GiantSpaceRobot / tsRNAsearch

Nextflow DSL2 tRNA and ncRNA fragment identification pipeline for small RNA-seq data
MIT License
7 stars 3 forks source link

error while installing packages #15

Open alirizaaribas-ibg opened 2 years ago

alirizaaribas-ibg commented 2 years ago

Hello, I had lots of erros while installing. I tried to install manually. How can I solve these? conda env create -f tsRNAsearch/environment.yml is stuck at solving environment phase.

(base) conda env create -f environment.yml
Collecting package metadata (repodata.json): done
Solving environment: \

Here are working, step1:

conda create -y -n tsrnasearch_env python=2.7.15 r=3.5.1
conda activate tsrnasearch_env
conda install -y curl=7.64.0
conda install -y -c bioconda cutadapt=1.18
conda install -y -c bioconda fastqc=0.11.9
conda install -y -c conda-forge ghostscript=9.22
conda install -y -c conda-forge libgit2=0.27.8
conda install -y numpy=1.15.4
conda install -y openssl=1.0.2u
conda install -y pandoc=2.10
conda install -y pip=20.1.1
conda install -y pigz=2.3.4
conda install -y python=2.7.15
conda install -y -c r r=3.5.1
conda install -y -c r r-boot=1.3_20
conda install -y -c r r-checkpoint=0.4.4
conda install -y -c r r-class=7.3_14
conda install -y -c r r-cluster=2.0.7_1
conda install -y -c r r-codetools=0.2_15
conda install -y -c r r-curl=3.2
conda install -y -c r r-deployrrserve=9.0.0
conda install -y -c r r-doparallel=1.0.13
conda install -y -c r r-foreach=1.5.0
conda install -y -c r r-foreign=0.8_70
conda install -y -c r r-iterators=1.0.10
conda install -y -c r r-jsonlite=1.5
conda install -y -c r r-kernsmooth=2.23_15
conda install -y -c r r-lattice=0.20_35
conda install -y -c r r-mass=7.3_49
conda install -y -c r r-matrix=1.2_14
conda install -y -c r r-mgcv=1.8_23
conda install -y -c r r-microsoftr=3.5.0.108
conda install -y -c r r-nlme=3.1_137
conda install -y -c r r-nnet=7.3_12
conda install -y -c r r-png=0.1_7
conda install -y -c r r-r6=2.2.2
conda install -y -c r r-recommended=3.5.1
conda install -y -c r r-revoioq=10.0.0
conda install -y -c r r-revomods=11.0.0
conda install -y -c r r-revoutils=11.0.0
conda install -y -c r r-revoutilsmath=11.0.0
conda install -y -c r r-rpart=4.1_13
conda install -y -c r r-runit=0.4.26
conda install -y -c r r-spatial=7.3_11
conda install -y -c r r-survival=2.41_3
conda install -y -c r samtools=1.9
conda install -y -c r star=2.5.2b
conda install -y -c r subread=2.0.1=hed695b0_0
conda install -y -c r trim-galore=0.4.1
pip install multiqc==0.4
conda install -c bioconda nextflow

Here are not working, step2: Rscript bin/InstallPackages.R

Rscript bin/InstallPackages_GeneralVersions.R
Loading required package: BiocManager
Loading required package: git2r
Loading required package: ggplot2
Loading required package: ggrepel
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Loading required package: EnhancedVolcano
[1] "Installing EnhancedVolcano..."
Bioconductor version 3.8 (BiocManager 1.30.1), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'EnhancedVolcano'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Error in library(EnhancedVolcano) :
  there is no package called ‘EnhancedVolcano’
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘EnhancedVolcano’
2: packages ‘BiocVersion’, ‘EnhancedVolcano’ are not available (for R version 3.5.1)
Execution halted

Alternatively:

Rscript bin/InstallPackages.R
Loading required package: BiocManager
Loading required package: devtools

Attaching package: ‘devtools’

The following object is masked from ‘package:BiocManager’:

    install

Loading required package: git2r
Loading required package: ggplot2
Loading required package: ggrepel
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Loading required package: EnhancedVolcano
[1] "Installing EnhancedVolcano..."
Bioconductor version 3.8 (BiocManager 1.30.1), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'EnhancedVolcano'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Error in library(EnhancedVolcano) :
  there is no package called ‘EnhancedVolcano’
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘EnhancedVolcano’
2: packages ‘BiocVersion’, ‘EnhancedVolcano’ are not available (for R version 3.5.1)
Execution halted