work_env-building.md
Table of Contents
#TODO Make sure this doc is at parity with the doc in 2023_expression
#DONE Add in the creation of the htseq_env and/or gff3_env
#TODO Move section on additions to Trinity_env to the main notebook for building Trinity_env (elsewhere in repo)
Code: Get situated, make directory for featureCounts work, etc.
#!/bin/bash
#DONTRUN #CONTINUE
grabnode # 16, etc.
if [[ "${CONDA_DEFAULT_ENV}" != "base" ]]; then
conda deactivate
fi
Trinity_env
mkdir 2023-0215/
transcriptome &&
{
cd "results/2023-0215/" \
|| echo "cd'ing failed; check on this..."
}Code: Install featureCounts in Trinity_env
#!/bin/bash
#DONTRUN #CONTINUE
mamba install -c bioconda subreadPrinted: Install featureCounts in Trinity_env
❯ mamba install -c bioconda subread
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|/
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.1.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['subread']
pkgs/r/linux-64 No change
pkgs/r/noarch No change
pkgs/main/noarch 819.1kB @ 2.6MB/s 0.3s
bioconda/noarch 4.2MB @ 2.7MB/s 1.9s
pkgs/main/linux-64 5.2MB @ 2.8MB/s 5.3s
bioconda/linux-64 4.5MB @ 806.0kB/s 6.6s
Pinned packages:
- python 3.10.*
Transaction
Prefix: /home/kalavatt/miniconda3/envs/Trinity_env
Updating specs:
- subread
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
──────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────
+ subread 2.0.3 h7132678_1 bioconda/linux-64 25MB
Summary:
Install: 1 packages
Total download: 25MB
──────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
subread 24.7MB @ 35.9MB/s 1.1s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: doneContains programs for 4tU-seq analyses
Code: Create a new environment, expression_env: Create the environment on KrisMac
#!/bin/bash
#DONTRUN #CONTINUE
if [[ "${CONDA_DEFAULT_ENV}" != "base" ]]; then
conda deactivate
fi
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
mamba create \
-n expression_env \
-c conda-forge \
r-base \
r-tidyverse \
mamba
source activate expression_env
mamba install -c bioconda bioconductor-deseq2
mamba install -c bioconda subread
mamba install \
-c bioconda \
bioconductor-enhancedvolcano bioconductor-pcatoolsPrinted: Create a new environment for normalization work, install programs, etc.: Create the environment on KrisMac
❯ mamba create \
> -n expression_env \
> -c conda-forge \
> r-base \
> r-tidyverse \
> mamba
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
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██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.3.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['r-base', 'r-tidyverse', 'mamba']
bioconda/linux-64 Using cache
bioconda/noarch Using cache
pkgs/main/linux-64 No change
pkgs/main/noarch No change
pkgs/r/linux-64 No change
pkgs/r/noarch No change
conda-forge/noarch 11.3MB @ 2.7MB/s 4.9s
conda-forge/linux-64 29.8MB @ 4.9MB/s 8.0s
Transaction
Prefix: /home/kalavatt/miniconda3/envs/expression_env
Updating specs:
- r-base
- r-tidyverse
- mamba
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────────────────────
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+ sed 4.8 he412f7d_0 conda-forge/linux-64 Cached
+ setuptools 67.3.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ sysroot_linux-64 2.12 he073ed8_15 conda-forge/noarch Cached
+ tk 8.6.12 h27826a3_0 conda-forge/linux-64 Cached
+ tktable 2.10 hb7b940f_3 conda-forge/linux-64 Cached
+ toolz 0.12.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tqdm 4.64.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tzdata 2022g h191b570_0 conda-forge/noarch Cached
+ urllib3 1.26.14 pyhd8ed1ab_0 conda-forge/noarch Cached
+ wheel 0.38.4 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xorg-kbproto 1.0.7 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-libice 1.0.10 h7f98852_0 conda-forge/linux-64 Cached
+ xorg-libsm 1.2.3 hd9c2040_1000 conda-forge/linux-64 Cached
+ xorg-libx11 1.7.2 h7f98852_0 conda-forge/linux-64 Cached
+ xorg-libxau 1.0.9 h7f98852_0 conda-forge/linux-64 Cached
+ xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge/linux-64 Cached
+ xorg-libxext 1.3.4 h7f98852_1 conda-forge/linux-64 Cached
+ xorg-libxrender 0.9.10 h7f98852_1003 conda-forge/linux-64 Cached
+ xorg-libxt 1.2.1 h7f98852_2 conda-forge/linux-64 Cached
+ xorg-renderproto 0.11.1 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-xextproto 7.3.0 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-xproto 7.0.31 h7f98852_1007 conda-forge/linux-64 Cached
+ xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached
+ yaml-cpp 0.7.0 h27087fc_2 conda-forge/linux-64 Cached
+ zlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
+ zstandard 0.19.0 py311hbe0fcd7_1 conda-forge/linux-64 Cached
+ zstd 1.5.2 h3eb15da_6 conda-forge/linux-64 Cached
Summary:
Install: 237 packages
Total download: 0 B
───────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
To activate this environment, use
$ mamba activate expression_env
To deactivate an active environment, use
$ mamba
❯ mamba install -c bioconda bioconductor-deseq2
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.3.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bioconductor-deseq2']
bioconda/noarch 4.2MB @ 4.6MB/s 1.1s
bioconda/linux-64 4.5MB @ 4.0MB/s 1.3s
pkgs/main/linux-64 5.2MB @ 2.7MB/s 2.4s
pkgs/r/noarch 1.3MB @ 602.5kB/s 1.6s
pkgs/main/noarch 819.1kB @ 313.2kB/s 1.5s
pkgs/r/linux-64 1.4MB @ 524.7kB/s 0.9s
conda-forge/noarch 11.3MB @ 3.6MB/s 3.5s
conda-forge/linux-64 29.8MB @ 4.2MB/s 8.1s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /home/kalavatt/miniconda3/envs/expression_env
Updating specs:
- bioconductor-deseq2
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────────────────────────────────
+ argcomplete 2.0.0 pyhd8ed1ab_0 conda-forge/noarch 35kB
+ bioconductor-annotate 1.76.0 r42hdfd78af_0 bioconda/noarch 2MB
+ bioconductor-annotationdbi 1.60.0 r42hdfd78af_0 bioconda/noarch 5MB
+ bioconductor-biobase 2.58.0 r42hc0cfd56_0 bioconda/linux-64 2MB
+ bioconductor-biocgenerics 0.44.0 r42hdfd78af_0 bioconda/noarch 665kB
+ bioconductor-biocparallel 1.32.5 r42hc247a5b_0 bioconda/linux-64 2MB
+ bioconductor-biostrings 2.66.0 r42hc0cfd56_0 bioconda/linux-64 14MB
+ bioconductor-data-packages 20230202 hdfd78af_0 bioconda/noarch 144kB
+ bioconductor-delayedarray 0.24.0 r42hc0cfd56_0 bioconda/linux-64 2MB
+ bioconductor-deseq2 1.38.0 r42hc247a5b_0 bioconda/linux-64 3MB
+ bioconductor-genefilter 1.80.0 r42h38f54d8_0 bioconda/linux-64 1MB
+ bioconductor-geneplotter 1.76.0 r42hdfd78af_0 bioconda/noarch 2MB
+ bioconductor-genomeinfodb 1.34.8 r42hdfd78af_0 bioconda/noarch 4MB
+ bioconductor-genomeinfodbdata 1.2.9 r42hdfd78af_0 bioconda/noarch 8kB
+ bioconductor-genomicranges 1.50.0 r42hc0cfd56_0 bioconda/linux-64 2MB
+ bioconductor-iranges 2.32.0 r42hc0cfd56_0 bioconda/linux-64 3MB
+ bioconductor-keggrest 1.38.0 r42hdfd78af_0 bioconda/noarch 199kB
+ bioconductor-matrixgenerics 1.10.0 r42hdfd78af_0 bioconda/noarch 353kB
+ bioconductor-s4vectors 0.36.0 r42hc0cfd56_0 bioconda/linux-64 2MB
+ bioconductor-summarizedexperiment 1.28.0 r42hdfd78af_0 bioconda/noarch 3MB
+ bioconductor-xvector 0.38.0 r42hc0cfd56_0 bioconda/linux-64 738kB
+ bioconductor-zlibbioc 1.44.0 r42hc0cfd56_0 bioconda/linux-64 74kB
+ importlib-metadata 4.13.0 pyha770c72_0 conda-forge/noarch 26kB
+ importlib_metadata 4.13.0 hd8ed1ab_0 conda-forge/noarch 9kB
+ jq 1.5 0 bioconda/linux-64 1MB
+ libgcc 7.2.0 h69d50b8_2 conda-forge/linux-64 312kB
+ pyyaml 6.0 py311hd4cff14_5 conda-forge/linux-64 207kB
+ r-bh 1.81.0_1 r42hc72bb7e_0 conda-forge/noarch 11MB
+ r-bitops 1.0_7 r42h06615bd_1 conda-forge/linux-64 46kB
+ r-codetools 0.2_19 r42hc72bb7e_0 conda-forge/noarch 108kB
+ r-formatr 1.14 r42hc72bb7e_0 conda-forge/noarch 165kB
+ r-futile.logger 1.4.3 r42hc72bb7e_1004 conda-forge/noarch 111kB
+ r-futile.options 1.0.1 r42hc72bb7e_1003 conda-forge/noarch 29kB
+ r-lambda.r 1.2.4 r42hc72bb7e_2 conda-forge/noarch 124kB
+ r-locfit 1.5_9.7 r42h133d619_0 conda-forge/linux-64 551kB
+ r-matrixstats 0.63.0 r42h06615bd_0 conda-forge/linux-64 445kB
+ r-plogr 0.2.0 r42hc72bb7e_1004 conda-forge/noarch 21kB
+ r-png 0.1_8 r42h10cf519_0 conda-forge/linux-64 58kB
+ r-rcpparmadillo 0.11.4.4.0 r42h358215d_0 conda-forge/linux-64 873kB
+ r-rcurl 1.98_1.10 r42h133d619_0 conda-forge/linux-64 817kB
+ r-rsqlite 2.2.20 r42h38f115c_0 conda-forge/linux-64 1MB
+ r-snow 0.4_4 r42hc72bb7e_1 conda-forge/noarch 117kB
+ r-survival 3.5_3 r42h133d619_0 conda-forge/linux-64 6MB
+ r-xml 3.99_0.13 r42hed7f998_0 conda-forge/linux-64 2MB
+ r-xtable 1.8_4 r42hc72bb7e_4 conda-forge/noarch 717kB
+ toml 0.10.2 pyhd8ed1ab_0 conda-forge/noarch 18kB
+ xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge/noarch 14kB
+ yaml 0.2.5 h7f98852_2 conda-forge/linux-64 89kB
+ yq 3.1.0 pyhd8ed1ab_0 conda-forge/noarch 22kB
+ zipp 3.14.0 pyhd8ed1ab_0 conda-forge/noarch 17kB
Summary:
Install: 50 packages
Total download: 76MB
─────────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
bioconductor-s4vectors 2.3MB @ 30.2MB/s 0.1s
bioconductor-biocgenerics 664.5kB @ 6.3MB/s 0.1s
yaml 89.1kB @ 643.1kB/s 0.0s
bioconductor-zlibbioc 74.5kB @ 499.8kB/s 0.2s
r-snow 117.0kB @ 576.0kB/s 0.1s
pyyaml 207.0kB @ 983.0kB/s 0.1s
xmltodict 13.6kB @ 60.5kB/s 0.0s
r-locfit 551.0kB @ 2.2MB/s 0.2s
r-plogr 21.2kB @ 78.1kB/s 0.1s
r-lambda.r 123.9kB @ 452.7kB/s 0.1s
argcomplete 35.2kB @ 116.3kB/s 0.0s
bioconductor-iranges 2.5MB @ 8.2MB/s 0.3s
r-futile.logger 111.1kB @ 360.6kB/s 0.1s
bioconductor-matrixgenerics 352.7kB @ 960.6kB/s 0.1s
bioconductor-biobase 2.5MB @ 6.2MB/s 0.6s
bioconductor-keggrest 199.5kB @ 386.5kB/s 0.3s
bioconductor-xvector 737.8kB @ 1.3MB/s 0.2s
bioconductor-genomicranges 2.3MB @ 4.0MB/s 0.3s
bioconductor-genomeinfodb 4.3MB @ 7.1MB/s 0.3s
zipp 17.3kB @ 20.3kB/s 0.2s
bioconductor-deseq2 2.9MB @ 3.4MB/s 0.6s
r-rcpparmadillo 873.0kB @ 907.6kB/s 0.4s
importlib_metadata 9.1kB @ 9.5kB/s 0.1s
bioconductor-biocparallel 1.7MB @ 1.3MB/s 0.4s
bioconductor-delayedarray 2.5MB @ 1.9MB/s 0.4s
r-rsqlite 1.2MB @ 880.6kB/s 0.5s
r-survival 5.9MB @ 4.0MB/s 1.2s
r-bh 11.4MB @ 7.0MB/s 1.2s
bioconductor-genefilter 1.2MB @ 690.8kB/s 0.4s
r-matrixstats 444.8kB @ 241.5kB/s 0.4s
r-codetools 108.1kB @ 58.6kB/s 0.4s
toml 18.4kB @ 10.0kB/s 0.4s
bioconductor-geneplotter 1.5MB @ 830.8kB/s 0.7s
importlib-metadata 25.5kB @ 12.1kB/s 0.3s
jq 1.2MB @ 555.9kB/s 0.4s
yq 22.4kB @ 10.6kB/s 0.4s
bioconductor-data-packages 144.5kB @ 68.2kB/s 0.5s
r-png 58.3kB @ 24.5kB/s 0.3s
bioconductor-genomeinfodbdata 7.9kB @ 3.3kB/s 0.3s
bioconductor-summarizedexperiment 2.8MB @ 1.1MB/s 0.3s
r-futile.options 28.8kB @ 10.8kB/s 0.4s
r-xml 1.7MB @ 613.4kB/s 0.6s
bioconductor-annotate 1.8MB @ 608.3kB/s 0.6s
libgcc 311.7kB @ 102.6kB/s 0.4s
bioconductor-annotationdbi 5.2MB @ 1.6MB/s 1.1s
r-bitops 45.7kB @ 13.9kB/s 0.3s
r-rcurl 817.2kB @ 248.4kB/s 0.5s
r-xtable 717.4kB @ 217.8kB/s 0.3s
bioconductor-biostrings 14.2MB @ 4.3MB/s 1.4s
r-formatr 165.2kB @ 46.7kB/s 0.2s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c bioconda subread
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.3.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['subread']
bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pkgs/r/linux-64 No change
pkgs/main/linux-64 No change
pkgs/main/noarch No change
pkgs/r/noarch No change
Pinned packages:
- python 3.11.*
Transaction
Prefix: /home/kalavatt/miniconda3/envs/expression_env
Updating specs:
- subread
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
──────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────
+ subread 2.0.3 h7132678_1 bioconda/linux-64 25MB
Summary:
Install: 1 packages
Total download: 25MB
──────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
subread 24.7MB @ 40.9MB/s 0.7s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install \
> -c bioconda \
> bioconductor-enhancedvolcano bioconductor-pcatools
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.3.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bioconductor-enhancedvolcano', 'bioconductor-pcatools']
bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pkgs/main/linux-64 No change
pkgs/main/noarch No change
pkgs/r/linux-64 No change
pkgs/r/noarch No change
Pinned packages:
- python 3.11.*
Transaction
Prefix: /home/kalavatt/miniconda3/envs/expression_env
Updating specs:
- bioconductor-enhancedvolcano
- bioconductor-pcatools
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────────────────────────
+ bioconductor-beachmat 2.14.0 r42hc247a5b_0 bioconda/linux-64 1MB
+ bioconductor-biocsingular 1.14.0 r42hc247a5b_0 bioconda/linux-64 993kB
+ bioconductor-delayedmatrixstats 1.20.0 r42hdfd78af_0 bioconda/noarch 740kB
+ bioconductor-enhancedvolcano 1.16.0 r42hdfd78af_0 bioconda/noarch 5MB
+ bioconductor-pcatools 2.10.0 r42hc247a5b_0 bioconda/linux-64 5MB
+ bioconductor-scaledmatrix 1.6.0 r42hdfd78af_0 bioconda/noarch 653kB
+ bioconductor-sparsematrixstats 1.10.0 r42hc247a5b_0 bioconda/linux-64 1MB
+ r-cowplot 1.1.1 r42hc72bb7e_1 conda-forge/noarch 1MB
+ r-dqrng 0.3.0 r42h7525677_1 conda-forge/linux-64 173kB
+ r-ggrepel 0.9.3 r42h38f115c_0 conda-forge/linux-64 268kB
+ r-irlba 2.3.5.1 r42h5f7b363_0 conda-forge/linux-64 317kB
+ r-plyr 1.8.8 r42h7525677_0 conda-forge/linux-64 855kB
+ r-reshape2 1.4.4 r42h7525677_2 conda-forge/linux-64 135kB
+ r-rsvd 1.0.5 r42hc72bb7e_1 conda-forge/noarch 4MB
+ r-sitmo 2.0.2 r42h7525677_1 conda-forge/linux-64 165kB
Summary:
Install: 15 packages
Total download: 22MB
─────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
bioconductor-delayedmatrixstats 739.6kB @ 10.1MB/s 0.1s
bioconductor-scaledmatrix 652.9kB @ 6.2MB/s 0.1s
bioconductor-beachmat 1.3MB @ 11.5MB/s 0.1s
r-irlba 316.6kB @ 2.2MB/s 0.0s
bioconductor-biocsingular 992.9kB @ 6.6MB/s 0.1s
bioconductor-sparsematrixstats 1.2MB @ 5.3MB/s 0.2s
r-plyr 855.3kB @ 3.7MB/s 0.1s
r-cowplot 1.4MB @ 6.0MB/s 0.2s
r-reshape2 135.2kB @ 543.4kB/s 0.1s
r-ggrepel 268.0kB @ 993.0kB/s 0.3s
r-rsvd 3.6MB @ 11.2MB/s 0.1s
r-dqrng 173.1kB @ 495.0kB/s 0.1s
r-sitmo 165.0kB @ 427.7kB/s 0.1s
bioconductor-enhancedvolcano 5.1MB @ 7.8MB/s 0.4s
bioconductor-pcatools 5.0MB @ 5.4MB/s 0.7s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: doneCode: Create a new environment, expression_env: Create the environment on WorkMac
#!/bin/bash
#DONTRUN #CONTINUE
if [[ "${CONDA_DEFAULT_ENV}" != "base" ]]; then
conda deactivate
fi
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
create_x86_conda_environment \
expression_env \
-c conda-forge \
r-base \
r-tidyverse \
mamba
# create_x86_conda_environment:
#+ Create a conda environment using x86 architecture
#+
#+ The first argument is environment name; all subsequent arguments will be
#+ passed to `conda create`
#+
#+ example usage: create_x86_conda_environment myenv_x86 python=3.9
source activate expression_env
mamba install -c bioconda bioconductor-deseq2
mamba install -c bioconda subread
mamba install \
-c bioconda \
bioconductor-enhancedvolcano bioconductor-pcatools
mamba install -c conda-forge r-markdown # Needed by RStudio on WorkMac...
mamba install -c conda-forge r-roxygen2 #TODO Copy in installation text...
mamba install -c bioconda bioconductor-sva
mamba install -c conda-forge r-ggalt
mamba install -c conda-forge r-rjson
mamba install -c bioconda bioconductor-rtracklayerPrinted: Create a new environment for normalization work, install programs, etc.: Create the environment on WorkMac
❯ create_x86_conda_environment \
> expression_env \
> -c conda-forge \
> r-base \
> r-tidyverse \
> mamba
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 22.9.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/kalavatt/mambaforge/envs/expression_env
added / updated specs:
- mamba
- r-base
- r-tidyverse
The following packages will be downloaded:
package | build
---------------------------|-----------------
brotlipy-0.7.0 |py311h5547dcb_1005 370 KB conda-forge
cffi-1.15.1 | py311ha86e640_3 274 KB conda-forge
compiler-rt_osx-64-14.0.6 | h8d5cb93_0 3.4 MB
conda-23.1.0 | py311h6eed73b_0 1.2 MB conda-forge
conda-package-handling-2.0.2| pyh38be061_0 247 KB conda-forge
conda-package-streaming-0.7.0| pyhd8ed1ab_1 17 KB conda-forge
cryptography-39.0.1 | py311h61927ef_0 1.1 MB conda-forge
curl-7.88.1 | h6df9250_0 140 KB conda-forge
fmt-9.1.0 | hb8565cd_0 179 KB conda-forge
fontconfig-2.14.2 | h5bb23bf_0 232 KB conda-forge
gfortran_impl_osx-64-11.3.0| h1f927f5_28 17.5 MB conda-forge
jpeg-9e | hb7f2c08_3 226 KB conda-forge
libarchive-3.6.2 | h6d8d9f1_0 706 KB conda-forge
libcurl-7.88.1 | h6df9250_0 335 KB conda-forge
libcxx-15.0.7 | h71dddab_0 1.1 MB conda-forge
libdeflate-1.17 | hac1461d_0 66 KB conda-forge
libgfortran-5.0.0 |10_4_0_h97931a8_28 144 KB conda-forge
libgfortran-devel_osx-64-11.3.0| h824d247_28 418 KB conda-forge
libgfortran5-11.3.0 | h082f757_28 1.4 MB conda-forge
libmamba-1.3.1 | h9d281b0_1 1.2 MB conda-forge
libmambapy-1.3.1 | py311hcc19a12_1 231 KB conda-forge
libsolv-0.7.23 | hbc0c0cd_0 402 KB conda-forge
libtiff-4.5.0 | hee9004a_2 383 KB conda-forge
llvm-openmp-15.0.7 | h61d9ccf_0 287 KB conda-forge
lz4-c-1.9.4 | hf0c8a7f_0 153 KB conda-forge
lzo-2.10 | haf1e3a3_1000 190 KB conda-forge
mamba-1.3.1 | py311h8082e30_1 63 KB conda-forge
mpc-1.3.1 | h81bd1dd_0 107 KB conda-forge
openssl-3.0.8 | hfd90126_0 2.2 MB conda-forge
pango-1.50.13 | hbd9bf65_0 407 KB conda-forge
pip-23.0.1 | pyhd8ed1ab_0 1.3 MB conda-forge
pluggy-1.0.0 | pyhd8ed1ab_5 16 KB conda-forge
pycosat-0.6.4 | py311h5547dcb_1 113 KB conda-forge
pyopenssl-23.0.0 | pyhd8ed1ab_0 124 KB conda-forge
python-3.11.0 |he7542f4_1_cpython 14.7 MB conda-forge
python_abi-3.11 | 3_cp311 6 KB conda-forge
r-backports-1.4.1 | r42h815d134_1 109 KB conda-forge
r-base-4.2.2 | h841e2fe_3 23.3 MB conda-forge
r-broom-1.0.3 | r42hc72bb7e_0 1.7 MB conda-forge
r-cachem-1.0.7 | r42h815d134_0 72 KB conda-forge
r-callr-3.7.3 | r42hc72bb7e_0 429 KB conda-forge
r-cellranger-1.1.0 | r42hc72bb7e_1005 110 KB conda-forge
r-cli-3.6.0 | r42h49197e3_0 1.2 MB conda-forge
r-clipr-0.8.0 | r42hc72bb7e_1 68 KB conda-forge
r-colorspace-2.1_0 | r42h815d134_0 2.4 MB conda-forge
r-conflicted-1.2.0 | r42h785f33e_0 62 KB conda-forge
r-data.table-1.14.8 | r42h557251b_0 1.8 MB conda-forge
r-dbplyr-2.3.1 | r42hc72bb7e_0 1.0 MB conda-forge
r-dplyr-1.1.0 | r42h49197e3_0 1.3 MB conda-forge
r-dtplyr-1.3.0 | r42hc72bb7e_0 348 KB conda-forge
r-farver-2.1.1 | r42h49197e3_1 1.4 MB conda-forge
r-fastmap-1.1.1 | r42h49197e3_0 69 KB conda-forge
r-forcats-1.0.0 | r42hc72bb7e_0 414 KB conda-forge
r-fs-1.6.1 | r42h49197e3_0 269 KB conda-forge
r-gargle-1.3.0 | r42h785f33e_0 519 KB conda-forge
r-ggplot2-3.4.1 | r42hc72bb7e_0 3.9 MB conda-forge
r-googledrive-2.0.0 | r42hc72bb7e_1 1.8 MB conda-forge
r-googlesheets4-1.0.1 | r42h785f33e_1 498 KB conda-forge
r-gtable-0.3.1 | r42hc72bb7e_1 174 KB conda-forge
r-haven-2.5.1 | r42h49197e3_0 383 KB conda-forge
r-httr-1.4.5 | r42hc72bb7e_0 477 KB conda-forge
r-ids-1.0.1 | r42hc72bb7e_2 127 KB conda-forge
r-isoband-0.2.7 | r42h49197e3_1 1.6 MB conda-forge
r-knitr-1.42 | r42hc72bb7e_1 1.2 MB conda-forge
r-labeling-0.4.2 | r42hc72bb7e_2 68 KB conda-forge
r-lubridate-1.9.2 | r42h815d134_1 942 KB conda-forge
r-mass-7.3_58.2 | r42h815d134_0 1.1 MB conda-forge
r-mgcv-1.8_41 | r42h40f944a_0 3.2 MB conda-forge
r-modelr-0.1.10 | r42hc72bb7e_0 220 KB conda-forge
r-munsell-0.5.0 | r42hc72bb7e_1005 248 KB conda-forge
r-nlme-3.1_162 | r42h1e4e481_0 2.2 MB conda-forge
r-processx-3.8.0 | r42h815d134_0 318 KB conda-forge
r-ps-1.7.2 | r42h815d134_0 315 KB conda-forge
r-ragg-1.2.5 | r42hd0b13e6_0 386 KB conda-forge
r-rcpp-1.0.10 | r42h49197e3_0 1.9 MB conda-forge
r-readr-2.1.4 | r42h49197e3_0 724 KB conda-forge
r-readxl-1.4.2 | r42h3ae43e4_0 712 KB conda-forge
r-rematch-1.0.1 | r42hc72bb7e_1005 20 KB conda-forge
r-rematch2-2.1.2 | r42hc72bb7e_2 54 KB conda-forge
r-reprex-2.0.2 | r42hc72bb7e_1 499 KB conda-forge
r-rstudioapi-0.14 | r42hc72bb7e_1 301 KB conda-forge
r-rvest-1.0.3 | r42hc72bb7e_1 216 KB conda-forge
r-sass-0.4.5 | r42h49197e3_0 2.0 MB conda-forge
r-scales-1.2.1 | r42hc72bb7e_1 612 KB conda-forge
r-selectr-0.4_2 | r42hc72bb7e_2 463 KB conda-forge
r-stringi-1.7.12 | r42h7183e51_0 836 KB conda-forge
r-systemfonts-1.0.4 | r42h1372bf0_1 253 KB conda-forge
r-textshaping-0.3.6 | r42h12cd53d_4 99 KB conda-forge
r-tidyr-1.3.0 | r42h49197e3_0 1.1 MB conda-forge
r-tidyverse-2.0.0 | r42h785f33e_0 415 KB conda-forge
r-timechange-0.2.0 | r42h49197e3_0 177 KB conda-forge
r-tinytex-0.44 | r42hc72bb7e_0 139 KB conda-forge
r-tzdb-0.3.0 | r42h49197e3_1 531 KB conda-forge
r-utf8-1.2.3 | r42h815d134_0 135 KB conda-forge
r-uuid-1.1_0 | r42h815d134_1 50 KB conda-forge
r-vctrs-0.5.2 | r42h49197e3_0 1.2 MB conda-forge
r-viridislite-0.4.1 | r42hc72bb7e_1 1.3 MB conda-forge
r-vroom-1.6.1 | r42h49197e3_0 781 KB conda-forge
r-xfun-0.37 | r42h49197e3_0 393 KB conda-forge
r-yaml-2.3.7 | r42h815d134_0 104 KB conda-forge
reproc-14.2.4 | hb7f2c08_0 27 KB conda-forge
reproc-cpp-14.2.4 | hf0c8a7f_0 19 KB conda-forge
requests-2.28.2 | pyhd8ed1ab_0 55 KB conda-forge
ruamel.yaml-0.17.21 | py311h5547dcb_2 248 KB conda-forge
ruamel.yaml.clib-0.2.7 | py311h5547dcb_1 115 KB conda-forge
setuptools-67.4.0 | pyhd8ed1ab_0 567 KB conda-forge
tzdata-2022g | h191b570_0 106 KB conda-forge
urllib3-1.26.14 | pyhd8ed1ab_0 110 KB conda-forge
yaml-cpp-0.7.0 | hf0c8a7f_2 139 KB conda-forge
zstandard-0.19.0 | py311hebd4beb_1 405 KB conda-forge
zstd-1.5.2 | hbc0c0cd_6 399 KB conda-forge
------------------------------------------------------------
Total: 123.2 MB
The following NEW packages will be INSTALLED:
_r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 None
brotlipy conda-forge/osx-64::brotlipy-0.7.0-py311h5547dcb_1005 None
bwidget conda-forge/osx-64::bwidget-1.9.14-h694c41f_1 None
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4 None
c-ares conda-forge/osx-64::c-ares-1.18.1-h0d85af4_0 None
ca-certificates conda-forge/osx-64::ca-certificates-2022.12.7-h033912b_0 None
cairo conda-forge/osx-64::cairo-1.16.0-h904041c_1014 None
cctools_osx-64 conda-forge/osx-64::cctools_osx-64-973.0.1-hcc6d90d_11 None
certifi conda-forge/noarch::certifi-2022.12.7-pyhd8ed1ab_0 None
cffi conda-forge/osx-64::cffi-1.15.1-py311ha86e640_3 None
charset-normalizer conda-forge/noarch::charset-normalizer-2.1.1-pyhd8ed1ab_0 None
clang conda-forge/osx-64::clang-14.0.6-h694c41f_0 None
clang-14 conda-forge/osx-64::clang-14-14.0.6-default_h55ffa42_0 None
clang_osx-64 conda-forge/osx-64::clang_osx-64-14.0.6-h3113cd8_4 None
clangxx conda-forge/osx-64::clangxx-14.0.6-default_h55ffa42_0 None
clangxx_osx-64 conda-forge/osx-64::clangxx_osx-64-14.0.6-h6f97653_4 None
colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0 None
compiler-rt conda-forge/osx-64::compiler-rt-14.0.6-h613da45_0 None
compiler-rt_osx-64 pkgs/main/osx-64::compiler-rt_osx-64-14.0.6-h8d5cb93_0 None
conda conda-forge/osx-64::conda-23.1.0-py311h6eed73b_0 None
conda-package-han~ conda-forge/noarch::conda-package-handling-2.0.2-pyh38be061_0 None
conda-package-str~ conda-forge/noarch::conda-package-streaming-0.7.0-pyhd8ed1ab_1 None
cryptography conda-forge/osx-64::cryptography-39.0.1-py311h61927ef_0 None
curl conda-forge/osx-64::curl-7.88.1-h6df9250_0 None
expat conda-forge/osx-64::expat-2.5.0-hf0c8a7f_0 None
fmt conda-forge/osx-64::fmt-9.1.0-hb8565cd_0 None
font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0 None
font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0 None
font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0 None
font-ttf-ubuntu conda-forge/noarch::font-ttf-ubuntu-0.83-hab24e00_0 None
fontconfig conda-forge/osx-64::fontconfig-2.14.2-h5bb23bf_0 None
fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0 None
fonts-conda-forge conda-forge/noarch::fonts-conda-forge-1-0 None
freetype conda-forge/osx-64::freetype-2.12.1-h3f81eb7_1 None
fribidi conda-forge/osx-64::fribidi-1.0.10-hbcb3906_0 None
gettext conda-forge/osx-64::gettext-0.21.1-h8a4c099_0 None
gfortran_impl_osx~ conda-forge/osx-64::gfortran_impl_osx-64-11.3.0-h1f927f5_28 None
gfortran_osx-64 conda-forge/osx-64::gfortran_osx-64-11.3.0-h18f7dce_0 None
gmp conda-forge/osx-64::gmp-6.2.1-h2e338ed_0 None
graphite2 conda-forge/osx-64::graphite2-1.3.13-h2e338ed_1001 None
gsl conda-forge/osx-64::gsl-2.7-h93259b0_0 None
harfbuzz conda-forge/osx-64::harfbuzz-6.0.0-h08f8713_0 None
icu conda-forge/osx-64::icu-70.1-h96cf925_0 None
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0 None
isl conda-forge/osx-64::isl-0.25-hb486fe8_0 None
jpeg conda-forge/osx-64::jpeg-9e-hb7f2c08_3 None
krb5 conda-forge/osx-64::krb5-1.20.1-h049b76e_0 None
ld64_osx-64 conda-forge/osx-64::ld64_osx-64-609-hfd63004_11 None
lerc conda-forge/osx-64::lerc-4.0.0-hb486fe8_0 None
libarchive conda-forge/osx-64::libarchive-3.6.2-h6d8d9f1_0 None
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas None
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas None
libclang-cpp14 conda-forge/osx-64::libclang-cpp14-14.0.6-default_h55ffa42_0 None
libcurl conda-forge/osx-64::libcurl-7.88.1-h6df9250_0 None
libcxx conda-forge/osx-64::libcxx-15.0.7-h71dddab_0 None
libdeflate conda-forge/osx-64::libdeflate-1.17-hac1461d_0 None
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2 None
libev conda-forge/osx-64::libev-4.33-haf1e3a3_1 None
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 None
libgfortran conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_28 None
libgfortran-devel~ conda-forge/noarch::libgfortran-devel_osx-64-11.3.0-h824d247_28 None
libgfortran5 conda-forge/osx-64::libgfortran5-11.3.0-h082f757_28 None
libglib conda-forge/osx-64::libglib-2.74.1-h4c723e1_1 None
libiconv conda-forge/osx-64::libiconv-1.17-hac89ed1_0 None
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas None
libllvm14 conda-forge/osx-64::libllvm14-14.0.6-h5b596cc_1 None
libmamba conda-forge/osx-64::libmamba-1.3.1-h9d281b0_1 None
libmambapy conda-forge/osx-64::libmambapy-1.3.1-py311hcc19a12_1 None
libnghttp2 conda-forge/osx-64::libnghttp2-1.51.0-he2ab024_0 None
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3 None
libpng conda-forge/osx-64::libpng-1.6.39-ha978bb4_0 None
libsolv conda-forge/osx-64::libsolv-0.7.23-hbc0c0cd_0 None
libsqlite conda-forge/osx-64::libsqlite-3.40.0-ha978bb4_0 None
libssh2 conda-forge/osx-64::libssh2-1.10.0-h47af595_3 None
libtiff conda-forge/osx-64::libtiff-4.5.0-hee9004a_2 None
libwebp-base conda-forge/osx-64::libwebp-base-1.2.4-h775f41a_0 None
libxml2 conda-forge/osx-64::libxml2-2.10.3-hb9e07b5_0 None
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4 None
llvm-openmp conda-forge/osx-64::llvm-openmp-15.0.7-h61d9ccf_0 None
llvm-tools conda-forge/osx-64::llvm-tools-14.0.6-h5b596cc_1 None
lz4-c conda-forge/osx-64::lz4-c-1.9.4-hf0c8a7f_0 None
lzo conda-forge/osx-64::lzo-2.10-haf1e3a3_1000 None
make conda-forge/osx-64::make-4.3-h22f3db7_1 None
mamba conda-forge/osx-64::mamba-1.3.1-py311h8082e30_1 None
mpc conda-forge/osx-64::mpc-1.3.1-h81bd1dd_0 None
mpfr conda-forge/osx-64::mpfr-4.1.0-h0f52abe_1 None
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1 None
openssl conda-forge/osx-64::openssl-3.0.8-hfd90126_0 None
pandoc conda-forge/osx-64::pandoc-2.19.2-h694c41f_1 None
pango conda-forge/osx-64::pango-1.50.13-hbd9bf65_0 None
pcre2 conda-forge/osx-64::pcre2-10.40-h1c4e4bc_0 None
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0 None
pixman conda-forge/osx-64::pixman-0.40.0-hbcb3906_0 None
pluggy conda-forge/noarch::pluggy-1.0.0-pyhd8ed1ab_5 None
pybind11-abi conda-forge/noarch::pybind11-abi-4-hd8ed1ab_3 None
pycosat conda-forge/osx-64::pycosat-0.6.4-py311h5547dcb_1 None
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0 None
pyopenssl conda-forge/noarch::pyopenssl-23.0.0-pyhd8ed1ab_0 None
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6 None
python conda-forge/osx-64::python-3.11.0-he7542f4_1_cpython None
python_abi conda-forge/osx-64::python_abi-3.11-3_cp311 None
r-askpass conda-forge/osx-64::r-askpass-1.1-r42h815d134_3 None
r-assertthat conda-forge/noarch::r-assertthat-0.2.1-r42hc72bb7e_3 None
r-backports conda-forge/osx-64::r-backports-1.4.1-r42h815d134_1 None
r-base conda-forge/osx-64::r-base-4.2.2-h841e2fe_3 None
r-base64enc conda-forge/osx-64::r-base64enc-0.1_3-r42h815d134_1005 None
r-bit conda-forge/osx-64::r-bit-4.0.5-r42h815d134_0 None
r-bit64 conda-forge/osx-64::r-bit64-4.0.5-r42h815d134_1 None
r-blob conda-forge/noarch::r-blob-1.2.3-r42hc72bb7e_1 None
r-broom conda-forge/noarch::r-broom-1.0.3-r42hc72bb7e_0 None
r-bslib conda-forge/noarch::r-bslib-0.4.2-r42hc72bb7e_0 None
r-cachem conda-forge/osx-64::r-cachem-1.0.7-r42h815d134_0 None
r-callr conda-forge/noarch::r-callr-3.7.3-r42hc72bb7e_0 None
r-cellranger conda-forge/noarch::r-cellranger-1.1.0-r42hc72bb7e_1005 None
r-cli conda-forge/osx-64::r-cli-3.6.0-r42h49197e3_0 None
r-clipr conda-forge/noarch::r-clipr-0.8.0-r42hc72bb7e_1 None
r-colorspace conda-forge/osx-64::r-colorspace-2.1_0-r42h815d134_0 None
r-conflicted conda-forge/noarch::r-conflicted-1.2.0-r42h785f33e_0 None
r-cpp11 conda-forge/noarch::r-cpp11-0.4.3-r42hc72bb7e_0 None
r-crayon conda-forge/noarch::r-crayon-1.5.2-r42hc72bb7e_1 None
r-curl conda-forge/osx-64::r-curl-4.3.3-r42h815d134_1 None
r-data.table conda-forge/osx-64::r-data.table-1.14.8-r42h557251b_0 None
r-dbi conda-forge/noarch::r-dbi-1.1.3-r42hc72bb7e_1 None
r-dbplyr conda-forge/noarch::r-dbplyr-2.3.1-r42hc72bb7e_0 None
r-digest conda-forge/osx-64::r-digest-0.6.31-r42h49197e3_0 None
r-dplyr conda-forge/osx-64::r-dplyr-1.1.0-r42h49197e3_0 None
r-dtplyr conda-forge/noarch::r-dtplyr-1.3.0-r42hc72bb7e_0 None
r-ellipsis conda-forge/osx-64::r-ellipsis-0.3.2-r42h815d134_1 None
r-evaluate conda-forge/noarch::r-evaluate-0.20-r42hc72bb7e_0 None
r-fansi conda-forge/osx-64::r-fansi-1.0.4-r42h815d134_0 None
r-farver conda-forge/osx-64::r-farver-2.1.1-r42h49197e3_1 None
r-fastmap conda-forge/osx-64::r-fastmap-1.1.1-r42h49197e3_0 None
r-forcats conda-forge/noarch::r-forcats-1.0.0-r42hc72bb7e_0 None
r-fs conda-forge/osx-64::r-fs-1.6.1-r42h49197e3_0 None
r-gargle conda-forge/noarch::r-gargle-1.3.0-r42h785f33e_0 None
r-generics conda-forge/noarch::r-generics-0.1.3-r42hc72bb7e_1 None
r-ggplot2 conda-forge/noarch::r-ggplot2-3.4.1-r42hc72bb7e_0 None
r-glue conda-forge/osx-64::r-glue-1.6.2-r42h815d134_1 None
r-googledrive conda-forge/noarch::r-googledrive-2.0.0-r42hc72bb7e_1 None
r-googlesheets4 conda-forge/noarch::r-googlesheets4-1.0.1-r42h785f33e_1 None
r-gtable conda-forge/noarch::r-gtable-0.3.1-r42hc72bb7e_1 None
r-haven conda-forge/osx-64::r-haven-2.5.1-r42h49197e3_0 None
r-highr conda-forge/noarch::r-highr-0.10-r42hc72bb7e_0 None
r-hms conda-forge/noarch::r-hms-1.1.2-r42hc72bb7e_1 None
r-htmltools conda-forge/osx-64::r-htmltools-0.5.4-r42h49197e3_0 None
r-httr conda-forge/noarch::r-httr-1.4.5-r42hc72bb7e_0 None
r-ids conda-forge/noarch::r-ids-1.0.1-r42hc72bb7e_2 None
r-isoband conda-forge/osx-64::r-isoband-0.2.7-r42h49197e3_1 None
r-jquerylib conda-forge/noarch::r-jquerylib-0.1.4-r42hc72bb7e_1 None
r-jsonlite conda-forge/osx-64::r-jsonlite-1.8.4-r42h815d134_0 None
r-knitr conda-forge/noarch::r-knitr-1.42-r42hc72bb7e_1 None
r-labeling conda-forge/noarch::r-labeling-0.4.2-r42hc72bb7e_2 None
r-lattice conda-forge/osx-64::r-lattice-0.20_45-r42h815d134_1 None
r-lifecycle conda-forge/noarch::r-lifecycle-1.0.3-r42hc72bb7e_1 None
r-lubridate conda-forge/osx-64::r-lubridate-1.9.2-r42h815d134_1 None
r-magrittr conda-forge/osx-64::r-magrittr-2.0.3-r42h815d134_1 None
r-mass conda-forge/osx-64::r-mass-7.3_58.2-r42h815d134_0 None
r-matrix conda-forge/osx-64::r-matrix-1.5_3-r42hce01bf1_0 None
r-memoise conda-forge/noarch::r-memoise-2.0.1-r42hc72bb7e_1 None
r-mgcv conda-forge/osx-64::r-mgcv-1.8_41-r42h40f944a_0 None
r-mime conda-forge/osx-64::r-mime-0.12-r42h815d134_1 None
r-modelr conda-forge/noarch::r-modelr-0.1.10-r42hc72bb7e_0 None
r-munsell conda-forge/noarch::r-munsell-0.5.0-r42hc72bb7e_1005 None
r-nlme conda-forge/osx-64::r-nlme-3.1_162-r42h1e4e481_0 None
r-openssl conda-forge/osx-64::r-openssl-2.0.5-r42hfeb9312_0 None
r-pillar conda-forge/noarch::r-pillar-1.8.1-r42hc72bb7e_1 None
r-pkgconfig conda-forge/noarch::r-pkgconfig-2.0.3-r42hc72bb7e_2 None
r-prettyunits conda-forge/noarch::r-prettyunits-1.1.1-r42hc72bb7e_2 None
r-processx conda-forge/osx-64::r-processx-3.8.0-r42h815d134_0 None
r-progress conda-forge/noarch::r-progress-1.2.2-r42hc72bb7e_3 None
r-ps conda-forge/osx-64::r-ps-1.7.2-r42h815d134_0 None
r-purrr conda-forge/osx-64::r-purrr-1.0.1-r42h815d134_0 None
r-r6 conda-forge/noarch::r-r6-2.5.1-r42hc72bb7e_1 None
r-ragg conda-forge/osx-64::r-ragg-1.2.5-r42hd0b13e6_0 None
r-rappdirs conda-forge/osx-64::r-rappdirs-0.3.3-r42h815d134_1 None
r-rcolorbrewer conda-forge/noarch::r-rcolorbrewer-1.1_3-r42h785f33e_1 None
r-rcpp conda-forge/osx-64::r-rcpp-1.0.10-r42h49197e3_0 None
r-readr conda-forge/osx-64::r-readr-2.1.4-r42h49197e3_0 None
r-readxl conda-forge/osx-64::r-readxl-1.4.2-r42h3ae43e4_0 None
r-rematch conda-forge/noarch::r-rematch-1.0.1-r42hc72bb7e_1005 None
r-rematch2 conda-forge/noarch::r-rematch2-2.1.2-r42hc72bb7e_2 None
r-reprex conda-forge/noarch::r-reprex-2.0.2-r42hc72bb7e_1 None
r-rlang conda-forge/osx-64::r-rlang-1.0.6-r42h49197e3_1 None
r-rmarkdown conda-forge/noarch::r-rmarkdown-2.20-r42hc72bb7e_0 None
r-rstudioapi conda-forge/noarch::r-rstudioapi-0.14-r42hc72bb7e_1 None
r-rvest conda-forge/noarch::r-rvest-1.0.3-r42hc72bb7e_1 None
r-sass conda-forge/osx-64::r-sass-0.4.5-r42h49197e3_0 None
r-scales conda-forge/noarch::r-scales-1.2.1-r42hc72bb7e_1 None
r-selectr conda-forge/noarch::r-selectr-0.4_2-r42hc72bb7e_2 None
r-stringi conda-forge/osx-64::r-stringi-1.7.12-r42h7183e51_0 None
r-stringr conda-forge/noarch::r-stringr-1.5.0-r42h785f33e_0 None
r-sys conda-forge/osx-64::r-sys-3.4.1-r42h815d134_0 None
r-systemfonts conda-forge/osx-64::r-systemfonts-1.0.4-r42h1372bf0_1 None
r-textshaping conda-forge/osx-64::r-textshaping-0.3.6-r42h12cd53d_4 None
r-tibble conda-forge/osx-64::r-tibble-3.1.8-r42h815d134_1 None
r-tidyr conda-forge/osx-64::r-tidyr-1.3.0-r42h49197e3_0 None
r-tidyselect conda-forge/osx-64::r-tidyselect-1.2.0-r42hbe3e9c8_0 None
r-tidyverse conda-forge/noarch::r-tidyverse-2.0.0-r42h785f33e_0 None
r-timechange conda-forge/osx-64::r-timechange-0.2.0-r42h49197e3_0 None
r-tinytex conda-forge/noarch::r-tinytex-0.44-r42hc72bb7e_0 None
r-tzdb conda-forge/osx-64::r-tzdb-0.3.0-r42h49197e3_1 None
r-utf8 conda-forge/osx-64::r-utf8-1.2.3-r42h815d134_0 None
r-uuid conda-forge/osx-64::r-uuid-1.1_0-r42h815d134_1 None
r-vctrs conda-forge/osx-64::r-vctrs-0.5.2-r42h49197e3_0 None
r-viridislite conda-forge/noarch::r-viridislite-0.4.1-r42hc72bb7e_1 None
r-vroom conda-forge/osx-64::r-vroom-1.6.1-r42h49197e3_0 None
r-withr conda-forge/noarch::r-withr-2.5.0-r42hc72bb7e_1 None
r-xfun conda-forge/osx-64::r-xfun-0.37-r42h49197e3_0 None
r-xml2 conda-forge/osx-64::r-xml2-1.3.3-r42h3576887_2 None
r-yaml conda-forge/osx-64::r-yaml-2.3.7-r42h815d134_0 None
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0 None
reproc conda-forge/osx-64::reproc-14.2.4-hb7f2c08_0 None
reproc-cpp conda-forge/osx-64::reproc-cpp-14.2.4-hf0c8a7f_0 None
requests conda-forge/noarch::requests-2.28.2-pyhd8ed1ab_0 None
ruamel.yaml conda-forge/osx-64::ruamel.yaml-0.17.21-py311h5547dcb_2 None
ruamel.yaml.clib conda-forge/osx-64::ruamel.yaml.clib-0.2.7-py311h5547dcb_1 None
setuptools conda-forge/noarch::setuptools-67.4.0-pyhd8ed1ab_0 None
sigtool conda-forge/osx-64::sigtool-0.1.3-h88f4db0_0 None
tapi conda-forge/osx-64::tapi-1100.0.11-h9ce4665_0 None
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0 None
tktable conda-forge/osx-64::tktable-2.10-h49f0cf7_3 None
toolz conda-forge/noarch::toolz-0.12.0-pyhd8ed1ab_0 None
tqdm conda-forge/noarch::tqdm-4.64.1-pyhd8ed1ab_0 None
tzdata conda-forge/noarch::tzdata-2022g-h191b570_0 None
urllib3 conda-forge/noarch::urllib3-1.26.14-pyhd8ed1ab_0 None
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0 None
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0 None
yaml-cpp conda-forge/osx-64::yaml-cpp-0.7.0-hf0c8a7f_2 None
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4 None
zstandard conda-forge/osx-64::zstandard-0.19.0-py311hebd4beb_1 None
zstd conda-forge/osx-64::zstd-1.5.2-hbc0c0cd_6 None
Proceed ([y]/n)? y
Downloading and Extracting Packages
conda-package-stream | 17 KB | ######################################################################### 100%
r-systemfonts-1.0.4 | 253 KB | ######################################################################### 100%
r-fastmap-1.1.1 | 69 KB | ######################################################################### 100%
r-rematch2-2.1.2 | 54 KB | ######################################################################### 100%
r-fs-1.6.1 | 269 KB | ######################################################################### 100%
r-ids-1.0.1 | 127 KB | ######################################################################### 100%
r-googledrive-2.0.0 | 1.8 MB | ######################################################################### 100%
urllib3-1.26.14 | 110 KB | ######################################################################### 100%
openssl-3.0.8 | 2.2 MB | ######################################################################### 100%
libmamba-1.3.1 | 1.2 MB | ######################################################################### 100%
r-modelr-0.1.10 | 220 KB | ######################################################################### 100%
libsolv-0.7.23 | 402 KB | ######################################################################### 100%
r-gtable-0.3.1 | 174 KB | ######################################################################### 100%
libcurl-7.88.1 | 335 KB | ######################################################################### 100%
r-readr-2.1.4 | 724 KB | ######################################################################### 100%
r-callr-3.7.3 | 429 KB | ######################################################################### 100%
r-dbplyr-2.3.1 | 1.0 MB | ######################################################################### 100%
compiler-rt_osx-64-1 | 3.4 MB | ######################################################################### 100%
r-clipr-0.8.0 | 68 KB | ######################################################################### 100%
libarchive-3.6.2 | 706 KB | ######################################################################### 100%
r-forcats-1.0.0 | 414 KB | ######################################################################### 100%
r-dtplyr-1.3.0 | 348 KB | ######################################################################### 100%
r-vroom-1.6.1 | 781 KB | ######################################################################### 100%
ruamel.yaml.clib-0.2 | 115 KB | ######################################################################### 100%
r-mass-7.3_58.2 | 1.1 MB | ######################################################################### 100%
zstd-1.5.2 | 399 KB | ######################################################################### 100%
r-ragg-1.2.5 | 386 KB | ######################################################################### 100%
r-readxl-1.4.2 | 712 KB | ######################################################################### 100%
r-munsell-0.5.0 | 248 KB | ######################################################################### 100%
reproc-14.2.4 | 27 KB | ######################################################################### 100%
cryptography-39.0.1 | 1.1 MB | ######################################################################### 100%
yaml-cpp-0.7.0 | 139 KB | ######################################################################### 100%
r-tzdb-0.3.0 | 531 KB | ######################################################################### 100%
r-cli-3.6.0 | 1.2 MB | ######################################################################### 100%
r-viridislite-0.4.1 | 1.3 MB | ######################################################################### 100%
r-scales-1.2.1 | 612 KB | ######################################################################### 100%
llvm-openmp-15.0.7 | 287 KB | ######################################################################### 100%
libcxx-15.0.7 | 1.1 MB | ######################################################################### 100%
r-httr-1.4.5 | 477 KB | ######################################################################### 100%
r-farver-2.1.1 | 1.4 MB | ######################################################################### 100%
reproc-cpp-14.2.4 | 19 KB | ######################################################################### 100%
pluggy-1.0.0 | 16 KB | ######################################################################### 100%
libgfortran-devel_os | 418 KB | ######################################################################### 100%
r-utf8-1.2.3 | 135 KB | ######################################################################### 100%
lz4-c-1.9.4 | 153 KB | ######################################################################### 100%
r-conflicted-1.2.0 | 62 KB | ######################################################################### 100%
pango-1.50.13 | 407 KB | ######################################################################### 100%
r-selectr-0.4_2 | 463 KB | ######################################################################### 100%
tzdata-2022g | 106 KB | ######################################################################### 100%
r-uuid-1.1_0 | 50 KB | ######################################################################### 100%
libgfortran-5.0.0 | 144 KB | ######################################################################### 100%
pyopenssl-23.0.0 | 124 KB | ######################################################################### 100%
r-ggplot2-3.4.1 | 3.9 MB | ######################################################################### 100%
pycosat-0.6.4 | 113 KB | ######################################################################### 100%
r-haven-2.5.1 | 383 KB | ######################################################################### 100%
r-stringi-1.7.12 | 836 KB | ######################################################################### 100%
r-isoband-0.2.7 | 1.6 MB | ######################################################################### 100%
r-rematch-1.0.1 | 20 KB | ######################################################################### 100%
r-rstudioapi-0.14 | 301 KB | ######################################################################### 100%
python-3.11.0 | 14.7 MB | ######################################################################### 100%
libdeflate-1.17 | 66 KB | ######################################################################### 100%
r-xfun-0.37 | 393 KB | ######################################################################### 100%
zstandard-0.19.0 | 405 KB | ######################################################################### 100%
libtiff-4.5.0 | 383 KB | ######################################################################### 100%
r-knitr-1.42 | 1.2 MB | ######################################################################### 100%
r-dplyr-1.1.0 | 1.3 MB | ######################################################################### 100%
r-rvest-1.0.3 | 216 KB | ######################################################################### 100%
r-rcpp-1.0.10 | 1.9 MB | ######################################################################### 100%
libmambapy-1.3.1 | 231 KB | ######################################################################### 100%
r-tidyverse-2.0.0 | 415 KB | ######################################################################### 100%
requests-2.28.2 | 55 KB | ######################################################################### 100%
python_abi-3.11 | 6 KB | ######################################################################### 100%
r-timechange-0.2.0 | 177 KB | ######################################################################### 100%
lzo-2.10 | 190 KB | ######################################################################### 100%
fontconfig-2.14.2 | 232 KB | ######################################################################### 100%
r-textshaping-0.3.6 | 99 KB | ######################################################################### 100%
r-sass-0.4.5 | 2.0 MB | ######################################################################### 100%
r-lubridate-1.9.2 | 942 KB | ######################################################################### 100%
mpc-1.3.1 | 107 KB | ######################################################################### 100%
r-ps-1.7.2 | 315 KB | ######################################################################### 100%
ruamel.yaml-0.17.21 | 248 KB | ######################################################################### 100%
r-colorspace-2.1_0 | 2.4 MB | ######################################################################### 100%
r-data.table-1.14.8 | 1.8 MB | ######################################################################### 100%
r-labeling-0.4.2 | 68 KB | ######################################################################### 100%
r-nlme-3.1_162 | 2.2 MB | ######################################################################### 100%
r-processx-3.8.0 | 318 KB | ######################################################################### 100%
r-vctrs-0.5.2 | 1.2 MB | ######################################################################### 100%
gfortran_impl_osx-64 | 17.5 MB | ######################################################################### 100%
r-mgcv-1.8_41 | 3.2 MB | ######################################################################### 100%
r-googlesheets4-1.0. | 498 KB | ######################################################################### 100%
fmt-9.1.0 | 179 KB | ######################################################################### 100%
r-yaml-2.3.7 | 104 KB | ######################################################################### 100%
r-reprex-2.0.2 | 499 KB | ######################################################################### 100%
pip-23.0.1 | 1.3 MB | ######################################################################### 100%
libgfortran5-11.3.0 | 1.4 MB | ######################################################################### 100%
conda-package-handli | 247 KB | ######################################################################### 100%
setuptools-67.4.0 | 567 KB | ######################################################################### 100%
mamba-1.3.1 | 63 KB | ######################################################################### 100%
curl-7.88.1 | 140 KB | ######################################################################### 100%
r-tidyr-1.3.0 | 1.1 MB | ######################################################################### 100%
conda-23.1.0 | 1.2 MB | ######################################################################### 100%
r-tinytex-0.44 | 139 KB | ######################################################################### 100%
cffi-1.15.1 | 274 KB | ######################################################################### 100%
r-base-4.2.2 | 23.3 MB | ######################################################################### 100%
jpeg-9e | 226 KB | ######################################################################### 100%
r-backports-1.4.1 | 109 KB | ######################################################################### 100%
r-cachem-1.0.7 | 72 KB | ######################################################################### 100%
r-gargle-1.3.0 | 519 KB | ######################################################################### 100%
brotlipy-0.7.0 | 370 KB | ######################################################################### 100%
r-cellranger-1.1.0 | 110 KB | ######################################################################### 100%
r-broom-1.0.3 | 1.7 MB | ######################################################################### 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate expression_env
#
# To deactivate an active environment, use
#
# $ conda deactivate
Retrieving notices: ...working... done
❯ source activate expression_env
❯ con-env
# conda environments:
#
/Users/kalavatt/mambaforge/envs/Trinity_env
base * /Users/kalavatt/mambaforge/envs/expression_env
/Users/kalavatt/mambaforge/envs/r413_env
/Users/kalavatt/mambaforge/envs/spyder_env
❯ mamba install -c bioconda bioconductor-deseq2
mamba install -c bioconda subread
mamba install \
-c bioconda \
bioconductor-enhancedvolcano bioconductor-pcatools
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.3.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bioconductor-deseq2']
bioconda/osx-64 3.8MB @ 3.7MB/s 1.1s
bioconda/noarch 4.2MB @ 3.6MB/s 1.2s
pkgs/main/osx-64 5.0MB @ 3.8MB/s 1.4s
pkgs/r/noarch 1.3MB @ 906.8kB/s 0.4s
pkgs/main/noarch 819.1kB @ 552.4kB/s 0.2s
pkgs/r/osx-64 820.9kB @ 512.5kB/s 0.5s
conda-forge/noarch 11.4MB @ 4.0MB/s 3.1s
conda-forge/osx-64 27.1MB @ 4.2MB/s 7.1s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- bioconductor-deseq2
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────────────────────
+ argcomplete 2.0.0 pyhd8ed1ab_0 conda-forge/noarch 35kB
+ bioconductor-annotate 1.76.0 r42hdfd78af_0 bioconda/noarch 2MB
+ bioconductor-annotationdbi 1.60.0 r42hdfd78af_0 bioconda/noarch 5MB
+ bioconductor-biobase 2.58.0 r42h3be46a4_0 bioconda/osx-64 3MB
+ bioconductor-biocgenerics 0.44.0 r42hdfd78af_0 bioconda/noarch 665kB
+ bioconductor-biocparallel 1.32.5 r42hb890f52_0 bioconda/osx-64 2MB
+ bioconductor-biostrings 2.66.0 r42h3be46a4_0 bioconda/osx-64 14MB
+ bioconductor-data-packages 20230202 hdfd78af_0 bioconda/noarch 144kB
+ bioconductor-delayedarray 0.24.0 r42h3be46a4_0 bioconda/osx-64 3MB
+ bioconductor-deseq2 1.38.0 r42hb890f52_0 bioconda/osx-64 3MB
+ bioconductor-genefilter 1.80.0 r42h238a2e4_0 bioconda/osx-64 1MB
+ bioconductor-geneplotter 1.76.0 r42hdfd78af_0 bioconda/noarch 2MB
+ bioconductor-genomeinfodb 1.34.8 r42hdfd78af_0 bioconda/noarch 4MB
+ bioconductor-genomeinfodbdata 1.2.9 r42hdfd78af_0 bioconda/noarch 8kB
+ bioconductor-genomicranges 1.50.0 r42h3be46a4_0 bioconda/osx-64 2MB
+ bioconductor-iranges 2.32.0 r42h3be46a4_0 bioconda/osx-64 3MB
+ bioconductor-keggrest 1.38.0 r42hdfd78af_0 bioconda/noarch 199kB
+ bioconductor-matrixgenerics 1.10.0 r42hdfd78af_0 bioconda/noarch 353kB
+ bioconductor-s4vectors 0.36.0 r42h3be46a4_0 bioconda/osx-64 2MB
+ bioconductor-summarizedexperiment 1.28.0 r42hdfd78af_0 bioconda/noarch 3MB
+ bioconductor-xvector 0.38.0 r42h3be46a4_0 bioconda/osx-64 737kB
+ bioconductor-zlibbioc 1.44.0 r42h3be46a4_0 bioconda/osx-64 73kB
+ importlib-metadata 4.13.0 pyha770c72_0 conda-forge/noarch 26kB
+ importlib_metadata 4.13.0 hd8ed1ab_0 conda-forge/noarch 9kB
+ jq 1.5 0 bioconda/osx-64 309kB
+ libgcc 4.8.5 1 conda-forge/osx-64 804kB
+ pyyaml 6.0 py311h5547dcb_5 conda-forge/osx-64 198kB
+ r-bh 1.81.0_1 r42hc72bb7e_0 conda-forge/noarch 11MB
+ r-bitops 1.0_7 r42h815d134_1 conda-forge/osx-64 44kB
+ r-codetools 0.2_19 r42hc72bb7e_0 conda-forge/noarch 108kB
+ r-formatr 1.14 r42hc72bb7e_0 conda-forge/noarch 165kB
+ r-futile.logger 1.4.3 r42hc72bb7e_1004 conda-forge/noarch 111kB
+ r-futile.options 1.0.1 r42hc72bb7e_1003 conda-forge/noarch 29kB
+ r-lambda.r 1.2.4 r42hc72bb7e_2 conda-forge/noarch 124kB
+ r-locfit 1.5_9.7 r42h815d134_0 conda-forge/osx-64 573kB
+ r-matrixstats 0.63.0 r42h815d134_0 conda-forge/osx-64 452kB
+ r-plogr 0.2.0 r42hc72bb7e_1004 conda-forge/noarch 21kB
+ r-png 0.1_8 r42hbf2103b_0 conda-forge/osx-64 57kB
+ r-rcpparmadillo 0.11.4.4.0 r42hf5e6a41_0 conda-forge/osx-64 883kB
+ r-rcurl 1.98_1.10 r42h815d134_0 conda-forge/osx-64 815kB
+ r-rsqlite 2.2.20 r42h49197e3_0 conda-forge/osx-64 1MB
+ r-snow 0.4_4 r42hc72bb7e_1 conda-forge/noarch 117kB
+ r-survival 3.5_3 r42h815d134_0 conda-forge/osx-64 6MB
+ r-xml 3.99_0.13 r42h67ce8dc_0 conda-forge/osx-64 2MB
+ r-xtable 1.8_4 r42hc72bb7e_4 conda-forge/noarch 717kB
+ toml 0.10.2 pyhd8ed1ab_0 conda-forge/noarch 18kB
+ xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge/noarch 14kB
+ yaml 0.2.5 h0d85af4_2 conda-forge/osx-64 84kB
+ yq 3.1.1 pyhd8ed1ab_0 conda-forge/noarch 23kB
+ zipp 3.15.0 pyhd8ed1ab_0 conda-forge/noarch 17kB
Summary:
Install: 50 packages
Total download: 76MB
───────────────────────────────────────────────────────────────────────────────────────────────────
bioconductor-biocgenerics 664.5kB @ 10.3MB/s 0.1s
bioconductor-zlibbioc 73.2kB @ 862.9kB/s 0.1s
bioconductor-s4vectors 2.3MB @ 23.5MB/s 0.1s
bioconductor-iranges 2.5MB @ 19.5MB/s 0.1s
pyyaml 197.9kB @ 1.5MB/s 0.0s
bioconductor-biobase 2.5MB @ 17.7MB/s 0.1s
libgcc 804.3kB @ 5.7MB/s 0.1s
r-snow 117.0kB @ 755.2kB/s 0.0s
toml 18.4kB @ 113.6kB/s 0.0s
r-formatr 165.2kB @ 973.5kB/s 0.0s
zipp 17.2kB @ 98.5kB/s 0.0s
argcomplete 35.2kB @ 194.1kB/s 0.0s
yq 22.6kB @ 113.7kB/s 0.0s
bioconductor-biocparallel 1.7MB @ 8.4MB/s 0.0s
bioconductor-keggrest 199.5kB @ 957.5kB/s 0.0s
r-png 57.4kB @ 229.4kB/s 0.0s
bioconductor-annotate 1.8MB @ 6.5MB/s 0.1s
bioconductor-genomeinfodb 4.3MB @ 14.6MB/s 0.1s
r-rcurl 815.2kB @ 2.5MB/s 0.0s
r-codetools 108.1kB @ 329.0kB/s 0.0s
r-survival 6.0MB @ 18.2MB/s 0.3s
r-plogr 21.2kB @ 59.4kB/s 0.0s
importlib_metadata 9.1kB @ 24.9kB/s 0.0s
bioconductor-data-packages 144.5kB @ 372.4kB/s 0.0s
bioconductor-genomicranges 2.2MB @ 5.3MB/s 0.1s
r-matrixstats 451.9kB @ 963.3kB/s 0.0s
r-locfit 573.3kB @ 1.2MB/s 0.2s
jq 309.3kB @ 650.1kB/s 0.1s
importlib-metadata 25.5kB @ 50.9kB/s 0.0s
yaml 84.2kB @ 166.5kB/s 0.0s
bioconductor-genomeinfodbdata 7.9kB @ 14.7kB/s 0.0s
bioconductor-matrixgenerics 352.7kB @ 638.6kB/s 0.1s
bioconductor-deseq2 2.9MB @ 5.0MB/s 0.4s
r-bitops 44.3kB @ 74.5kB/s 0.0s
r-lambda.r 123.9kB @ 198.9kB/s 0.0s
r-rcpparmadillo 883.4kB @ 1.3MB/s 0.2s
bioconductor-annotationdbi 5.2MB @ 7.1MB/s 0.2s
r-xtable 717.4kB @ 914.1kB/s 0.1s
r-bh 11.4MB @ 14.0MB/s 0.2s
r-futile.logger 111.1kB @ 136.2kB/s 0.0s
xmltodict 13.6kB @ 16.0kB/s 0.0s
bioconductor-geneplotter 1.5MB @ 1.7MB/s 0.5s
bioconductor-summarizedexperiment 2.8MB @ 3.1MB/s 0.1s
bioconductor-genefilter 1.1MB @ 1.3MB/s 0.2s
r-rsqlite 1.2MB @ 1.3MB/s 0.3s
r-futile.options 28.8kB @ 31.3kB/s 0.0s
bioconductor-xvector 737.3kB @ 782.5kB/s 0.0s
bioconductor-biostrings 14.2MB @ 13.2MB/s 0.2s
r-xml 1.7MB @ 1.5MB/s 0.2s
bioconductor-delayedarray 2.5MB @ 2.1MB/s 0.3s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c bioconda subread
__ __ __ __
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██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.3.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['subread']
bioconda/osx-64 Using cache
bioconda/noarch Using cache
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
pkgs/r/noarch No change
pkgs/r/osx-64 No change
pkgs/main/osx-64 No change
pkgs/main/noarch 819.4kB @ 2.4MB/s 0.4s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- subread
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────
+ subread 2.0.3 h740a0af_1 bioconda/osx-64 12MB
Summary:
Install: 1 packages
Total download: 12MB
────────────────────────────────────────────────────────────
Confirm changes: [Y/n]
mamba install \
-c bioconda \
bioconductor-enhancedvolcano bioconductor-pcatools
subread 12.3MB @ 33.3MB/s 0.4s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
\ __ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
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/ / \ / \ / \ / \ \____
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███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.3.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bioconductor-enhancedvolcano', 'bioconductor-pcatools']
bioconda/osx-64 Using cache
bioconda/noarch Using cache
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
pkgs/main/osx-64 Using cache
pkgs/main/noarch Using cache
pkgs/r/osx-64 Using cache
pkgs/r/noarch Using cache
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- bioconductor-enhancedvolcano
- bioconductor-pcatools
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────────────
+ bioconductor-beachmat 2.14.0 r42hb890f52_0 bioconda/osx-64 1MB
+ bioconductor-biocsingular 1.14.0 r42hb890f52_0 bioconda/osx-64 995kB
+ bioconductor-delayedmatrixstats 1.20.0 r42hdfd78af_0 bioconda/noarch 740kB
+ bioconductor-enhancedvolcano 1.16.0 r42hdfd78af_0 bioconda/noarch 5MB
+ bioconductor-pcatools 2.10.0 r42hb890f52_0 bioconda/osx-64 5MB
+ bioconductor-scaledmatrix 1.6.0 r42hdfd78af_0 bioconda/noarch 653kB
+ bioconductor-sparsematrixstats 1.10.0 r42hb890f52_0 bioconda/osx-64 1MB
+ r-cowplot 1.1.1 r42hc72bb7e_1 conda-forge/noarch 1MB
+ r-dqrng 0.3.0 r42h49197e3_1 conda-forge/osx-64 164kB
+ r-ggrepel 0.9.3 r42h49197e3_0 conda-forge/osx-64 261kB
+ r-irlba 2.3.5.1 r42hce01bf1_0 conda-forge/osx-64 320kB
+ r-plyr 1.8.8 r42h49197e3_0 conda-forge/osx-64 856kB
+ r-reshape2 1.4.4 r42h49197e3_2 conda-forge/osx-64 132kB
+ r-rsvd 1.0.5 r42hc72bb7e_1 conda-forge/noarch 4MB
+ r-sitmo 2.0.2 r42h49197e3_1 conda-forge/osx-64 160kB
Summary:
Install: 15 packages
Total download: 22MB
───────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
bioconductor-sparsematrixstats 1.2MB @ 11.5MB/s 0.1s
bioconductor-scaledmatrix 652.9kB @ 6.1MB/s 0.1s
r-sitmo 160.5kB @ 1.5MB/s 0.1s
bioconductor-delayedmatrixstats 739.6kB @ 6.2MB/s 0.1s
bioconductor-beachmat 1.3MB @ 10.0MB/s 0.1s
r-irlba 319.6kB @ 2.0MB/s 0.1s
r-reshape2 131.5kB @ 804.9kB/s 0.0s
r-ggrepel 260.8kB @ 1.5MB/s 0.0s
r-rsvd 3.6MB @ 20.3MB/s 0.1s
r-dqrng 163.7kB @ 838.1kB/s 0.0s
r-plyr 856.0kB @ 4.0MB/s 0.0s
bioconductor-biocsingular 994.8kB @ 4.1MB/s 0.1s
r-cowplot 1.4MB @ 4.8MB/s 0.2s
bioconductor-enhancedvolcano 5.1MB @ 12.9MB/s 0.2s
bioconductor-pcatools 5.0MB @ 7.5MB/s 0.5s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c conda-forge r-markdown
__ __ __ __
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|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.27.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['r-markdown']
bioconda/noarch 4.2MB @ 4.4MB/s 1.1s
pkgs/main/osx-64 5.0MB @ 4.3MB/s 1.3s
bioconda/osx-64 3.8MB @ 2.8MB/s 1.4s
pkgs/r/noarch 1.3MB @ 901.1kB/s 0.5s
pkgs/r/osx-64 820.9kB @ 556.7kB/s 0.3s
pkgs/main/noarch 819.4kB @ 501.6kB/s 0.3s
conda-forge/noarch 11.4MB @ 4.9MB/s 2.6s
conda-forge/osx-64 27.1MB @ 4.3MB/s 7.0s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- r-markdown
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────
+ r-commonmark 1.8.1 r42h815d134_0 conda-forge/osx-64 Cached
+ r-markdown 1.5 r42hc72bb7e_0 conda-forge/noarch 122kB
Summary:
Install: 2 packages
Total download: 122kB
─────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
r-markdown 122.1kB @ 597.3kB/s 0.2s
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c bioconda bioconductor-sva
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.27.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bioconductor-sva']
bioconda/osx-64 3.8MB @ 4.8MB/s 0.9s
pkgs/r/noarch No change
bioconda/noarch 4.2MB @ 4.2MB/s 1.1s
pkgs/main/osx-64 5.2MB @ 4.7MB/s 1.2s
pkgs/r/osx-64 No change
pkgs/main/noarch 820.1kB @ 673.2kB/s 0.3s
conda-forge/noarch 11.7MB @ 4.5MB/s 2.8s
conda-forge/osx-64 27.6MB @ 5.0MB/s 6.2s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- bioconductor-sva
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────
+ bioconductor-sva 3.46.0 r42h3be46a4_0 bioconda/osx-64 489kB
Summary:
Install: 1 packages
Total download: 489kB
─────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
bioconductor-sva 488.8kB @ 1.9MB/s 0.3s
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c conda-forge r-ggalt
__ __ __ __
/ \ / \ / \ / \
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/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.27.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['r-ggalt']
bioconda/osx-64 No change
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/r/osx-64 No change
bioconda/noarch 4.2MB @ 4.6MB/s 1.0s
pkgs/main/osx-64 5.2MB @ 4.9MB/s 1.2s
conda-forge/noarch 11.7MB @ 5.2MB/s 2.5s
conda-forge/osx-64 27.6MB @ 4.8MB/s 6.4s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- r-ggalt
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────────
+ proj 9.1.1 hf909084_2 conda-forge/osx-64 3MB
+ r-ash 1.0_15 r42h1e4e481_1007 conda-forge/osx-64 45kB
+ r-crosstalk 1.2.0 r42hc72bb7e_1 conda-forge/noarch 377kB
+ r-extrafont 0.18 r42ha770c72_1 conda-forge/noarch 69kB
+ r-extrafontdb 1.0 r42hc72bb7e_1004 conda-forge/noarch 20kB
+ r-ggalt 0.4.0 r42ha770c72_3 conda-forge/noarch 2MB
+ r-hexbin 1.28.3 r42h1e4e481_0 conda-forge/osx-64 2MB
+ r-htmlwidgets 1.6.2 r42hc72bb7e_0 conda-forge/noarch 424kB
+ r-later 1.3.0 r42hf00d5e6_1 conda-forge/osx-64 116kB
+ r-lazyeval 0.2.2 r42h815d134_3 conda-forge/osx-64 168kB
+ r-maps 3.4.1 r42h815d134_1 conda-forge/osx-64 2MB
+ r-plotly 4.10.1 r42hc72bb7e_0 conda-forge/noarch 3MB
+ r-proj4 1.0_12 r42h2df1cd0_1 conda-forge/osx-64 37kB
+ r-promises 1.2.0.1 r42h49197e3_1 conda-forge/osx-64 2MB
+ r-rttf2pt1 1.3.12 r42h815d134_0 conda-forge/osx-64 109kB
+ sqlite 3.40.0 h9ae0607_0 conda-forge/osx-64 Cached
Summary:
Install: 16 packages
Total download: 15MB
─────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
r-lazyeval 167.8kB @ 3.0MB/s 0.1s
r-maps 2.4MB @ 26.6MB/s 0.1s
r-htmlwidgets 424.0kB @ 4.8MB/s 0.0s
proj 2.6MB @ 19.5MB/s 0.0s
r-later 115.6kB @ 779.7kB/s 0.1s
r-rttf2pt1 108.9kB @ 673.2kB/s 0.2s
r-extrafontdb 20.3kB @ 65.8kB/s 0.2s
r-ash 44.8kB @ 141.7kB/s 0.3s
r-ggalt 2.4MB @ 7.1MB/s 0.2s
r-proj4 37.4kB @ 111.1kB/s 0.2s
r-plotly 3.0MB @ 8.9MB/s 0.3s
r-extrafont 69.0kB @ 164.3kB/s 0.1s
r-crosstalk 376.9kB @ 861.5kB/s 0.1s
r-promises 1.6MB @ 3.5MB/s 0.1s
r-hexbin 1.6MB @ 3.4MB/s 0.2s
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c conda-forge r-rjson
__ __ __ __
/ \ / \ / \ / \
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/ / \ / \ / \ / \ \____
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/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.27.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['r-rjson']
pkgs/main/osx-64 No change
bioconda/osx-64 No change
pkgs/r/noarch No change
bioconda/noarch No change
pkgs/r/osx-64 No change
pkgs/main/noarch No change
conda-forge/noarch 11.7MB @ 5.0MB/s 2.6s
conda-forge/osx-64 27.6MB @ 5.1MB/s 6.1s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- r-rjson
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────
+ r-rjson 0.2.21 r42h49197e3_2 conda-forge/osx-64 167kB
Summary:
Install: 1 packages
Total download: 167kB
───────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- r-rjson
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────
+ r-rjson 0.2.21 r42h49197e3_2 conda-forge/osx-64 167kB
Summary:
Install: 1 packages
Total download: 167kB
r-rjson 167.4kB @ 341.8kB/s 0.5s
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c bioconda bioconductor-rtracklayer
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.27.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bioconductor-rtracklayer']
bioconda/osx-64 3.8MB @ 4.4MB/s 0.9s
pkgs/r/noarch No change
pkgs/main/noarch No change
bioconda/noarch 4.2MB @ 4.3MB/s 1.1s
pkgs/r/osx-64 No change
pkgs/main/osx-64 5.2MB @ 4.8MB/s 1.2s
conda-forge/noarch 11.7MB @ 4.5MB/s 2.9s
conda-forge/osx-64 27.6MB @ 5.0MB/s 6.2s
Pinned packages:
- python 3.11.*
warning libmamba Invalid package cache, file '/Users/kalavatt/mambaforge/pkgs/r-base-4.2.2-h841e2fe_3/lib/R/doc/html/packages.html' has incorrect size
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/expression_env
Updating specs:
- bioconductor-rtracklayer
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────
+ bioconductor-biocio 1.8.0 r42hdfd78af_0 bioconda/noarch 429kB
+ bioconductor-genomicalignments 1.34.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-rhtslib 2.0.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-rsamtools 2.14.0 r42hb890f52_0 bioconda/osx-64 Cached
+ bioconductor-rtracklayer 1.58.0 r42h6e925bd_1 bioconda/osx-64 6MB
+ r-restfulr 0.0.15 r42h9f1ad2d_1 bioconda/osx-64 440kB
Change:
────────────────────────────────────────────────────────────────────────────────────────────────
- krb5 1.20.1 h049b76e_0 conda-forge
+ krb5 1.20.1 h0165f36_0 conda-forge/osx-64 1MB
- libarchive 3.6.2 h6d8d9f1_0 conda-forge
+ libarchive 3.6.2 h7181a6f_0 conda-forge/osx-64 728kB
- libssh2 1.10.0 h47af595_3 conda-forge
+ libssh2 1.10.0 h7535e13_3 conda-forge/osx-64 Cached
- python 3.11.0 he7542f4_1_cpython conda-forge
+ python 3.11.0 h4150a38_1_cpython conda-forge/osx-64 15MB
- sigtool 0.1.3 h88f4db0_0 conda-forge
+ sigtool 0.1.3 h57ddcff_0 conda-forge/osx-64 Cached
Downgrade:
────────────────────────────────────────────────────────────────────────────────────────────────
- cryptography 39.0.2 py311h61927ef_0 conda-forge
+ cryptography 39.0.0 py311h8661239_0 conda-forge/osx-64 1MB
- curl 7.88.1 h6df9250_0 conda-forge
+ curl 7.87.0 haf73cf8_0 conda-forge/osx-64 141kB
- libcurl 7.88.1 h6df9250_0 conda-forge
+ libcurl 7.87.0 haf73cf8_0 conda-forge/osx-64 331kB
- libmamba 1.3.1 h9d281b0_2 conda-forge
+ libmamba 1.2.0 h1ca9962_0 conda-forge/osx-64 1MB
- libmambapy 1.3.1 py311hcc19a12_2 conda-forge
+ libmambapy 1.2.0 py311h8020b13_0 conda-forge/osx-64 237kB
- libnghttp2 1.52.0 he2ab024_0 conda-forge
+ libnghttp2 1.51.0 h0dd9d14_0 conda-forge/osx-64 609kB
- mamba 1.3.1 py311h8082e30_2 conda-forge
+ mamba 1.2.0 py311h280fce9_0 conda-forge/osx-64 65kB
- openssl 3.1.0 hfd90126_0 conda-forge
+ openssl 1.1.1t hfd90126_0 conda-forge/osx-64 2MB
- r-base 4.2.3 h841e2fe_0 conda-forge
+ r-base 4.2.2 h841e2fe_3 conda-forge/osx-64 Cached
- r-openssl 2.0.6 r42hfeb9312_0 conda-forge
+ r-openssl 2.0.5 r42h13d56fc_0 conda-forge/osx-64 626kB
Summary:
Install: 6 packages
Change: 5 packages
Downgrade: 10 packages
Total download: 30MB
────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
libarchive 727.7kB @ 8.5MB/s 0.1s
openssl 1.7MB @ 18.6MB/s 0.1s
libnghttp2 609.3kB @ 6.1MB/s 0.1s
krb5 1.1MB @ 10.9MB/s 0.1s
libcurl 331.2kB @ 2.5MB/s 0.0s
python 15.3MB @ 50.6MB/s 0.3s
mamba 65.4kB @ 215.6kB/s 0.2s
curl 141.3kB @ 431.0kB/s 0.0s
libmambapy 237.1kB @ 716.2kB/s 0.2s
bioconductor-biocio 429.4kB @ 1.2MB/s 0.3s
r-restfulr 440.1kB @ 788.7kB/s 0.2s
r-openssl 626.4kB @ 1.0MB/s 0.3s
bioconductor-rtracklayer 5.6MB @ 9.1MB/s 0.5s
cryptography 1.2MB @ 1.7MB/s 0.4s
libmamba 1.2MB @ 1.5MB/s 0.5s
Preparing transaction: done
Verifying transaction: /
SafetyError: The package for r-base located at /Users/kalavatt/mambaforge/pkgs/r-base-4.2.2-h841e2fe_3
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
reported size: 3423 bytes
actual size: 41091 bytes
done
Executing transaction: doneCode: Add appropriate shortcut to .zaliases and .bash_aliases
#!/bin/bash
# .zaliases
alias expression_env="source activate expression_env"
alias R-expression="(
source activate expression_env
open -na /Applications/RStudio.app
)"
# .bash_aliases
alias expression_env="source activate expression_env"Code: Get situated
#!/bin/bash
tmux new -s install
tmux attach -t install
grabnode # 1, defaults
transcriptome &&
{
cd "results/2023-0215" \
|| echo "cd'ing failed; check on this..."
}
if [[ "${CONDA_DEFAULT_ENV}" != "base" ]]; then
conda deactivate
fiNeed the following packages
- https://anaconda.org/bioconda/agat
- https://anaconda.org/bioconda/gffcompare
- https://anaconda.org/bioconda/subread (
featureCounts) - https://anaconda.org/bioconda/htseq (
htseq-count) - https://anaconda.org/bioconda/bioconductor-rtracklayer
- https://anaconda.org/bioconda/bioconductor-genomicranges
- https://anaconda.org/conda-forge/markdown
- https://anaconda.org/conda-forge/r-markdown
- https://anaconda.org/conda-forge/r-tidyverse
Code: Set up gff3_env
#!/bin/bash
# Local installation, WorkMac
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
# conda config --set channel_priority strict
create_x86_conda_environment gff3_env
mamba install \
-c bioconda \
bioconductor-genomicalignments \
bioconductor-genomicranges \
bioconductor-rtracklayer
mamba install \
-c conda-forge \
python==3.10 \
bioconductor-rtracklayer==1.58.0
mamba install \
-c bioconda \
gffcompare \
gffread \
htseq \
bioconductor-rtracklayer==1.58.0
mamba install \
-c conda-forge \
markdown \
parallel \
r-markdown \
r-tidyverse \
rename \
ucsc-liftover \
bioconductor-rtracklayer==1.58.0
mamba install \
-c conda-forge \
r-complexupset \
bioconductor-rtracklayer==1.58.0
mamba install \
-c bioconda \
igv \
bioconductor-rtracklayer==1.58.0
# mamba create -n gff3_env \
# --yes \
# -c bioconda \
# agat \
# gffcompare \
# subread \
# htseq \
# bioconductor-rtracklayer \
# bioconductor-genomicranges
#
# source activate gff3_env
#
# mamba install \
# --yes \
# -c conda-forge \
# markdown \
# r-markdown \
# r-tidyverse \
# bioconductor-rtracklayer==1.58.0
#
# mamba install \
# --yes \
# -c conda-forge \
# parallel \
# rename \
# gffread \
# ucsc-liftover \
# bioconductor-rtracklayer==1.58.0Printed: Set up gff3_env
❯ create_x86_conda_environment gff3_env
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.1.0
latest version: 23.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.3.1
## Package Plan ##
environment location: /Users/kalavatt/mambaforge/envs/gff3_env
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate gff3_env
#
# To deactivate an active environment, use
#
# $ conda deactivate
❯ mamba install \
> -c bioconda \
> bioconductor-genomicalignments \
> bioconductor-genomicranges \
> bioconductor-rtracklayer
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bioconductor-genomicalignments', 'bioconductor-genomicranges', 'bioconductor-rtracklayer']
bioconda/noarch No change
bioconda/osx-64 No change
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/r/osx-64 No change
pkgs/main/osx-64 5.2MB @ 5.3MB/s 1.1s
conda-forge/noarch 11.9MB @ 2.8MB/s 4.5s
conda-forge/osx-64 27.8MB @ 5.0MB/s 6.3s
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/gff3_env
Updating specs:
- bioconductor-genomicalignments
- bioconductor-genomicranges
- bioconductor-rtracklayer
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────────────
+ _r-mutex 1.0.1 anacondar_1 conda-forge/noarch Cached
+ argcomplete 3.0.5 pyhd8ed1ab_0 conda-forge/noarch Cached
+ bioconductor-biobase 2.58.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-biocgenerics 0.44.0 r42hdfd78af_0 bioconda/noarch Cached
+ bioconductor-biocio 1.8.0 r42hdfd78af_0 bioconda/noarch Cached
+ bioconductor-biocparallel 1.32.5 r42hb890f52_0 bioconda/osx-64 Cached
+ bioconductor-biostrings 2.66.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-data-packages 20230202 hdfd78af_0 bioconda/noarch Cached
+ bioconductor-delayedarray 0.24.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-genomeinfodb 1.34.8 r42hdfd78af_0 bioconda/noarch Cached
+ bioconductor-genomeinfodbdata 1.2.9 r42hdfd78af_0 bioconda/noarch Cached
+ bioconductor-genomicalignments 1.34.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-genomicranges 1.50.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-iranges 2.32.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-matrixgenerics 1.10.0 r42hdfd78af_0 bioconda/noarch Cached
+ bioconductor-rhtslib 2.0.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-rsamtools 2.14.0 r42hb890f52_0 bioconda/osx-64 Cached
+ bioconductor-rtracklayer 1.58.0 r42h6e925bd_1 bioconda/osx-64 Cached
+ bioconductor-s4vectors 0.36.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-summarizedexperiment 1.28.0 r42hdfd78af_0 bioconda/noarch Cached
+ bioconductor-xvector 0.38.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bioconductor-zlibbioc 1.44.0 r42h3be46a4_0 bioconda/osx-64 Cached
+ bwidget 1.9.14 h694c41f_1 conda-forge/osx-64 Cached
+ bzip2 1.0.8 h0d85af4_4 conda-forge/osx-64 Cached
+ c-ares 1.18.1 h0d85af4_0 conda-forge/osx-64 Cached
+ ca-certificates 2022.12.7 h033912b_0 conda-forge/osx-64 Cached
+ cairo 1.16.0 h904041c_1014 conda-forge/osx-64 Cached
+ cctools_osx-64 973.0.1 h5676edf_13 conda-forge/osx-64 Cached
+ clang 16.0.1 h49458c0_0 conda-forge/osx-64 Cached
+ clang-16 16.0.1 default_hd25f202_0 conda-forge/osx-64 Cached
+ clang_osx-64 16.0.1 hac0a0c4_1 conda-forge/osx-64 Cached
+ clangxx 16.0.1 default_hd25f202_0 conda-forge/osx-64 Cached
+ clangxx_osx-64 16.0.1 h950475c_1 conda-forge/osx-64 Cached
+ compiler-rt 16.0.1 h613da45_0 conda-forge/osx-64 Cached
+ compiler-rt_osx-64 16.0.1 h613da45_0 conda-forge/noarch Cached
+ curl 7.87.0 haf73cf8_0 conda-forge/osx-64 Cached
+ expat 2.5.0 hf0c8a7f_1 conda-forge/osx-64 Cached
+ font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge/noarch Cached
+ font-ttf-inconsolata 3.000 h77eed37_0 conda-forge/noarch Cached
+ font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge/noarch Cached
+ font-ttf-ubuntu 0.83 hab24e00_0 conda-forge/noarch Cached
+ fontconfig 2.14.2 h5bb23bf_0 conda-forge/osx-64 Cached
+ fonts-conda-ecosystem 1 0 conda-forge/noarch Cached
+ fonts-conda-forge 1 0 conda-forge/noarch Cached
+ freetype 2.12.1 h3f81eb7_1 conda-forge/osx-64 Cached
+ fribidi 1.0.10 hbcb3906_0 conda-forge/osx-64 Cached
+ gettext 0.21.1 h8a4c099_0 conda-forge/osx-64 Cached
+ gfortran_impl_osx-64 11.3.0 h1f927f5_31 conda-forge/osx-64 Cached
+ gfortran_osx-64 11.3.0 h18f7dce_1 conda-forge/osx-64 Cached
+ gmp 6.2.1 h2e338ed_0 conda-forge/osx-64 Cached
+ graphite2 1.3.13 h2e338ed_1001 conda-forge/osx-64 Cached
+ gsl 2.7 h93259b0_0 conda-forge/osx-64 Cached
+ harfbuzz 6.0.0 h08f8713_0 conda-forge/osx-64 Cached
+ icu 70.1 h96cf925_0 conda-forge/osx-64 Cached
+ isl 0.25 hb486fe8_0 conda-forge/osx-64 Cached
+ jpeg 9e hb7f2c08_3 conda-forge/osx-64 Cached
+ jq 1.5 0 bioconda/osx-64 Cached
+ krb5 1.20.1 h0165f36_0 conda-forge/osx-64 Cached
+ ld64_osx-64 609 hbfe4790_13 conda-forge/osx-64 Cached
+ lerc 4.0.0 hb486fe8_0 conda-forge/osx-64 Cached
+ libblas 3.9.0 16_osx64_openblas conda-forge/osx-64 Cached
+ libcblas 3.9.0 16_osx64_openblas conda-forge/osx-64 Cached
+ libclang-cpp16 16.0.1 default_hd25f202_0 conda-forge/osx-64 Cached
+ libcurl 7.87.0 haf73cf8_0 conda-forge/osx-64 Cached
+ libcxx 16.0.1 h71dddab_0 conda-forge/osx-64 Cached
+ libdeflate 1.17 hac1461d_0 conda-forge/osx-64 Cached
+ libedit 3.1.20191231 h0678c8f_2 conda-forge/osx-64 Cached
+ libev 4.33 haf1e3a3_1 conda-forge/osx-64 Cached
+ libexpat 2.5.0 hf0c8a7f_1 conda-forge/osx-64 Cached
+ libffi 3.4.2 h0d85af4_5 conda-forge/osx-64 Cached
+ libgcc 4.8.5 1 conda-forge/osx-64 Cached
+ libgfortran 5.0.0 11_3_0_h97931a8_31 conda-forge/osx-64 Cached
+ libgfortran-devel_osx-64 11.3.0 h824d247_31 conda-forge/noarch Cached
+ libgfortran5 12.2.0 he409387_31 conda-forge/osx-64 Cached
+ libglib 2.74.1 h4c723e1_1 conda-forge/osx-64 Cached
+ libiconv 1.17 hac89ed1_0 conda-forge/osx-64 Cached
+ liblapack 3.9.0 16_osx64_openblas conda-forge/osx-64 Cached
+ libllvm16 16.0.1 h7001e86_0 conda-forge/osx-64 Cached
+ libnghttp2 1.51.0 h0dd9d14_0 conda-forge/osx-64 Cached
+ libopenblas 0.3.21 openmp_h429af6e_3 conda-forge/osx-64 Cached
+ libpng 1.6.39 ha978bb4_0 conda-forge/osx-64 Cached
+ libsqlite 3.40.0 ha978bb4_0 conda-forge/osx-64 Cached
+ libssh2 1.10.0 h7535e13_3 conda-forge/osx-64 Cached
+ libtiff 4.5.0 hee9004a_2 conda-forge/osx-64 Cached
+ libwebp-base 1.3.0 hb7f2c08_0 conda-forge/osx-64 Cached
+ libxml2 2.10.3 h201ad9d_4 conda-forge/osx-64 Cached
+ libzlib 1.2.13 hfd90126_4 conda-forge/osx-64 Cached
+ llvm-openmp 16.0.1 h61d9ccf_0 conda-forge/osx-64 Cached
+ llvm-tools 16.0.1 h7001e86_0 conda-forge/osx-64 Cached
+ make 4.3 h22f3db7_1 conda-forge/osx-64 Cached
+ mpc 1.3.1 h81bd1dd_0 conda-forge/osx-64 Cached
+ mpfr 4.2.0 h4f9bd69_0 conda-forge/osx-64 Cached
+ ncurses 6.3 h96cf925_1 conda-forge/osx-64 Cached
+ openssl 1.1.1t hfd90126_0 conda-forge/osx-64 Cached
+ pango 1.50.14 hbd9bf65_0 conda-forge/osx-64 Cached
+ pcre2 10.40 h1c4e4bc_0 conda-forge/osx-64 Cached
+ pip 23.0.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pixman 0.40.0 hbcb3906_0 conda-forge/osx-64 Cached
+ python 3.11.0 h4150a38_1_cpython conda-forge/osx-64 Cached
+ python_abi 3.11 3_cp311 conda-forge/osx-64 Cached
+ pyyaml 6.0 py311h5547dcb_5 conda-forge/osx-64 Cached
+ r-base 4.2.2 h841e2fe_3 conda-forge/osx-64 Cached
+ r-bh 1.81.0_1 r42hc72bb7e_0 conda-forge/noarch Cached
+ r-bitops 1.0_7 r42h815d134_1 conda-forge/osx-64 Cached
+ r-codetools 0.2_19 r42hc72bb7e_0 conda-forge/noarch Cached
+ r-cpp11 0.4.3 r42hc72bb7e_0 conda-forge/noarch Cached
+ r-crayon 1.5.2 r42hc72bb7e_1 conda-forge/noarch Cached
+ r-formatr 1.14 r42hc72bb7e_0 conda-forge/noarch Cached
+ r-futile.logger 1.4.3 r42hc72bb7e_1004 conda-forge/noarch Cached
+ r-futile.options 1.0.1 r42hc72bb7e_1003 conda-forge/noarch Cached
+ r-lambda.r 1.2.4 r42hc72bb7e_2 conda-forge/noarch Cached
+ r-lattice 0.21_8 r42h815d134_0 conda-forge/osx-64 Cached
+ r-matrix 1.5_4 r42hce01bf1_0 conda-forge/osx-64 Cached
+ r-matrixstats 0.63.0 r42h815d134_0 conda-forge/osx-64 Cached
+ r-rcurl 1.98_1.10 r42h815d134_0 conda-forge/osx-64 Cached
+ r-restfulr 0.0.15 r42h9f1ad2d_1 bioconda/osx-64 Cached
+ r-rjson 0.2.21 r42h49197e3_2 conda-forge/osx-64 Cached
+ r-snow 0.4_4 r42hc72bb7e_1 conda-forge/noarch Cached
+ r-xml 3.99_0.14 r42h67ce8dc_0 conda-forge/osx-64 Cached
+ r-yaml 2.3.7 r42h815d134_0 conda-forge/osx-64 Cached
+ readline 8.2 h9e318b2_1 conda-forge/osx-64 Cached
+ setuptools 67.6.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ sigtool 0.1.3 h57ddcff_0 conda-forge/osx-64 Cached
+ tapi 1100.0.11 h9ce4665_0 conda-forge/osx-64 Cached
+ tk 8.6.12 h5dbffcc_0 conda-forge/osx-64 Cached
+ tktable 2.10 h49f0cf7_3 conda-forge/osx-64 Cached
+ toml 0.10.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tomlkit 0.11.7 pyha770c72_0 conda-forge/noarch Cached
+ typing 3.10.0.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tzdata 2023c h71feb2d_0 conda-forge/noarch Cached
+ wheel 0.40.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xz 5.2.6 h775f41a_0 conda-forge/osx-64 Cached
+ yaml 0.2.5 h0d85af4_2 conda-forge/osx-64 Cached
+ yq 3.2.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ zlib 1.2.13 hfd90126_4 conda-forge/osx-64 Cached
+ zstd 1.5.2 hbc0c0cd_6 conda-forge/osx-64 Cached
Summary:
Install: 137 packages
Total download: 0 B
────────────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install \
> -c conda-forge \
> python==3.10 \
> bioconductor-rtracklayer==1.58.0
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['python==3.10', 'bioconductor-rtracklayer==1.58.0']
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
bioconda/osx-64 Using cache
bioconda/noarch Using cache
pkgs/r/osx-64 No change
pkgs/main/osx-64 No change
pkgs/r/noarch No change
pkgs/main/noarch No change
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/gff3_env
Updating specs:
- python==3.10
- bioconductor-rtracklayer==1.58.0
- ca-certificates
- openssl
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────────────────────
+ sqlite 3.40.0 h9ae0607_0 conda-forge/osx-64 Cached
Change:
──────────────────────────────────────────────────────────────────────────────
- pyyaml 6.0 py311h5547dcb_5 conda-forge
+ pyyaml 6.0 py310h90acd4f_5 conda-forge/osx-64 Cached
Reinstall:
──────────────────────────────────────────────────────────────────────────────
o argcomplete 3.0.5 pyhd8ed1ab_0 conda-forge
o pip 23.0.1 pyhd8ed1ab_0 conda-forge
o setuptools 67.6.1 pyhd8ed1ab_0 conda-forge
o toml 0.10.2 pyhd8ed1ab_0 conda-forge
o tomlkit 0.11.7 pyha770c72_0 conda-forge
o typing 3.10.0.0 pyhd8ed1ab_0 conda-forge
o wheel 0.40.0 pyhd8ed1ab_0 conda-forge
o xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
o yq 3.2.1 pyhd8ed1ab_0 conda-forge
Downgrade:
──────────────────────────────────────────────────────────────────────────────
- python 3.11.0 h4150a38_1_cpython conda-forge
+ python 3.10.0 h1248fe1_3_cpython conda-forge/osx-64 Cached
- python_abi 3.11 3_cp311 conda-forge
+ python_abi 3.10 3_cp310 conda-forge/osx-64 Cached
Summary:
Install: 1 packages
Change: 1 packages
Reinstall: 9 packages
Downgrade: 2 packages
Total download: 0 B
──────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install \
> -c bioconda \
> gffcompare \
> gffread \
> htseq \
> bioconductor-rtracklayer==1.58.0
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['gffcompare', 'gffread', 'htseq', 'bioconductor-rtracklayer==1.58.0']
bioconda/osx-64 Using cache
bioconda/noarch Using cache
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
pkgs/main/osx-64 No change
pkgs/r/noarch No change
pkgs/r/osx-64 No change
pkgs/main/noarch No change
Pinned packages:
- python 3.10.*
warning libmamba Invalid package cache, file '/Users/kalavatt/mambaforge/pkgs/r-base-4.2.2-h6e3643f_2/lib/R/doc/html/packages.html' has incorrect size
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/gff3_env
Updating specs:
- gffcompare
- gffread
- htseq
- bioconductor-rtracklayer==1.58.0
- ca-certificates
- openssl
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────
+ brotli 1.0.9 hb7f2c08_8 conda-forge/osx-64 Cached
+ brotli-bin 1.0.9 hb7f2c08_8 conda-forge/osx-64 Cached
+ certifi 2022.12.7 pyhd8ed1ab_0 conda-forge/noarch Cached
+ contourpy 1.0.7 py310ha23aa8a_0 conda-forge/osx-64 Cached
+ cycler 0.11.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ fonttools 4.39.3 py310h90acd4f_0 conda-forge/osx-64 Cached
+ gffcompare 0.12.6 hb3ea9af_0 bioconda/osx-64 Cached
+ gffread 0.12.7 h6151dfb_1 bioconda/osx-64 Cached
+ htseq 2.0.2 py310hec0d4ff_0 bioconda/osx-64 Cached
+ kiwisolver 1.4.4 py310ha23aa8a_1 conda-forge/osx-64 Cached
+ lcms2 2.14 h90f4b2a_0 conda-forge/osx-64 Cached
+ libbrotlicommon 1.0.9 hb7f2c08_8 conda-forge/osx-64 Cached
+ libbrotlidec 1.0.9 hb7f2c08_8 conda-forge/osx-64 Cached
+ libbrotlienc 1.0.9 hb7f2c08_8 conda-forge/osx-64 Cached
+ libxcb 1.13 h0d85af4_1004 conda-forge/osx-64 Cached
+ matplotlib-base 3.7.1 py310he725631_0 conda-forge/osx-64 Cached
+ munkres 1.0.7 py_1 bioconda/noarch Cached
+ numpy 1.24.2 py310h788a5b3_0 conda-forge/osx-64 Cached
+ openjpeg 2.5.0 h5d0d7b0_1 conda-forge/osx-64 Cached
+ packaging 23.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pillow 9.2.0 py310hffcf78b_3 conda-forge/osx-64 Cached
+ pthread-stubs 0.4 hc929b4f_1001 conda-forge/osx-64 Cached
+ pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pysam 0.20.0 py310h958c131_0 bioconda/osx-64 Cached
+ python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ six 1.16.0 pyh6c4a22f_0 conda-forge/noarch Cached
+ unicodedata2 15.0.0 py310h90acd4f_0 conda-forge/osx-64 Cached
+ xorg-libxau 1.0.9 h35c211d_0 conda-forge/osx-64 Cached
+ xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge/osx-64 Cached
Change:
────────────────────────────────────────────────────────────────────────────────
- r-base 4.2.2 h841e2fe_3 conda-forge
+ r-base 4.2.2 h6e3643f_2 conda-forge/osx-64 Cached
Downgrade:
────────────────────────────────────────────────────────────────────────────────
- libdeflate 1.17 hac1461d_0 conda-forge
+ libdeflate 1.13 h775f41a_0 conda-forge/osx-64 Cached
- libtiff 4.5.0 hee9004a_2 conda-forge
+ libtiff 4.4.0 h5e0c7b4_3 conda-forge/osx-64 Cached
Summary:
Install: 29 packages
Change: 1 packages
Downgrade: 2 packages
Total download: 0 B
────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: \
SafetyError: The package for r-base located at /Users/kalavatt/mambaforge/pkgs/r-base-4.2.2-h6e3643f_2
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
reported size: 3423 bytes
actual size: 11533 bytes
done
Executing transaction: done
❯ mamba install \
> -c conda-forge \
> markdown \
> parallel \
> r-markdown \
> r-tidyverse \
> rename \
> ucsc-liftover \
> bioconductor-rtracklayer==1.58.0
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['markdown', 'parallel', 'r-markdown', 'r-tidyverse', 'rename', 'ucsc-liftover', 'bioconductor-rtracklayer==1.58.0']
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
bioconda/osx-64 Using cache
bioconda/noarch Using cache
pkgs/r/osx-64 No change
pkgs/main/noarch No change
pkgs/r/noarch No change
pkgs/main/osx-64 No change
Pinned packages:
- python 3.10.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/gff3_env
Updating specs:
- markdown
- parallel
- r-markdown
- r-tidyverse
- rename
- ucsc-liftover
- bioconductor-rtracklayer==1.58.0
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────────────────────────
+ importlib-metadata 6.3.0 pyha770c72_0 conda-forge/noarch 25kB
+ libuuid 2.38.1 hb7f2c08_0 conda-forge/osx-64 30kB
+ markdown 3.4.3 pyhd8ed1ab_0 conda-forge/noarch 71kB
+ mysql-connector-c 6.1.11 h0f02589_1007 conda-forge/osx-64 5MB
+ pandoc 3.1.1 h9d075a6_0 conda-forge/osx-64 15MB
+ parallel 20230322 h694c41f_0 conda-forge/osx-64 2MB
+ perl 5.32.1 2_h0d85af4_perl5 conda-forge/osx-64 14MB
+ r-askpass 1.1 r42h815d134_3 conda-forge/osx-64 29kB
+ r-assertthat 0.2.1 r42hc72bb7e_3 conda-forge/noarch 73kB
+ r-backports 1.4.1 r42h815d134_1 conda-forge/osx-64 112kB
+ r-base64enc 0.1_3 r42h815d134_1005 conda-forge/osx-64 45kB
+ r-bit 4.0.5 r42h815d134_0 conda-forge/osx-64 1MB
+ r-bit64 4.0.5 r42h815d134_1 conda-forge/osx-64 545kB
+ r-blob 1.2.4 r42hc72bb7e_0 conda-forge/noarch 66kB
+ r-broom 1.0.4 r42hc72bb7e_0 conda-forge/noarch 2MB
+ r-bslib 0.4.2 r42hc72bb7e_0 conda-forge/noarch 4MB
+ r-cachem 1.0.7 r42h815d134_0 conda-forge/osx-64 73kB
+ r-callr 3.7.3 r42hc72bb7e_0 conda-forge/noarch 439kB
+ r-cellranger 1.1.0 r42hc72bb7e_1005 conda-forge/noarch 112kB
+ r-cli 3.6.1 r42h49197e3_0 conda-forge/osx-64 1MB
+ r-clipr 0.8.0 r42hc72bb7e_1 conda-forge/noarch 70kB
+ r-colorspace 2.1_0 r42h815d134_0 conda-forge/osx-64 3MB
+ r-commonmark 1.9.0 r42h815d134_0 conda-forge/osx-64 122kB
+ r-curl 4.3.3 r42h815d134_1 conda-forge/osx-64 709kB
+ r-data.table 1.14.8 r42h557251b_0 conda-forge/osx-64 2MB
+ r-dbi 1.1.3 r42hc72bb7e_1 conda-forge/noarch 789kB
+ r-dbplyr 2.3.2 r42hc72bb7e_0 conda-forge/noarch 1MB
+ r-digest 0.6.31 r42h49197e3_0 conda-forge/osx-64 184kB
+ r-dplyr 1.1.1 r42h49197e3_0 conda-forge/osx-64 1MB
+ r-dtplyr 1.3.1 r42hc72bb7e_0 conda-forge/noarch 357kB
+ r-ellipsis 0.3.2 r42h815d134_1 conda-forge/osx-64 42kB
+ r-evaluate 0.20 r42hc72bb7e_0 conda-forge/noarch 87kB
+ r-fansi 1.0.4 r42h815d134_0 conda-forge/osx-64 309kB
+ r-farver 2.1.1 r42h49197e3_1 conda-forge/osx-64 1MB
+ r-fastmap 1.1.1 r42h49197e3_0 conda-forge/osx-64 71kB
+ r-forcats 1.0.0 r42hc72bb7e_0 conda-forge/noarch 424kB
+ r-fs 1.6.1 r42h49197e3_0 conda-forge/osx-64 276kB
+ r-gargle 1.3.0 r42h785f33e_0 conda-forge/noarch 531kB
+ r-generics 0.1.3 r42hc72bb7e_1 conda-forge/noarch 95kB
+ r-ggplot2 3.4.2 r42hc72bb7e_0 conda-forge/noarch 4MB
+ r-glue 1.6.2 r42h815d134_1 conda-forge/osx-64 157kB
+ r-googledrive 2.1.0 r42hc72bb7e_0 conda-forge/noarch 1MB
+ r-googlesheets4 1.1.0 r42h785f33e_0 conda-forge/noarch 508kB
+ r-gtable 0.3.3 r42hc72bb7e_0 conda-forge/noarch 221kB
+ r-haven 2.5.2 r42h49197e3_0 conda-forge/osx-64 352kB
+ r-highr 0.10 r42hc72bb7e_0 conda-forge/noarch 57kB
+ r-hms 1.1.3 r42hc72bb7e_0 conda-forge/noarch 107kB
+ r-htmltools 0.5.5 r42h49197e3_0 conda-forge/osx-64 353kB
+ r-httr 1.4.5 r42hc72bb7e_0 conda-forge/noarch 488kB
+ r-ids 1.0.1 r42hc72bb7e_2 conda-forge/noarch 130kB
+ r-isoband 0.2.7 r42h49197e3_1 conda-forge/osx-64 2MB
+ r-jquerylib 0.1.4 r42hc72bb7e_1 conda-forge/noarch 379kB
+ r-jsonlite 1.8.4 r42h815d134_0 conda-forge/osx-64 629kB
+ r-knitr 1.42 r42hc72bb7e_1 conda-forge/noarch 1MB
+ r-labeling 0.4.2 r42hc72bb7e_2 conda-forge/noarch 70kB
+ r-lifecycle 1.0.3 r42hc72bb7e_1 conda-forge/noarch 128kB
+ r-lubridate 1.9.2 r42h815d134_1 conda-forge/osx-64 964kB
+ r-magrittr 2.0.3 r42h815d134_1 conda-forge/osx-64 219kB
+ r-markdown 1.6 r42hc72bb7e_0 conda-forge/noarch 179kB
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+ r-memoise 2.0.1 r42hc72bb7e_1 conda-forge/noarch 59kB
+ r-mgcv 1.8_42 r42h40f944a_0 conda-forge/osx-64 3MB
+ r-mime 0.12 r42h815d134_1 conda-forge/osx-64 52kB
+ r-modelr 0.1.11 r42hc72bb7e_0 conda-forge/noarch 221kB
+ r-munsell 0.5.0 r42hc72bb7e_1005 conda-forge/noarch 254kB
+ r-nlme 3.1_162 r42h1e4e481_0 conda-forge/osx-64 2MB
+ r-openssl 2.0.5 r42h13d56fc_0 conda-forge/osx-64 626kB
+ r-pillar 1.9.0 r42hc72bb7e_0 conda-forge/noarch 617kB
+ r-pkgconfig 2.0.3 r42hc72bb7e_2 conda-forge/noarch 27kB
+ r-prettyunits 1.1.1 r42hc72bb7e_2 conda-forge/noarch 43kB
+ r-processx 3.8.0 r42h815d134_0 conda-forge/osx-64 325kB
+ r-progress 1.2.2 r42hc72bb7e_3 conda-forge/noarch 94kB
+ r-ps 1.7.4 r42h815d134_0 conda-forge/osx-64 304kB
+ r-purrr 1.0.1 r42h815d134_0 conda-forge/osx-64 482kB
+ r-r6 2.5.1 r42hc72bb7e_1 conda-forge/noarch 93kB
+ r-rappdirs 0.3.3 r42h815d134_1 conda-forge/osx-64 52kB
+ r-rcolorbrewer 1.1_3 r42h785f33e_1 conda-forge/noarch 67kB
+ r-rcpp 1.0.10 r42h49197e3_0 conda-forge/osx-64 2MB
+ r-readr 2.1.4 r42h49197e3_0 conda-forge/osx-64 741kB
+ r-readxl 1.4.2 r42h3ae43e4_0 conda-forge/osx-64 729kB
+ r-rematch 1.0.1 r42hc72bb7e_1005 conda-forge/noarch 21kB
+ r-rematch2 2.1.2 r42hc72bb7e_2 conda-forge/noarch 55kB
+ r-reprex 2.0.2 r42hc72bb7e_1 conda-forge/noarch 511kB
+ r-rlang 1.1.0 r42h49197e3_0 conda-forge/osx-64 2MB
+ r-rmarkdown 2.14 r42h6115d3f_0 pkgs/r/noarch 3MB
+ r-rstudioapi 0.14 r42hc72bb7e_1 conda-forge/noarch 309kB
+ r-rvest 1.0.3 r42hc72bb7e_1 conda-forge/noarch 221kB
+ r-sass 0.4.5 r42h49197e3_0 conda-forge/osx-64 2MB
+ r-scales 1.2.1 r42hc72bb7e_1 conda-forge/noarch 627kB
+ r-selectr 0.4_2 r42hc72bb7e_2 conda-forge/noarch 474kB
+ r-stringi 1.7.12 r42h7183e51_0 conda-forge/osx-64 856kB
+ r-stringr 1.5.0 r42h785f33e_0 conda-forge/noarch 294kB
+ r-sys 3.4.1 r42h815d134_0 conda-forge/osx-64 48kB
+ r-tibble 3.2.1 r42h815d134_1 conda-forge/osx-64 609kB
+ r-tidyr 1.3.0 r42h49197e3_0 conda-forge/osx-64 1MB
+ r-tidyselect 1.2.0 r42hbe3e9c8_0 conda-forge/osx-64 222kB
+ r-tidyverse 1.3.2 r42hc72bb7e_1 conda-forge/noarch 448kB
+ r-timechange 0.2.0 r42h49197e3_0 conda-forge/osx-64 181kB
+ r-tinytex 0.44 r42hc72bb7e_0 conda-forge/noarch 142kB
+ r-tzdb 0.3.0 r42h49197e3_1 conda-forge/osx-64 544kB
+ r-utf8 1.2.3 r42h815d134_0 conda-forge/osx-64 138kB
+ r-uuid 1.1_0 r42h815d134_1 conda-forge/osx-64 51kB
+ r-vctrs 0.6.1 r42h49197e3_0 conda-forge/osx-64 1MB
+ r-viridislite 0.4.1 r42hc72bb7e_1 conda-forge/noarch 1MB
+ r-vroom 1.6.1 r42h49197e3_0 conda-forge/osx-64 800kB
+ r-withr 2.5.0 r42hc72bb7e_1 conda-forge/noarch 246kB
+ r-xfun 0.38 r42h49197e3_0 conda-forge/osx-64 418kB
+ r-xml2 1.3.3 r42h3576887_2 conda-forge/osx-64 330kB
+ rename 1.601 hdfd78af_1 bioconda/noarch 13kB
+ ucsc-liftover 377 h516baf0_2 bioconda/osx-64 861kB
+ zipp 3.15.0 pyhd8ed1ab_0 conda-forge/noarch 17kB
Summary:
Install: 111 packages
Total download: 103MB
──────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
libuuid 29.6kB @ 731.2kB/s 0.0s
r-mime 51.9kB @ 1.2MB/s 0.0s
r-magrittr 219.1kB @ 4.6MB/s 0.1s
r-backports 111.9kB @ 1.3MB/s 0.0s
r-jsonlite 628.6kB @ 7.0MB/s 0.1s
r-base64enc 44.6kB @ 373.7kB/s 0.0s
r-rappdirs 52.0kB @ 335.7kB/s 0.0s
r-rcpp 2.0MB @ 10.7MB/s 0.1s
r-digest 183.7kB @ 823.6kB/s 0.0s
r-farver 1.5MB @ 6.0MB/s 0.1s
r-sys 48.4kB @ 186.9kB/s 0.0s
mysql-connector-c 4.6MB @ 17.0MB/s 0.3s
r-xml2 329.7kB @ 1.2MB/s 0.0s
r-cachem 73.4kB @ 258.8kB/s 0.0s
r-pkgconfig 26.6kB @ 86.2kB/s 0.0s
r-withr 245.9kB @ 790.5kB/s 0.0s
r-openssl 626.4kB @ 2.0MB/s 0.1s
perl 14.0MB @ 42.7MB/s 0.3s
r-highr 57.1kB @ 163.4kB/s 0.0s
r-dbi 789.4kB @ 2.2MB/s 0.0s
r-lifecycle 128.1kB @ 353.9kB/s 0.0s
r-viridislite 1.3MB @ 3.6MB/s 0.1s
r-httr 488.0kB @ 1.3MB/s 0.0s
r-jquerylib 378.6kB @ 965.3kB/s 0.0s
r-gtable 221.3kB @ 557.6kB/s 0.0s
r-gargle 531.2kB @ 1.3MB/s 0.0s
pandoc 14.7MB @ 35.7MB/s 0.4s
r-progress 94.4kB @ 212.9kB/s 0.0s
r-pillar 617.4kB @ 1.4MB/s 0.0s
r-sass 2.1MB @ 4.5MB/s 0.1s
r-vctrs 1.3MB @ 2.7MB/s 0.1s
r-vroom 799.7kB @ 1.6MB/s 0.0s
r-cellranger 112.2kB @ 227.1kB/s 0.0s
r-bslib 4.1MB @ 8.2MB/s 0.1s
r-tidyr 1.1MB @ 2.2MB/s 0.1s
r-dbplyr 1.1MB @ 2.1MB/s 0.0s
r-xfun 417.8kB @ 770.6kB/s 0.0s
r-broom 1.8MB @ 3.3MB/s 0.1s
r-curl 709.0kB @ 1.3MB/s 0.0s
r-uuid 51.2kB @ 89.8kB/s 0.0s
r-ggplot2 4.1MB @ 7.2MB/s 0.1s
r-timechange 181.5kB @ 312.0kB/s 0.0s
r-stringi 855.8kB @ 1.4MB/s 0.0s
r-ellipsis 42.1kB @ 68.5kB/s 0.0s
r-mass 1.1MB @ 1.8MB/s 0.1s
r-nlme 2.3MB @ 3.7MB/s 0.1s
r-askpass 28.5kB @ 45.2kB/s 0.0s
r-generics 94.5kB @ 147.8kB/s 0.0s
r-rstudioapi 308.6kB @ 481.9kB/s 0.0s
r-rcolorbrewer 66.9kB @ 103.1kB/s 0.0s
r-tinytex 142.4kB @ 217.6kB/s 0.0s
r-memoise 59.0kB @ 89.3kB/s 0.0s
r-prettyunits 43.3kB @ 65.1kB/s 0.0s
markdown 70.9kB @ 105.4kB/s 0.0s
r-processx 325.3kB @ 477.4kB/s 0.0s
r-hms 106.7kB @ 156.0kB/s 0.0s
r-purrr 482.1kB @ 701.1kB/s 0.0s
r-haven 352.2kB @ 507.2kB/s 0.2s
r-tibble 609.5kB @ 853.6kB/s 0.0s
r-reprex 511.2kB @ 708.3kB/s 0.0s
r-tidyverse 448.2kB @ 615.7kB/s 0.0s
r-googledrive 1.2MB @ 1.6MB/s 0.0s
r-glue 157.1kB @ 210.2kB/s 0.0s
r-fs 275.8kB @ 365.3kB/s 0.0s
r-rmarkdown 2.8MB @ 3.7MB/s 0.1s
r-bit 1.2MB @ 1.5MB/s 0.1s
r-data.table 1.9MB @ 2.3MB/s 0.1s
parallel 1.9MB @ 2.3MB/s 0.1s
r-assertthat 73.2kB @ 90.7kB/s 0.0s
r-ids 130.2kB @ 160.4kB/s 0.0s
r-r6 92.6kB @ 113.4kB/s 0.1s
r-scales 627.1kB @ 758.7kB/s 0.0s
r-blob 66.0kB @ 79.6kB/s 0.0s
r-googlesheets4 507.7kB @ 593.4kB/s 0.0s
r-rvest 221.2kB @ 257.2kB/s 0.0s
r-dplyr 1.4MB @ 1.6MB/s 0.0s
r-htmltools 353.0kB @ 407.9kB/s 0.1s
r-commonmark 121.7kB @ 138.7kB/s 0.0s
r-utf8 138.0kB @ 156.2kB/s 0.0s
r-fastmap 70.6kB @ 79.6kB/s 0.0s
zipp 17.2kB @ 19.2kB/s 0.0s
r-rlang 1.5MB @ 1.7MB/s 0.0s
r-labeling 70.0kB @ 77.1kB/s 0.0s
r-munsell 254.3kB @ 279.8kB/s 0.0s
rename 13.4kB @ 14.6kB/s 0.0s
r-rematch2 54.9kB @ 59.3kB/s 0.0s
r-callr 439.1kB @ 468.4kB/s 0.0s
r-readr 741.0kB @ 786.6kB/s 0.0s
r-ps 304.0kB @ 318.6kB/s 0.0s
r-cli 1.3MB @ 1.3MB/s 0.0s
r-evaluate 86.7kB @ 90.2kB/s 0.0s
r-bit64 544.6kB @ 564.8kB/s 0.0s
r-tidyselect 222.0kB @ 226.7kB/s 0.0s
importlib-metadata 25.3kB @ 25.7kB/s 0.0s
r-forcats 424.4kB @ 430.6kB/s 0.0s
r-clipr 69.8kB @ 69.3kB/s 0.0s
r-isoband 1.6MB @ 1.6MB/s 0.0s
r-readxl 728.8kB @ 708.1kB/s 0.1s
r-knitr 1.3MB @ 1.3MB/s 0.0s
r-selectr 473.9kB @ 455.7kB/s 0.0s
r-tzdb 543.9kB @ 516.8kB/s 0.0s
r-modelr 220.6kB @ 206.3kB/s 0.0s
r-rematch 20.8kB @ 19.4kB/s 0.0s
ucsc-liftover 860.8kB @ 791.2kB/s 0.1s
r-mgcv 3.3MB @ 3.0MB/s 0.1s
r-fansi 309.1kB @ 281.1kB/s 0.0s
r-markdown 178.6kB @ 162.0kB/s 0.0s
r-dtplyr 357.4kB @ 322.6kB/s 0.0s
r-stringr 294.3kB @ 260.8kB/s 0.0s
r-colorspace 2.5MB @ 2.2MB/s 0.1s
r-lubridate 964.5kB @ 799.1kB/s 0.4s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install \
> -c conda-forge \
> r-complexupset \
> bioconductor-rtracklayer==1.58.0
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['r-complexupset', 'bioconductor-rtracklayer==1.58.0']
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
bioconda/osx-64 Using cache
bioconda/noarch Using cache
pkgs/main/noarch No change
pkgs/main/osx-64 No change
pkgs/r/noarch No change
pkgs/r/osx-64 No change
Pinned packages:
- python 3.10.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/gff3_env
Updating specs:
- r-complexupset
- bioconductor-rtracklayer==1.58.0
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────
+ r-complexupset 1.3.3 r42hc72bb7e_1 conda-forge/noarch 3MB
+ r-patchwork 1.1.2 r42hc72bb7e_1 conda-forge/noarch 3MB
Summary:
Install: 2 packages
Total download: 6MB
─────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
r-patchwork 3.3MB @ 17.4MB/s 0.2s
r-complexupset 2.8MB @ 6.8MB/s 0.4s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c bioconda igv bioconductor-rtracklayer==1.58.0
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['igv', 'bioconductor-rtracklayer==1.58.0']
bioconda/osx-64 Using cache
bioconda/noarch Using cache
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
pkgs/main/noarch No change
pkgs/r/noarch No change
pkgs/r/osx-64 No change
pkgs/main/osx-64 No change
Pinned packages:
- python 3.10.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/gff3_env
Updating specs:
- igv
- bioconductor-rtracklayer==1.58.0
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────
+ igv 2.13.2 hdfd78af_0 bioconda/noarch 34MB
+ openjdk 17.0.3 hbc0c0cd_6 conda-forge/osx-64 165MB
Summary:
Install: 2 packages
Total download: 200MB
────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
igv 34.1MB @ 34.1MB/s 1.0s
openjdk 165.4MB @ 83.9MB/s 2.0s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c \
> conda-forge \
> r-plyr \
> bioconductor-rtracklayer==1.58.0
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['r-plyr', 'bioconductor-rtracklayer==1.58.0']
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
bioconda/osx-64 Using cache
bioconda/noarch Using cache
pkgs/main/noarch No change
pkgs/r/noarch No change
pkgs/r/osx-64 No change
pkgs/main/osx-64 No change
Pinned packages:
- python 3.10.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/gff3_env
Updating specs:
- r-plyr
- bioconductor-rtracklayer==1.58.0
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────────
+ r-plyr 1.8.8 r42h49197e3_0 conda-forge/osx-64 856kB
Summary:
Install: 1 packages
Total download: 856kB
──────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
r-plyr 856.0kB @ 3.2MB/s 0.3s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: doneCode: Add appropriate shortcut to .zaliases and .bash_aliases
#!/bin/bash
# .zaliases
alias gff3_env="source activate gff3_env"
alias R-gff3="(
source activate gff3_env
open -na /Applications/RStudio.app
)"
# .bash_aliases
alias gff3_env="source activate gff3_env"Code: Create an environment for running Python with spyder
#!/bin/bash
create_x86_conda_environment spyder_env
# source activate spyder_env
mamba install -c conda-forge spyder numpy
mamba install -c conda-forge pandas
mamba install -c conda-forge nltk #NOTE Don't need this
mamba install -c conda-forge pipePrinted:
❯ create_x86_conda_environment spyder_env
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.1.0
latest version: 23.3.1
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.3.1
## Package Plan ##
environment location: /Users/kalavatt/mambaforge/envs/spyder_env
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate spyder_env
#
# To deactivate an active environment, use
#
# $ conda deactivate
❯ mamba install -c conda-forge spyder numpy
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['spyder', 'numpy']
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
bioconda/osx-64 Using cache
bioconda/noarch Using cache
pkgs/r/osx-64 No change
pkgs/r/noarch No change
pkgs/main/osx-64 No change
pkgs/main/noarch No change
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/spyder_env
Updating specs:
- spyder
- numpy
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────────
+ alabaster 0.7.13 pyhd8ed1ab_0 conda-forge/noarch Cached
+ applaunchservices 0.3.0 pyhd8ed1ab_2 conda-forge/noarch Cached
+ appnope 0.1.3 pyhd8ed1ab_0 conda-forge/noarch Cached
+ arrow 1.2.3 pyhd8ed1ab_0 conda-forge/noarch Cached
+ astroid 2.15.3 py311h6eed73b_0 conda-forge/osx-64 Cached
+ asttokens 2.2.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ atomicwrites 1.4.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ attrs 22.2.0 pyh71513ae_0 conda-forge/noarch Cached
+ autopep8 2.0.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ babel 2.12.1 pyhd8ed1ab_1 conda-forge/noarch Cached
+ backcall 0.2.0 pyh9f0ad1d_0 conda-forge/noarch Cached
+ backports 1.0 pyhd8ed1ab_3 conda-forge/noarch Cached
+ backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge/noarch Cached
+ beautifulsoup4 4.12.2 pyha770c72_0 conda-forge/noarch Cached
+ binaryornot 0.4.4 py_1 conda-forge/noarch Cached
+ black 23.3.0 py311h6eed73b_0 conda-forge/osx-64 Cached
+ bleach 6.0.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ brotlipy 0.7.0 py311h5547dcb_1005 conda-forge/osx-64 Cached
+ bzip2 1.0.8 h0d85af4_4 conda-forge/osx-64 Cached
+ ca-certificates 2022.12.7 h033912b_0 conda-forge/osx-64 Cached
+ certifi 2022.12.7 pyhd8ed1ab_0 conda-forge/noarch Cached
+ cffi 1.15.1 py311ha86e640_3 conda-forge/osx-64 Cached
+ chardet 5.1.0 py311h6eed73b_0 conda-forge/osx-64 Cached
+ charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ click 8.1.3 unix_pyhd8ed1ab_2 conda-forge/noarch Cached
+ cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ colorama 0.4.6 pyhd8ed1ab_0 conda-forge/noarch Cached
+ comm 0.1.3 pyhd8ed1ab_0 conda-forge/noarch Cached
+ cookiecutter 2.1.1 pyh6c4a22f_0 conda-forge/noarch Cached
+ cryptography 40.0.2 py311h61927ef_0 conda-forge/osx-64 Cached
+ debugpy 1.6.7 py311h814d153_0 conda-forge/osx-64 Cached
+ decorator 5.1.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ diff-match-patch 20200713 pyh9f0ad1d_0 conda-forge/noarch Cached
+ dill 0.3.6 pyhd8ed1ab_1 conda-forge/noarch Cached
+ docstring-to-markdown 0.12 pyhd8ed1ab_0 conda-forge/noarch Cached
+ docutils 0.19 py311h6eed73b_1 conda-forge/osx-64 Cached
+ entrypoints 0.4 pyhd8ed1ab_0 conda-forge/noarch Cached
+ executing 1.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ flake8 6.0.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ gettext 0.21.1 h8a4c099_0 conda-forge/osx-64 Cached
+ giflib 5.2.1 hb7f2c08_3 conda-forge/osx-64 Cached
+ glib 2.76.1 hbc0c0cd_0 conda-forge/osx-64 Cached
+ glib-tools 2.76.1 hbc0c0cd_0 conda-forge/osx-64 Cached
+ gst-plugins-base 1.22.0 h37e1711_2 conda-forge/osx-64 Cached
+ gstreamer 1.22.0 h1d18e73_2 conda-forge/osx-64 Cached
+ icu 72.1 h7336db1_0 conda-forge/osx-64 Cached
+ idna 3.4 pyhd8ed1ab_0 conda-forge/noarch Cached
+ imagesize 1.4.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ importlib-metadata 6.5.0 pyha770c72_0 conda-forge/noarch Cached
+ importlib_metadata 6.5.0 hd8ed1ab_0 conda-forge/noarch Cached
+ importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ inflection 0.5.1 pyh9f0ad1d_0 conda-forge/noarch Cached
+ intervaltree 3.0.2 py_0 conda-forge/noarch Cached
+ ipykernel 6.22.0 pyh736e0ef_0 conda-forge/noarch Cached
+ ipython 8.12.0 pyhd1c38e8_0 conda-forge/noarch Cached
+ ipython_genutils 0.2.0 py_1 conda-forge/noarch Cached
+ isort 5.12.0 pyhd8ed1ab_1 conda-forge/noarch Cached
+ jaraco.classes 3.2.3 pyhd8ed1ab_0 conda-forge/noarch Cached
+ jedi 0.18.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ jellyfish 0.9.0 py311h5547dcb_2 conda-forge/osx-64 Cached
+ jinja2 3.1.2 pyhd8ed1ab_1 conda-forge/noarch Cached
+ jinja2-time 0.2.0 pyhd8ed1ab_3 conda-forge/noarch Cached
+ jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge/noarch Cached
+ jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ jupyter_core 5.3.0 py311h6eed73b_0 conda-forge/osx-64 Cached
+ jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ keyring 23.13.1 py311h6eed73b_0 conda-forge/osx-64 Cached
+ krb5 1.20.1 h049b76e_0 conda-forge/osx-64 Cached
+ lazy-object-proxy 1.9.0 py311h5547dcb_0 conda-forge/osx-64 Cached
+ lerc 4.0.0 hb486fe8_0 conda-forge/osx-64 Cached
+ libblas 3.9.0 16_osx64_openblas conda-forge/osx-64 Cached
+ libcblas 3.9.0 16_osx64_openblas conda-forge/osx-64 Cached
+ libclang 14.0.6 default_h55ffa42_0 conda-forge/osx-64 Cached
+ libclang13 14.0.6 default_hb5731bd_0 conda-forge/osx-64 Cached
+ libcxx 16.0.1 h71dddab_0 conda-forge/osx-64 Cached
+ libdeflate 1.18 hac1461d_0 conda-forge/osx-64 Cached
+ libedit 3.1.20191231 h0678c8f_2 conda-forge/osx-64 Cached
+ libexpat 2.5.0 hf0c8a7f_1 conda-forge/osx-64 Cached
+ libffi 3.4.2 h0d85af4_5 conda-forge/osx-64 Cached
+ libgfortran 5.0.0 11_3_0_h97931a8_31 conda-forge/osx-64 Cached
+ libgfortran5 12.2.0 he409387_31 conda-forge/osx-64 Cached
+ libglib 2.76.1 h4c723e1_0 conda-forge/osx-64 Cached
+ libiconv 1.17 hac89ed1_0 conda-forge/osx-64 Cached
+ libjpeg-turbo 2.1.5.1 hb7f2c08_0 conda-forge/osx-64 Cached
+ liblapack 3.9.0 16_osx64_openblas conda-forge/osx-64 Cached
+ libllvm14 14.0.6 h5b596cc_1 conda-forge/osx-64 Cached
+ libogg 1.3.4 h35c211d_1 conda-forge/osx-64 Cached
+ libopenblas 0.3.21 openmp_h429af6e_3 conda-forge/osx-64 Cached
+ libopus 1.3.1 hc929b4f_1 conda-forge/osx-64 Cached
+ libpng 1.6.39 ha978bb4_0 conda-forge/osx-64 Cached
+ libpq 15.2 h3640bf0_0 conda-forge/osx-64 Cached
+ libsodium 1.0.18 hbcb3906_1 conda-forge/osx-64 Cached
+ libspatialindex 1.9.3 he49afe7_4 conda-forge/osx-64 Cached
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+ libtiff 4.5.0 hedf67fa_6 conda-forge/osx-64 Cached
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+ sphinxcontrib-devhelp 1.0.2 py_0 conda-forge/noarch Cached
+ sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ sphinxcontrib-jsmath 1.0.1 py_0 conda-forge/noarch Cached
+ sphinxcontrib-qthelp 1.0.3 py_0 conda-forge/noarch Cached
+ sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge/noarch Cached
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+ text-unidecode 1.3 py_0 conda-forge/noarch Cached
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+ three-merge 0.1.1 pyh9f0ad1d_0 conda-forge/noarch Cached
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+ tomli 2.0.1 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ tzdata 2023c h71feb2d_0 conda-forge/noarch Cached
+ ujson 5.7.0 py311h814d153_0 conda-forge/osx-64 Cached
+ unidecode 1.3.6 pyhd8ed1ab_0 conda-forge/noarch Cached
+ urllib3 1.26.15 pyhd8ed1ab_0 conda-forge/noarch Cached
+ watchdog 3.0.0 py311h6fddac2_0 conda-forge/osx-64 Cached
+ wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge/noarch Cached
+ webencodings 0.5.1 py_1 conda-forge/noarch Cached
+ whatthepatch 1.0.4 pyhd8ed1ab_0 conda-forge/noarch Cached
+ wheel 0.40.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ wrapt 1.15.0 py311h5547dcb_0 conda-forge/osx-64 Cached
+ wurlitzer 3.0.3 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xz 5.2.6 h775f41a_0 conda-forge/osx-64 Cached
+ yaml 0.2.5 h0d85af4_2 conda-forge/osx-64 Cached
+ yapf 0.32.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ zeromq 4.3.4 he49afe7_1 conda-forge/osx-64 Cached
+ zipp 3.15.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ zstd 1.5.2 hbc0c0cd_6 conda-forge/osx-64 Cached
Summary:
Install: 229 packages
Total download: 8MB
────────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
numpy 7.5MB @ 33.7MB/s 0.2s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c conda-forge pandas
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██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['pandas']
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
bioconda/osx-64 Using cache
bioconda/noarch Using cache
pkgs/main/osx-64 No change
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/r/osx-64 No change
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/spyder_env
Updating specs:
- pandas
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────
+ pandas 2.0.0 py311hd84f3f5_0 conda-forge/osx-64 14MB
+ python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge/noarch 143kB
Summary:
Install: 2 packages
Total download: 14MB
───────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
python-tzdata 143.1kB @ 2.5MB/s 0.1s
pandas 14.1MB @ 74.7MB/s 0.2s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c conda-forge nltk
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['nltk']
bioconda/osx-64 No change
pkgs/main/osx-64 No change
bioconda/noarch No change
pkgs/main/noarch No change
pkgs/r/noarch No change
pkgs/r/osx-64 No change
conda-forge/noarch 11.9MB @ 4.2MB/s 3.1s
conda-forge/osx-64 27.9MB @ 4.9MB/s 6.3s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/spyder_env
Updating specs:
- nltk
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────
+ joblib 1.2.0 pyhd8ed1ab_0 conda-forge/noarch 210kB
+ nltk 3.8.1 pyhd8ed1ab_0 conda-forge/noarch 1MB
+ regex 2023.3.23 py311h5547dcb_0 conda-forge/osx-64 372kB
+ tqdm 4.65.0 pyhd8ed1ab_1 conda-forge/noarch Cached
Summary:
Install: 4 packages
Total download: 2MB
───────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
joblib 210.0kB @ 1.3MB/s 0.2s
nltk 1.1MB @ 6.0MB/s 0.2s
regex 372.0kB @ 1.9MB/s 0.2s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
❯ mamba install -c conda-forge pipe
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['pipe']
bioconda/osx-64 3.8MB @ 4.1MB/s 1.0s
bioconda/noarch 4.2MB @ 4.0MB/s 1.1s
pkgs/main/osx-64 5.3MB @ 4.5MB/s 1.3s
pkgs/r/noarch No change
pkgs/r/osx-64 No change
pkgs/main/noarch No change
conda-forge/noarch 12.0MB @ 4.5MB/s 2.9s
conda-forge/osx-64 27.9MB @ 4.5MB/s 6.9s
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/kalavatt/mambaforge/envs/spyder_env
Updating specs:
- pipe
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────
+ pipe 2.0 pyhd8ed1ab_0 conda-forge/noarch 13kB
Summary:
Install: 1 packages
Total download: 13kB
───────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
pipe 12.7kB @ 102.7kB/s 0.1s
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done