Seurat install error #2818
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As the error says, you have an issue with the patchwork package. I'm not sure where you installed patchwork from; the latest version of patchwork is version 1.0.0 while you have version 2.4 installed. You need to fix that to get Seurat loading properly. |
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Hi,
I've got the following error after trying to upgrade to the latest version of Seurat:
The install and session info is below. Any help would be greatly appreciated.
The downloaded binary packages are in
/var/folders/zs/c8q5z27524x284w8_z1y5n6xz5j2wq/T//Rtmpl015cI/downloaded_packages
The downloaded binary packages are in
/var/folders/zs/c8q5z27524x284w8_z1y5n6xz5j2wq/T//Rtmpl015cI/downloaded_packages
Old packages: 'class', 'foreign', 'lattice', 'nlme', 'nnet', 'survival'
Update all/some/none? [a/s/n]: install.packages('Seurat')
Update all/some/none? [a/s/n]: library(Seurat)
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
lattice 0.20-40 0.20-41 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/class_7.3-16.tgz'
Content type 'application/x-gzip' length 95922 bytes (93 KB)
downloaded 93 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/foreign_0.8-76.tgz'
Content type 'application/x-gzip' length 329258 bytes (321 KB)
downloaded 321 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/nlme_3.1-145.tgz'
Content type 'application/x-gzip' length 2382321 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/nnet_7.3-13.tgz'
Content type 'application/x-gzip' length 129105 bytes (126 KB)
downloaded 126 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/survival_3.1-11.tgz'
Content type 'application/x-gzip' length 7851286 bytes (7.5 MB)
downloaded 7.5 MB
The downloaded binary packages are in
/var/folders/zs/c8q5z27524x284w8_z1y5n6xz5j2wq/T//Rtmpl015cI/downloaded_packages
installing the source package ‘lattice’
trying URL 'https://cran.rstudio.com/src/contrib/lattice_0.20-41.tar.gz'
Content type 'application/x-gzip' length 389631 bytes (380 KB)
downloaded 380 KB
** package ‘lattice’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c threeDplot.c -o threeDplot.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o lattice.so init.o threeDplot.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-lattice/00new/lattice/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
The downloaded source packages are in
‘/private/var/folders/zs/c8q5z27524x284w8_z1y5n6xz5j2wq/T/Rtmpl015cI/downloaded_packages’
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] nlme_3.1-145 bitops_1.0-6 RcppAnnoy_0.0.16 RColorBrewer_1.1-2
[5] httr_1.4.1 numDeriv_2020.2-1 tools_3.6.3 R6_2.4.1
[9] irlba_2.3.3 KernSmooth_2.23-16 BiocGenerics_0.32.0 colorspace_1.4-2
[13] sn_1.6-1 npsurv_0.4-0 tidyselect_1.0.0 mnormt_1.5-6
[17] compiler_3.6.3 cli_2.0.2 Biobase_2.46.0 TFisher_0.2.0
[21] sandwich_2.5-2 caTools_1.18.0 scales_1.1.0 lmtest_0.9-37
[25] mvtnorm_1.1-0 ggridges_0.5.2 stringr_1.4.0 digest_0.6.25
[29] pkgconfig_2.0.3 bibtex_0.4.2.2 plotrix_3.7-7 rlang_0.4.5
[33] rstudioapi_0.11 zoo_1.8-8 jsonlite_1.6.1 ica_1.0-2
[37] gtools_3.8.2 dplyr_0.8.5 magrittr_1.5 patchwork_2.4
[41] Matrix_1.2-18 Rcpp_1.0.4 munsell_0.5.0 fansi_0.4.1
[45] ape_5.3 reticulate_1.15 lifecycle_0.2.0 stringi_1.4.6
[49] multcomp_1.4-12 gbRd_0.4-11 MASS_7.3-51.5 gplots_3.0.3
[53] Rtsne_0.15 plyr_1.8.6 grid_3.6.3 parallel_3.6.3
[57] gdata_2.18.0 listenv_0.8.0 ggrepel_0.8.2 crayon_1.3.4
[61] lattice_0.20-41 cowplot_1.0.0 splines_3.6.3 multtest_2.42.0
[65] knitr_1.28 pillar_1.4.3 igraph_1.2.5 future.apply_1.4.0
[69] codetools_0.2-16 stats4_3.6.3 leiden_0.3.3 mutoss_0.1-12
[73] glue_1.4.0 lsei_1.2-0 metap_1.3 BiocManager_1.30.10
[77] vctrs_0.2.4 Rdpack_0.11-1 gtable_0.3.0 RANN_2.6.1
[81] purrr_0.3.3 future_1.16.0 assertthat_0.2.1 ggplot2_3.3.0
[85] xfun_0.12 survival_3.1-11 tibble_3.0.0 cluster_2.1.0
[89] globals_0.12.5 fitdistrplus_1.0-14 TH.data_1.0-10 ellipsis_0.3.0
[93] ROCR_1.0-7
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