I am having issues downloading Bioconductor packages. For every package it says I get the following error:
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/geoffkerr/R/x86_64-pc-linux-gnu-library/4.0/packages/DESeq2’
The downloaded source packages are in
‘/tmp/Rtmp8Vayfz/downloaded_packages’
Installation path not writeable, unable to update packages: mgcv, spatial
Warning messages:
1: In install.packages(...) :
installation of package ‘openssl’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘httr’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘annotate’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘genefilter’ had non-zero exit status
5: In install.packages(...) :
installation of package ‘geneplotter’ had non-zero exit status
6: In install.packages(...) :
installation of package ‘DESeq2’ had non-zero exit status
I've checked to make sure that the directory has read/write privilages, and tried to manually install mgcv, spatial, but still come across this error. The BiocManager::install function is not working for any of the packages that I am trying to download. I've already tried some of the other suggestion mentions such as changing .libPaths() but that did not work. If anyone has any insight that would be great
Here is the session info:
> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8
[6] LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] spatial_7.3-13 mgcv_1.8-34 nlme_3.1-152
loaded via a namespace (and not attached):
[1] Biobase_2.50.0 viridis_0.5.1 tidyr_1.1.3 tidygraph_1.2.0 bit64_4.0.5 viridisLite_0.3.0
[7] splines_4.0.4 ggraph_2.0.5 assertthat_0.2.1 shadowtext_0.0.7 DO.db_2.9 BiocManager_1.30.10
[13] rvcheck_0.1.8 stats4_4.0.4 blob_1.2.1 ggrepel_0.9.1 pillar_1.5.1 RSQLite_2.2.4
[19] lattice_0.20-41 glue_1.4.2 digest_0.6.27 RColorBrewer_1.1-2 polyclip_1.10-0 qvalue_2.22.0
[25] colorspace_2.0-0 cowplot_1.1.1 Matrix_1.3-2 plyr_1.8.6 pkgconfig_2.0.3 purrr_0.3.4
[31] GO.db_3.12.1 scales_1.1.1 tweenr_1.0.1 enrichplot_1.10.2 BiocParallel_1.24.1 ggforce_0.3.3
[37] tibble_3.1.0 generics_0.1.0 farver_2.1.0 IRanges_2.24.1 ggplot2_3.3.3 ellipsis_0.3.1
[43] cachem_1.0.4 BiocGenerics_0.36.0 magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0 DOSE_3.16.0
[49] fansi_0.4.2 MASS_7.3-53.1 tools_4.0.4 data.table_1.14.0 lifecycle_1.0.0 stringr_1.4.0
[55] S4Vectors_0.28.1 munsell_0.5.0 AnnotationDbi_1.52.0 compiler_4.0.4 rlang_0.4.10 grid_4.0.4
[61] igraph_1.2.6 gtable_0.3.0 DBI_1.1.1 reshape2_1.4.4 graphlayouts_0.7.1 R6_2.5.0
[67] gridExtra_2.3 dplyr_1.0.5 fastmap_1.1.0 bit_4.0.4 utf8_1.1.4 fastmatch_1.1-0
[73] fgsea_1.16.0 GOSemSim_2.16.1 stringi_1.5.3 parallel_4.0.4 Rcpp_1.0.6 vctrs_0.3.6
[79] tidyselect_1.1.0 scatterpie_0.1.5
> BiocManager::version()
[1] ‘3.12’
> version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 0.4
year 2021
month 02
day 15
svn rev 80002
language R
version.string R version 4.0.4 (2021-02-15)
nickname Lost Library Book