Error: package or namespace load failed for ‘Seurat’ in loadNamespace

[JayalalKJ]

Hello Seurat people My goal is to load my Seurat object into R studio platform and run Monocle 3 for trajectory analysis. unfortunately, I can't open my Seurat object into the R environment after Loading the Monocle3.

My knowlege is limited for controling versions in R studio.

1. Anyone has developed .yml file to run both Monocle3 and Seurat woriking in conda environment
2. Do you have any tips for olve this--- ggplot compilation issue (See below)

Need help if anyone encountered tis issue before

library(monocle3)
library(Seurat)

Error: package or namespace load failed for ‘Seurat’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘ggplot2’ 3.2.1 is already loaded, but >= 3.3.0 is required

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS

Matrix products: default BLAS/LAPACK: /home/jay/anaconda3/envs/monocle4/lib/libopenblasp-r0.3.7.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=sv_SE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=sv_SE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=sv_SE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] lazyeval_0.2.2 monocle3_0.2.1 SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.0 [5] DelayedArray_0.12.0 BiocParallel_1.20.0 matrixStats_0.55.0 GenomicRanges_1.38.0
[9] GenomeInfoDb_1.22.0 IRanges_2.20.0 S4Vectors_0.24.0 Biobase_2.46.0
[13] BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] bitops_1.0-6 fs_1.3.1 usethis_1.5.1 devtools_2.2.1 RcppAnnoy_0.0.16
[6] RColorBrewer_1.1-2 rprojroot_1.3-2 tools_3.6.1 backports_1.1.5 R6_2.4.1
[11] KernSmooth_2.23-16 colorspace_1.4-1 withr_2.1.2 tidyselect_1.0.0 gridExtra_2.3
[16] prettyunits_1.1.1 processx_3.4.1 curl_4.3 compiler_3.6.1 cli_2.0.1
[21] desc_1.2.0 scales_1.1.0 callr_3.4.1 stringr_1.4.0 digest_0.6.23
[26] XVector_0.26.0 pkgconfig_2.0.3 sessioninfo_1.1.1 rlang_0.4.4 rstudioapi_0.10
[31] dplyr_0.8.4 RCurl_1.98-1.1 magrittr_1.5 GenomeInfoDbData_1.2.2 Matrix_1.2-18
[36] Rcpp_1.0.3 munsell_0.5.0 fansi_0.4.1 viridis_0.5.1 lifecycle_0.1.0
[41] stringi_1.4.3 yaml_2.2.1 MASS_7.3-51.5 zlibbioc_1.32.0 pkgbuild_1.0.6
[46] Rtsne_0.15 plyr_1.8.5 grid_3.6.1 listenv_0.8.0 crayon_1.3.4
[51] lattice_0.20-38 splines_3.6.1 cowplot_1.0.0 knitr_1.27 ps_1.3.0
[56] pillar_1.4.3 future.apply_1.6.0 reshape2_1.4.3 codetools_0.2-16 pkgload_1.0.2
[61] glue_1.3.1 remotes_2.1.0 testthat_2.3.1 gtable_0.3.0 RANN_2.6.1
[66] purrr_0.3.3 future_1.18.0 assertthat_0.2.1 ggplot2_3.3.2 xfun_0.12
[71] survival_3.1-8 viridisLite_0.3.0 tibble_2.1.3 memoise_1.1.0 cluster_2.1.0
[76] globals_0.12.5 fitdistrplus_1.1-1 ellipsis_0.3.0 ROCR_1.0-11

[Nur-Taz]

Have you tried updating/installing ggplot2 3.3.1?

[JayalalKJ]

Resolved it. conda env create -f .yml

1. Copy following codes in to .yml file

name: monocle3 channels:

• r
• ccb-sb
• conda-forge
• bioconda
• defaults dependencies:
• _libgcc_mutex=0.1=conda_forge
• _openmp_mutex=4.5=0_gnu
• _r-mutex=1.0.1=anacondar_1
• binutils_impl_linux-64=2.33.1=h53a641e_8
• binutils_linux-64=2.33.1=h9595d00_16
• bioconductor-annotate=1.64.0=r36_0
• bioconductor-annotationdbi=1.48.0=r36_0
• bioconductor-annotationfilter=1.10.0=r36_0
• bioconductor-annotationforge=1.28.0=r36_0
• bioconductor-batchelor=1.2.1=r36he1b5a44_0
• bioconductor-beachmat=2.2.0=r36he1b5a44_0
• bioconductor-biobase=2.46.0=r36h516909a_0
• bioconductor-biocfilecache=1.10.0=r36_0
• bioconductor-biocgenerics=0.32.0=r36_0
• bioconductor-biocneighbors=1.4.0=r36he1b5a44_0
• bioconductor-biocparallel=1.20.0=r36he1b5a44_0
• bioconductor-biocsingular=1.2.0=r36he1b5a44_0
• bioconductor-biomart=2.42.0=r36_0
• bioconductor-biostrings=2.54.0=r36h516909a_0
• bioconductor-biovizbase=1.34.0=r36h516909a_0
• bioconductor-bsgenome=1.54.0=r36_0
• bioconductor-category=2.52.0=r36_0
• bioconductor-complexheatmap=2.2.0=r36_0
• bioconductor-delayedarray=0.12.0=r36h516909a_0
• bioconductor-delayedmatrixstats=1.8.0=r36_0
• bioconductor-deseq2=1.26.0=r36he1b5a44_0
• bioconductor-diffbind=2.14.0=r36he1b5a44_0
• bioconductor-edger=3.28.0=r36he1b5a44_0
• bioconductor-ensdb.hsapiens.v75=2.99.0=r36_6
• bioconductor-ensembldb=2.10.0=r36_0
• bioconductor-genefilter=1.68.0=r36hc99cbb1_0
• bioconductor-geneplotter=1.64.0=r36_0
• bioconductor-genomeinfodb=1.22.0=r36_0
• bioconductor-genomeinfodbdata=1.2.2=r36_0
• bioconductor-genomicalignments=1.22.0=r36h516909a_0
• bioconductor-genomicfeatures=1.38.0=r36_0
• bioconductor-genomicinteractions=1.20.0=r36_0
• bioconductor-genomicranges=1.38.0=r36h516909a_0
• bioconductor-ggbio=1.34.0=r36_0
• bioconductor-go.db=3.10.0=r36_0
• bioconductor-gostats=2.52.0=r36_0
• bioconductor-graph=1.64.0=r36h516909a_0
• bioconductor-gseabase=1.48.0=r36_0
• bioconductor-gtrellis=1.18.0=r36_0
• bioconductor-gviz=1.30.0=r36_0
• bioconductor-hdf5array=1.14.0=r36h516909a_0
• bioconductor-homo.sapiens=1.3.1=r36_7
• bioconductor-interactionset=1.14.0=r36he1b5a44_0
• bioconductor-iranges=2.20.0=r36h516909a_0
• bioconductor-keggrest=1.26.0=r36_0
• bioconductor-limma=3.42.0=r36h516909a_0
• bioconductor-org.hs.eg.db=3.10.0=r36_0
• bioconductor-organismdbi=1.28.0=r36_0
• bioconductor-pcamethods=1.78.0=r36he1b5a44_0
• bioconductor-protgenerics=1.18.0=r36_0
• bioconductor-rbgl=1.62.1=r36he1b5a44_0
• bioconductor-rgraphviz=2.30.0=r36he1b5a44_0
• bioconductor-rhdf5=2.30.0=r36he1b5a44_0
• bioconductor-rhdf5lib=1.8.0=r36h516909a_0
• bioconductor-rhtslib=1.18.0=r36hdb70ac9_1
• bioconductor-rsamtools=2.2.0=r36he1b5a44_0
• bioconductor-rtracklayer=1.46.0=r36h516909a_0
• bioconductor-s4vectors=0.24.0=r36h516909a_0
• bioconductor-scater=1.14.0=r36he1b5a44_0
• bioconductor-shortread=1.44.0=r36he1b5a44_0
• bioconductor-singlecellexperiment=1.8.0=r36_0
• bioconductor-somaticsignatures=2.22.0=r36_0
• bioconductor-summarizedexperiment=1.16.0=r36_0
• bioconductor-systempiper=1.20.0=r36_0
• bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2=r36_7
• bioconductor-variantannotation=1.32.0=r36h516909a_0
• bioconductor-viper=1.20.0=r36_0
• bioconductor-xvector=0.26.0=r36h516909a_0
• bioconductor-yapsa=1.12.0=r36_0
• bioconductor-zlibbioc=1.32.0=r36h516909a_0
• boost-cpp=1.70.0=ha2d47e9_1
• bwidget=1.9.14=0
• bzip2=1.0.8=h516909a_2
• ca-certificates=2019.11.28=hecc5488_0
• cairo=1.16.0=h18b612c_1001
• certifi=2019.11.28=py37hc8dfbb8_1
• cfitsio=3.470=hb60a0a2_2
• colormath=3.0.0=py_2
• curl=7.68.0=hf8cf82a_0
• cyrus-sasl=2.1.27=he38ecfd_0
• dbus=1.13.6=he372182_0
• decorator=4.4.1=py_0
• expat=2.2.9=he1b5a44_2
• font-ttf-dejavu-sans-mono=2.37=hab24e00_0
• font-ttf-inconsolata=2.001=hab24e00_0
• font-ttf-source-code-pro=2.030=hab24e00_0
• font-ttf-ubuntu=0.83=hab24e00_0
• fontconfig=2.13.1=he4413a7_1000
• fonts-anaconda=1=h8fa9717_0
• freetype=2.10.0=he983fc9_1
• freexl=1.0.5=h14c3975_1002
• gcc_impl_linux-64=7.3.0=hd420e75_5
• gcc_linux-64=7.3.0=h553295d_16
• geos=3.7.2=he1b5a44_2
• geotiff=1.5.1=h560c3f3_2
• gettext=0.19.8.1=hc5be6a0_1002
• gfortran_impl_linux-64=7.3.0=hdf63c60_5
• gfortran_linux-64=7.3.0=h553295d_16
• giflib=5.1.7=h516909a_1
• glib=2.58.3=py37h6f030ca_1002
• gmp=6.2.0=he1b5a44_1
• graphite2=1.3.13=hf484d3e_1000
• gsl=2.5=h294904e_1
• gst-plugins-base=1.14.5=h0935bb2_1
• gstreamer=1.14.5=h36ae1b5_1
• gxx_impl_linux-64=7.3.0=hdf63c60_5
• gxx_linux-64=7.3.0=h553295d_16
• harfbuzz=1.8.8=hffaf4a1_0
• hdf4=4.2.13=hf30be14_1003
• hdf5=1.10.5=nompi_h3c11f04_1104
• icu=58.2=hf484d3e_1000
• jpeg=9c=h14c3975_1001
• json-c=0.13.1=h14c3975_1001
• kealib=1.4.12=hec59c27_0
• krb5=1.16.4=h2fd8d38_0
• ld_impl_linux-64=2.33.1=h53a641e_8
• libblas=3.8.0=14_openblas
• libcblas=3.8.0=14_openblas
• libcurl=7.68.0=hda55be3_0
• libdap4=3.20.4=hd3bb157_0
• libedit=3.1.20170329=hf8c457e_1001
• libffi=3.2.1=he1b5a44_1006
• libgcc-ng=9.2.0=h24d8f2e_2
• libgdal=2.4.2=h524de44_5
• libgfortran-ng=7.3.0=hdf63c60_5
• libgomp=9.2.0=h24d8f2e_2
• libiconv=1.15=h516909a_1005
• libkml=1.3.0=h4fcabce_1010
• liblapack=3.8.0=14_openblas
• libnetcdf=4.6.2=h303dfb8_1003
• libntlm=1.4=h516909a_1002
• libopenblas=0.3.7=h5ec1e0e_6
• libpng=1.6.37=hed695b0_0
• libpq=11.5=hd9ab2ff_1
• libspatialite=4.3.0a=he1bb1e1_1029
• libssh2=1.8.2=h22169c7_2
• libstdcxx-ng=9.2.0=hdf63c60_2
• libtiff=4.1.0=hc3755c2_3
• libuuid=2.32.1=h14c3975_1000
• libxcb=1.13=h14c3975_1002
• libxml2=2.9.9=h13577e0_2
• lz4-c=1.8.3=he1b5a44_1001
• make=4.2.1=h14c3975_2004
• mpfr=4.0.2=he80fd80_0
• ncurses=6.1=hf484d3e_1002
• networkx=2.4=py_0
• numpy=1.18.1=py37h95a1406_0
• openjdk=8.0.192=h14c3975_1003
• openjpeg=2.3.1=h981e76c_3
• openssl=1.1.1f=h516909a_0
• pandoc=2.9.1.1=0
• pango=1.40.14=he752989_2
• pcre=8.43=he1b5a44_0
• pip=20.0.2=py_2
• pixman=0.38.0=h516909a_1003
• poppler=0.67.0=h14e79db_8
• poppler-data=0.4.9=1
• postgresql=11.5=hc63931a_1
• proj4=6.1.0=he751ad9_2
• pthread-stubs=0.4=h14c3975_1001
• python=3.7.6=h357f687_2
• python_abi=3.7=1_cp37m
• qt=5.6.3=h8bf5577_3
• r-acepack=1.4.1=r36h9bbef5b_1004
• r-amap=0.8_18=r36h6786f55_0
• r-askpass=1.1=r36hcdcec82_1
• r-assertthat=0.2.1=r36h6115d3f_1
• r-backports=1.1.5=r36hcdcec82_0
• r-base=3.6.1=h8900bf8_2
• r-base64enc=0.1_3=r36hcdcec82_1003
• r-base64url=1.4=r36hcdcec82_1003
• r-batchtools=0.9.12=r36hcdcec82_0
• r-beeswarm=0.2.3=r36h6115d3f_1002
• r-bh=1.72.0_3=r36h6115d3f_0
• r-bibtex=0.4.2.2=r36hcdcec82_0
• r-biocmanager=1.30.10=r36h6115d3f_0
• r-bit=1.1_15.1=r36hcdcec82_0
• r-bit64=0.9_7=r36hcdcec82_1001
• r-bitops=1.0_6=r36hcdcec82_1003
• r-blob=1.2.1=r36h6115d3f_0
• r-boot=1.3_24=r36h6115d3f_0
• r-brew=1.0_6=r36h6115d3f_1002
• r-broom=0.5.4=r36h6115d3f_0
• r-cairo=1.5_10=r36hcdcec82_1
• r-callr=3.4.1=r36h6115d3f_0
• r-catools=1.18.0=r36h0357c0b_0
• r-cellranger=1.1.0=r36h6115d3f_1002
• r-checkmate=2.0.0=r36hcdcec82_0
• r-circlize=0.4.8=r36h6115d3f_0
• r-class=7.3_15=r36hcdcec82_1001
• r-classint=0.4_2=r36h9bbef5b_0
• r-cli=2.0.1=r36h6115d3f_0
• r-clipr=0.7.0=r36h6115d3f_0
• r-clisymbols=1.2.0=r36h6115d3f_1002
• r-clue=0.3_57=r36h516909a_1
• r-cluster=2.1.0=r36h9bbef5b_2
• r-coda=0.19_3=r36h6115d3f_1
• r-codetools=0.2_16=r36h6115d3f_1001
• r-colorspace=1.4_1=r36hcdcec82_1
• r-commonmark=1.7=r36hcdcec82_1001
• r-config=0.3=r36h6115d3f_1002
• r-corrplot=0.84=r36_1002
• r-covr=3.4.0=r36h0357c0b_0
• r-cowplot=1.0.0=r36h6115d3f_1
• r-crayon=1.3.4=r36h6115d3f_1002
• r-crosstalk=1.0.0=r36h6115d3f_1002
• r-curl=4.3=r36hcdcec82_0
• r-data.table=1.12.8=r36hcdcec82_0
• r-dbi=1.1.0=r36h6115d3f_0
• r-dbplyr=1.4.2=r36h6115d3f_1
• r-deldir=0.1_25=r36h9bbef5b_0
• r-dendextend=1.13.2=r36h6115d3f_0
• r-deoptimr=1.0_8=r36h6115d3f_1002
• r-desc=1.2.0=r36h6115d3f_1002
• r-devtools=2.2.1=r36h6115d3f_0
• r-dichromat=2.0_0=r36_2001
• r-digest=0.6.23=r36h0357c0b_0
• r-diptest=0.75_7=r36hcdcec82_1002
• r-doparallel=1.0.15=r36h6115d3f_0
• r-dplyr=0.8.4=r36h0357c0b_0
• r-dqrng=0.2.1=r36h0357c0b_1
• r-dt=0.12=r36h6115d3f_0
• r-e1071=1.7_3=r36h0357c0b_0
• r-ellipsis=0.3.0=r36hcdcec82_0
• r-evaluate=0.14=r36h6115d3f_1
• r-expm=0.999_4=r36hbf399a0_3
• r-fansi=0.4.1=r36hcdcec82_0
• r-farver=2.0.3=r36h0357c0b_0
• r-fastmap=1.0.1=r36h0357c0b_0
• r-flexmix=2.3_15=r36h6115d3f_1
• r-fnn=1.1.3=r36h0357c0b_1
• r-forcats=0.4.0=r36h6115d3f_1
• r-foreach=1.4.7=r36h6115d3f_0
• r-foreign=0.8_75=r36hcdcec82_0
• r-forge=0.2.0=r36h6115d3f_1
• r-formatr=1.7=r36h6115d3f_1
• r-formula=1.2_3=r36h6115d3f_1002
• r-fpc=2.2_5=r36h6115d3f_0
• r-fs=1.3.1=r36h0357c0b_1
• r-furrr=0.1.0=r36h6115d3f_1001
• r-futile.logger=1.4.3=r36h6115d3f_1002
• r-futile.options=1.0.1=r36h6115d3f_1001
• r-future=1.16.0=r36h6115d3f_0
• r-gdata=2.18.0=r36h6115d3f_1002
• r-generics=0.0.2=r36h6115d3f_1002
• r-getoptlong=0.1.8=r36h6115d3f_0
• r-ggally=1.4.0=r36h6115d3f_1001
• r-ggbeeswarm=0.6.0=r36_1002
• r-ggplot2=3.2.1=r36h6115d3f_0
• r-ggrastr=0.1.7=r36_1000
• r-ggrepel=0.8.1=r36h0357c0b_1
• r-ggsci=2.9=r36h6115d3f_1002
• r-gh=1.1.0=r36h6115d3f_0
• r-git2r=0.26.1=r36h5ca76e2_1
• r-globaloptions=0.1.1=r36_0
• r-globals=0.12.5=r36h6115d3f_0
• r-glue=1.3.1=r36hcdcec82_1
• r-gmodels=2.18.1=r36_1002
• r-gplots=3.0.1.2=r36h6115d3f_0
• r-gridbase=0.4_7=r36h6115d3f_1002
• r-gridextra=2.3=r36h6115d3f_1002
• r-grr=0.9.5=r36h0357c0b_1003
• r-gtable=0.3.0=r36h6115d3f_2
• r-gtools=3.8.1=r36hcdcec82_1003
• r-haven=2.2.0=r36hde08347_0
• r-hexbin=1.28.1=r36h9bbef5b_0
• r-highr=0.8=r36h6115d3f_1
• r-hmisc=4.3_0=r36h9bbef5b_0
• r-hms=0.5.3=r36h6115d3f_0
• r-htmltable=1.13.3=r36h6115d3f_0
• r-htmltools=0.4.0=r36h0357c0b_0
• r-htmlwidgets=1.5.1=r36h6115d3f_0
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• r-httr=1.4.1=r36h6115d3f_1
• r-hunspell=3.0=r36h0357c0b_1001
• r-hwriter=1.3.2=r36h6115d3f_1002
• r-igraph=1.2.4.2=r36h6786f55_0
• r-ini=0.3.1=r36h6115d3f_1002
• r-irlba=2.3.3=r36h7fa42b6_2
• r-iterators=1.0.12=r36h6115d3f_0
• r-jpeg=0.1_8.1=r36hcdcec82_0
• r-jsonlite=1.6.1=r36hcdcec82_0
• r-kableextra=1.1.0=r36h6115d3f_1
• r-kernlab=0.9_29=r36h0357c0b_0
• r-kernsmooth=2.23_16=r36h9bbef5b_0
• r-knitr=1.27=r36h6115d3f_0
• r-labeling=0.3=r36h6115d3f_1002
• r-lambda.r=1.2.4=r36h6115d3f_0
• r-later=1.0.0=r36h0357c0b_0
• r-lattice=0.20_38=r36hcdcec82_1002
• r-latticeextra=0.6_29=r36h6115d3f_0
• r-lazyeval=0.2.2=r36hcdcec82_1
• r-learnbayes=2.15.1=r36h6115d3f_1001
• r-leidenbase=0.1.0=r36hc99cbb1_0
• r-lifecycle=0.1.0=r36h6115d3f_0
• r-limsolve=1.5.6=r36h9bbef5b_0
• r-listenv=0.8.0=r36h6115d3f_0
• r-lmtest=0.9_37=r36h9bbef5b_2
• r-locfit=1.5_9.1=r36h516909a_1004
• r-lpsolve=5.6.15=r36hcdcec82_0
• r-lsei=1.2_0=r36h6e990d7_1004
• r-lubridate=1.7.4=r36h0357c0b_1002
• r-magrittr=1.5=r36h6115d3f_1002
• r-markdown=1.1=r36hcdcec82_0
• r-mass=7.3_51.5=r36hcdcec82_0
• r-matrix=1.2_18=r36hcdcec82_0
• r-matrix.utils=0.9.8=r36h6115d3f_0
• r-matrixstats=0.55.0=r36hcdcec82_0
• r-mclust=5.4.5=r36h9bbef5b_0
• r-memoise=1.1.0=r36h6115d3f_1003
• r-mgcv=1.8_31=r36hcdcec82_0
• r-mime=0.9=r36hcdcec82_0
• r-miniui=0.1.1.1=r36h6115d3f_1001
• r-mixtools=1.1.0=r36hcdcec82_1003
• r-modelr=0.1.5=r36h6115d3f_0
• r-modeltools=0.2_22=r36h6115d3f_1002
• r-mongolite=2.1.0=r36hcdcec82_1
• r-monocle3=0.2.1=r36hc9558a2_0
• r-munsell=0.5.0=r36h6115d3f_1002
• r-nlme=3.1_144=r36h9bbef5b_0
• r-nmf=0.21.0=r36h0357c0b_1003
• r-nnet=7.3_12=r36hcdcec82_1003
• r-odbc=1.2.2=r36h0357c0b_0
• r-openssl=1.4.1=r36h9c8475f_0
• r-packrat=0.5.0=r36h6115d3f_1001
• r-patchwork=1.0.0=r36h6115d3f_0
• r-pbapply=1.4_2=r36h6115d3f_0
• r-pbmcapply=1.5.0=r36hcdcec82_0
• r-pheatmap=1.0.12=r36h6115d3f_1
• r-pillar=1.4.3=r36h6115d3f_0
• r-pkgbuild=1.0.6=r36h6115d3f_0
• r-pkgconfig=2.0.3=r36h6115d3f_0
• r-pkgload=1.0.2=r36h0357c0b_1001
• r-pkgmaker=0.31=r36h6115d3f_0
• r-pki=0.1_5.1=r36hcdcec82_1003
• r-plogr=0.2.0=r36h6115d3f_1002
• r-plotly=4.9.2=r36h6115d3f_0
• r-plyr=1.8.5=r36h0357c0b_0
• r-pmcmr=4.3=r36h6115d3f_1002
• r-png=0.1_7=r36hcdcec82_1003
• r-prabclus=2.3_2=r36h6115d3f_0
• r-praise=1.0.0=r36h6115d3f_1003
• r-prettyunits=1.1.1=r36h6115d3f_0
• r-processx=3.4.1=r36hcdcec82_0
• r-profvis=0.3.6=r36hcdcec82_1
• r-progress=1.2.2=r36h6115d3f_1
• r-promises=1.1.0=r36h0357c0b_0
• r-proxy=0.4_23=r36hcdcec82_1
• r-pryr=0.1.4=r36h0357c0b_1003
• r-ps=1.3.0=r36hcdcec82_1001
• r-pscl=1.5.5=r36h516909a_0
• r-purrr=0.3.3=r36hcdcec82_0
• r-quadprog=1.5_8=r36h9bbef5b_0
• r-r.methodss3=1.7.1=r36h6115d3f_1002
• r-r.oo=1.23.0=r36h6115d3f_0
• r-r.utils=2.9.2=r36h6115d3f_0
• r-r2d3=0.2.3=r36h6115d3f_1001
• r-r6=2.4.1=r36h6115d3f_0
• r-rann=2.6.1=r36h0357c0b_1
• r-rappdirs=0.3.1=r36hcdcec82_1003
• r-raster=3.0_12=r36h0357c0b_0
• r-rcmdcheck=1.3.3=r36h6115d3f_2
• r-rcolorbrewer=1.1_2=r36h6115d3f_1002
• r-rcpp=1.0.3=r36h0357c0b_0
• r-rcppannoy=0.0.16=r36h0357c0b_0
• r-rcpparmadillo=0.9.800.4.0=r36h0357c0b_0
• r-rcppeigen=0.3.3.7.0=r36h0357c0b_0
• r-rcpphnsw=0.2.0=r36h0357c0b_0
• r-rcppparallel=5.0.0=r36h0357c0b_0
• r-rcppprogress=0.4.2=r36h6115d3f_0
• r-rcurl=1.98_1.1=r36hcdcec82_0
• r-readr=1.3.1=r36h0357c0b_1002
• r-readxl=1.3.1=r36h0357c0b_2
• r-registry=0.5_1=r36h6115d3f_1
• r-rematch=1.0.1=r36h6115d3f_1002
• r-remotes=2.1.0=r36h6115d3f_1
• r-reprex=0.3.0=r36h6115d3f_1
• r-reshape=0.8.8=r36hcdcec82_1
• r-reshape2=1.4.3=r36h0357c0b_1004
• r-reticulate=1.14=r36h0357c0b_0
• r-rex=1.1.2=r36h6115d3f_1001
• r-rhpcblasctl=0.20_17=r36hcdcec82_0
• r-rjava=0.9_11=r36hcdcec82_1
• r-rjdbc=0.2_7.1=r36h6115d3f_0
• r-rjson=0.2.20=r36h0357c0b_1001
• r-rjsonio=1.3_1.4=r36h0357c0b_0
• r-rlang=0.4.4=r36hcdcec82_0
• r-rmarkdown=2.1=r36h6115d3f_0
• r-rngtools=1.5=r36h6115d3f_0
• r-robustbase=0.93_5=r36h9bbef5b_2
• r-roxygen2=7.0.2=r36h0357c0b_0
• r-rpart=4.1_15=r36hcdcec82_1
• r-rprojroot=1.3_2=r36h6115d3f_1002
• r-rsample=0.0.5=r36h6115d3f_0
• r-rsconnect=0.8.16=r36h6115d3f_0
• r-rspectra=0.16_0=r36h0357c0b_0
• r-rsqlite=2.1.5=r36h0357c0b_0
• r-rstudioapi=0.10=r36h6115d3f_2
• r-rsvd=1.0.3=r36h6115d3f_0
• r-rtsne=0.15=r36he1b5a44_1
• r-rversions=2.0.1=r36h6115d3f_0
• r-rvest=0.3.5=r36h6115d3f_0
• r-scales=1.1.0=r36h6115d3f_0
• r-segmented=1.1_0=r36h6115d3f_0
• r-selectr=0.4_2=r36h6115d3f_0
• r-sessioninfo=1.1.1=r36h6115d3f_1001
• r-sf=0.7_6=r36h474ac88_3
• r-shape=1.4.4=r36_1002
• r-shiny=1.4.0=r36h6115d3f_0
• r-sitmo=2.0.1=r36h0357c0b_1
• r-slam=0.1_47=r36hcdcec82_0
• r-snow=0.4_3=r36h6115d3f_1001
• r-sourcetools=0.1.7=r36he1b5a44_1001
• r-sp=1.4_1=r36hcdcec82_0
• r-sparklyr=1.1.0=r36h6115d3f_0
• r-spdata=0.3.3=r36h6115d3f_0
• r-spdep=1.1_3=r36hc57f18f_1
• r-speedglm=0.3_2=r36_1002
• r-spelling=2.1=r36h6115d3f_1
• r-stringi=1.4.3=r36h29659fb_0
• r-stringr=1.4.0=r36h6115d3f_1
• r-survival=3.1_8=r36hcdcec82_0
• r-sys=3.3=r36hcdcec82_0
• r-testthat=2.3.1=r36h0357c0b_0
• r-tibble=2.1.3=r36hcdcec82_1
• r-tidyr=1.0.2=r36h0357c0b_0
• r-tidyselect=1.0.0=r36h6115d3f_0
• r-tidyverse=1.3.0=r36h6115d3f_1
• r-tinytex=0.19=r36h6115d3f_0
• r-umap=0.2.4.1=r36h0357c0b_0
• r-units=0.6_6=r36h0357c0b_0
• r-usethis=1.5.1=r36h6115d3f_1
• r-utf8=1.1.4=r36hcdcec82_1001
• r-uwot=0.1.8=r36h0357c0b_0
• r-vctrs=0.2.2=r36hcdcec82_0
• r-vipor=0.4.5=r36h6115d3f_1002
• r-viridis=0.5.1=r36h6115d3f_1003
• r-viridislite=0.3.0=r36h6115d3f_1002
• r-webshot=0.5.2=r36h6115d3f_0
• r-whisker=0.4=r36h6115d3f_0
• r-withr=2.1.2=r36h6115d3f_1001
• r-xfun=0.12=r36h6115d3f_0
• r-xml=3.98_1.20=r36hcdcec82_1
• r-xml2=1.2.2=r36h0357c0b_0
• r-xopen=1.0.0=r36h6115d3f_1002
• r-xtable=1.8_4=r36h6115d3f_2
• r-yaml=2.2.1=r36hcdcec82_0
• r-zeallot=0.1.0=r36h6115d3f_1001
• r-zoo=1.8_7=r36hcdcec82_0
• readline=8.0=hf8c457e_0
• rstudio=1.1.456=h6bb024c_1
• sed=4.7=h1bed415_1000
• setuptools=45.1.0=py37_0
• spectra=0.0.11=py_1
• sqlite=3.30.1=hcee41ef_0
• texlive-core=20180414=hc8d0b01_0
• tk=8.6.10=hed695b0_0
• tktable=2.10=h555a92e_3
• tzcode=2019a=h516909a_1002
• udunits2=2.2.27.6=h4e0c4b3_1001
• unixodbc=2.3.7=h227dcee_1000
• wheel=0.34.2=py_1
• xerces-c=3.2.2=hea5cb30_1003
• xorg-kbproto=1.0.7=h14c3975_1002
• xorg-libice=1.0.10=h516909a_0
• xorg-libsm=1.2.3=h84519dc_1000
• xorg-libx11=1.6.9=h516909a_0
• xorg-libxau=1.0.9=h14c3975_0
• xorg-libxdmcp=1.1.3=h516909a_0
• xorg-libxext=1.3.4=h516909a_0
• xorg-libxrender=0.9.10=h516909a_1002
• xorg-libxt=1.2.0=h516909a_0
• xorg-renderproto=0.11.1=h14c3975_1002
• xorg-xextproto=7.3.0=h14c3975_1002
• xorg-xproto=7.0.31=h14c3975_1007
• xz=5.2.4=h14c3975_1001
• zlib=1.2.11=h516909a_1006
• zstd=1.4.4=h3b9ef0a_1

• pip:

  • absl-py==0.9.0
  • astor==0.8.1
  • cachetools==4.0.0
  • chardet==3.0.4
  • gast==0.2.2
  • google-auth==1.10.1
  • google-auth-oauthlib==0.4.1
  • google-pasta==0.1.8
  • grpcio==1.26.0
  • h5py==2.10.0
  • idna==2.8
  • keras-applications==1.0.8
  • keras-preprocessing==1.1.0
  • markdown==3.1.1
  • oauthlib==3.1.0
  • opt-einsum==3.1.0
  • protobuf==3.11.2
  • pyasn1==0.4.8
  • pyasn1-modules==0.2.8
  • requests==2.22.0
  • requests-oauthlib==1.3.0
  • rsa==4.0
  • scipy==1.4.1
  • six==1.14.0
  • tensorboard==2.1.0
  • tensorflow==2.1.0
  • tensorflow-estimator==2.1.0
  • termcolor==1.1.0
  • urllib3==1.25.7
  • werkzeug==0.16.0
  • wrapt==1.11.2 prefix: /home/bq_mkohnen/my-envs/kidneyenv
  2. install with following command -> conda env create -f .yml 3. then, open rstudio from monocle 3 folder and install seurat3 from install packages (CRAN)