc
checking whether the C compiler works... no
The downloaded source packages are in
‘/private/var/folders/c_/l7vmby0n2xn04dwn723k1zh80000gp/T/RtmpiKmrK8/downloaded_packages’
There were 23 warnings (use warnings() to see them)
sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.3.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.18 ggplot2_3.3.6
loaded via a namespace (and not attached):
[1] magrittr_2.0.3 tidyselect_1.1.2 munsell_0.5.0 colorspace_2.0-3
[5] R6_2.5.1 rlang_1.0.2 fansi_1.0.3 dplyr_1.0.9
[9] tools_4.2.0 grid_4.2.0 gtable_0.3.0 utf8_1.2.2
[13] cli_3.3.0 DBI_1.1.2 withr_2.5.0 ellipsis_0.3.2
[17] assertthat_0.2.1 tibble_3.1.7 lifecycle_1.0.1 crayon_1.5.1
[21] purrr_0.3.4 vctrs_0.4.1 glue_1.6.2 compiler_4.2.0
[25] pillar_1.7.0 generics_0.1.2 scales_1.2.0 pkgconfig_2.0.3
