I’d put this in a comment as well but it doesn’t work in that format. I’m kinda hoping the actual comment has the solution so this question can be marked as a duplicate.
The output actually did give instructions, but it’s all smushed together and somewhat foreboding (which is somewhat appropriate given the proximity to Halloween).
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
says you need to know which linux distribution you have and install the libcurl OS package for it before trying to install the tidyverse.
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
* deb: libxml2-dev (Debian, Ubuntu, etc)
* rpm: libxml2-devel (Fedora, CentOS, RHEL)
* csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
says you need to know which linux distribution you have and install the libxml2 OS package for it before trying to install the tidyverse.
While you’re at it, make sure you have the openssl OS package installed as well.
Today we will learn how to fix error messages that you could find in your R development tool such as RStudio, Jupyter and others, when trying to invoke the tidyverse library without it being installed.
Understanding the error
- Open RStudio or Jupyter or other R script development environment.
- Create your script.
- Invoke the tidyverse environment : library(tidyverse)
- The Console will return the following exception message:
Error in library(tidyverse) : there is no package called ‘tidyverse’
Here’s a screenshot from the RStudio Console tab in my Windows computer. Same error will be thrown in Ubuntu and macOS.
The root cause is that you are trying to invoke tidyverse but the library is not yet installed in your computer. Reason for that is that when you install RStudio tidyverse is not installed by default and has to be added manually.
Fix the Error in library(tidyverse) in RStudio
Luckily, solving this error is pretty simple: we just need to install tidyverse:
install.packages('tidyverse')Important Note: Make sure to include the quotation marks around the library name. Failing to do so will invoke the following error: Error in install.packages : object ‘tidyverse’ not found
RStudio will install all the packages that compose tidyverse such as dplyr, purrr, broom, fs, reprex, highr, selectr, readr etc.
Next, you can invoke tidyverse and use its sub-packages in your R script:
library(tidyverse)
I ran the install.packages("tidyverse") and the installation was done.
At the end the following errors and warnings appeared:
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 61440 != reported length 104968
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
cannot open compressed file 'rprojroot/DESCRIPTION', probable reason 'No such file or directory'
Thank you @naumenko-sa for your kind help.
I upgraded successfully by ‘bcbio_nextgen.py upgrade -u skip —tools’. But, it’s still not working. Please see below.
Upgrading bcbio
Upgrading third party tools to latest versions
Reading packages from /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/tmpbcbio-install/cloudbiolinux/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
Checking for problematic or migrated packages in default environment
# Installing into conda environment default: age-metasv, arriba, bamtools=2.4.0, bamutil, bbmap, bcbio-prioritize, bcbio-variation, bcbio-variation-recall, bcftools, bedops, bedtools, bio-vcf, biobambam, bowtie, bowtie2, break-point-inspector, bwa, cage, cancerit-allelecount, chipseq-greylist, cnvkit, coincbc, cramtools, cufflinks, cyvcf2, deeptools, delly, duphold, ensembl-vep=100.*, express, extract-sv-reads, fastp, fastqc>=0.11.8=1, fgbio, freebayes, gatk, gatk4, geneimpacts, genesplicer, gffcompare, goleft, grabix, gridss, gsort, gvcfgenotyper, h5py, hisat2, hmftools-amber, hmftools-cobalt, hmftools-purple, hmmlearn, hts-nim-tools, htslib, impute2, kallisto>=0.43.1, kraken, ldc>=1.13.0, lofreq, macs2, maxentscan, mbuffer, minimap2, mintmap, mirdeep2=2.0.0.7, mirtop, moreutils, multiqc, multiqc-bcbio, ngs-disambiguate, novoalign, octopus>=0.5.1b, oncofuse, optitype>=1.3.4, pandoc=2.9.2, parallel, pbgzip, peddy, perl-sanger-cgp-battenberg, picard, pindel, pizzly, pyloh, pysam>=0.14.0, pythonpy, qsignature, qualimap, rapmap, razers3=3.5.0, rtg-tools, sailfish, salmon, sambamba, samblaster, samtools=1.9, scalpel, seq2c<2016, seqbuster, seqcluster, seqtk, sickle-trim, simple_sv_annotation, singlecell-barcodes, snap-aligner=1.0dev.97, snpeff=4.3.1t, solvebio, spades, staden_io_lib, star=2.6.1d, stringtie, subread, survivor, tdrmapper, tophat-recondition, trim-galore, ucsc-bedgraphtobigwig, ucsc-bedtobigbed, ucsc-bigbedinfo, ucsc-bigbedsummary, ucsc-bigbedtobed, ucsc-bigwiginfo, ucsc-bigwigsummary, ucsc-bigwigtobedgraph, ucsc-bigwigtowig, ucsc-fatotwobit, ucsc-gtftogenepred, ucsc-liftover, ucsc-wigtobigwig, umis, vardict-java, vardict<=2015, variantbam, varscan, vcfanno, vcflib, verifybamid2, viennarna, vqsr_cnn, vt, wham, anaconda-client, awscli, bzip2, ncurses, nodejs, p7zip, readline, s3gof3r, xz, perl-app-cpanminus, perl-archive-extract, perl-archive-zip, perl-bio-db-sam, perl-cgi, perl-dbi, perl-encode-locale, perl-file-fetch, perl-file-sharedir, perl-file-sharedir-install, perl-ipc-system-simple, perl-lwp-protocol-https, perl-lwp-simple, perl-statistics-descriptive, perl-time-hires, perl-vcftools-vcf, bioconductor-annotate, bioconductor-apeglm, bioconductor-biocgenerics, bioconductor-biocinstaller, bioconductor-biocstyle, bioconductor-biostrings, bioconductor-biovizbase, bioconductor-bsgenome.hsapiens.ucsc.hg19, bioconductor-bsgenome.hsapiens.ucsc.hg38, bioconductor-bubbletree, bioconductor-cn.mops, bioconductor-copynumber, bioconductor-degreport, bioconductor-deseq2, bioconductor-dexseq, bioconductor-dnacopy, bioconductor-genomeinfodbdata, bioconductor-genomicranges, bioconductor-iranges, bioconductor-limma, bioconductor-rtracklayer, bioconductor-snpchip, bioconductor-titancna, bioconductor-vsn>=3.50.0, r-base, r-basejump=0.7.2, r-bcbiornaseq>=0.2.7, r-cghflasso, r-chbutils, r-devtools, r-dplyr, r-dt, r-ggdendro, r-ggplot2, r-ggrepel>=0.7, r-gplots, r-gsalib, r-janitor, r-knitr, r-pheatmap, r-plyr, r-pscbs, r-reshape, r-rmarkdown, r-rsqlite, r-sleuth, r-snow, r-stringi, r-viridis>=0.5, r-wasabi, r=3.5.1, xorg-libxt
## Package Plan ##
environment location: /apps1/local/share/bcbio/anaconda
added / updated specs:
- age-metasv
- anaconda-client
- arriba
- awscli
- bamtools=2.4.0
- bamutil
- bbmap
- bcbio-prioritize
- bcbio-variation
- bcbio-variation-recall
- bcftools
- bedops
- bedtools
- bio-vcf
- biobambam
- bioconductor-annotate
- bioconductor-apeglm
- bioconductor-biocgenerics
- bioconductor-biocinstaller
- bioconductor-biocstyle
- bioconductor-biostrings
- bioconductor-biovizbase
- bioconductor-bsgenome.hsapiens.ucsc.hg19
- bioconductor-bsgenome.hsapiens.ucsc.hg38
- bioconductor-bubbletree
- bioconductor-cn.mops
- bioconductor-copynumber
- bioconductor-degreport
- bioconductor-deseq2
- bioconductor-dexseq
- bioconductor-dnacopy
- bioconductor-genomeinfodbdata
- bioconductor-genomicranges
- bioconductor-iranges
- bioconductor-limma
- bioconductor-rtracklayer
- bioconductor-snpchip
- bioconductor-titancna
- bioconductor-vsn[version='>=3.50.0']
- bowtie
- bowtie2
- break-point-inspector
- bwa
- bzip2
- cage
- cancerit-allelecount
- chipseq-greylist
- cnvkit
- coincbc
- cramtools
- cufflinks
- cyvcf2
- deeptools
- delly
- duphold
- ensembl-vep=100
- express
- extract-sv-reads
- fastp
- fastqc[version='>=0.11.8',build=1]
- fgbio
- freebayes
- gatk
- gatk4
- geneimpacts
- genesplicer
- gffcompare
- goleft
- grabix
- gridss
- gsort
- gvcfgenotyper
- h5py
- hisat2
- hmftools-amber
- hmftools-cobalt
- hmftools-purple
- hmmlearn
- hts-nim-tools
- htslib
- impute2
- kallisto[version='>=0.43.1']
- kraken
- ldc[version='>=1.13.0']
- lofreq
- macs2
- maxentscan
- mbuffer
- minimap2
- mintmap
- mirdeep2=2.0.0.7
- mirtop
- moreutils
- multiqc
- multiqc-bcbio
- ncurses
- ngs-disambiguate
- nodejs
- novoalign
- octopus[version='>=0.5.1b']
- oncofuse
- optitype[version='>=1.3.4']
- p7zip
- pandoc=2.9.2
- parallel
- pbgzip
- peddy
- perl-app-cpanminus
- perl-archive-extract
- perl-archive-zip
- perl-bio-db-sam
- perl-cgi
- perl-dbi
- perl-encode-locale
- perl-file-fetch
- perl-file-sharedir
- perl-file-sharedir-install
- perl-ipc-system-simple
- perl-lwp-protocol-https
- perl-lwp-simple
- perl-sanger-cgp-battenberg
- perl-statistics-descriptive
- perl-time-hires
- perl-vcftools-vcf
- picard
- pindel
- pizzly
- pyloh
- pysam[version='>=0.14.0']
- python=3
- pythonpy
- qsignature
- qualimap
- r-base
- r-basejump=0.7.2
- r-bcbiornaseq[version='>=0.2.7']
- r-cghflasso
- r-chbutils
- r-devtools
- r-dplyr
- r-dt
- r-ggdendro
- r-ggplot2
- r-ggrepel[version='>=0.7']
- r-gplots
- r-gsalib
- r-janitor
- r-knitr
- r-pheatmap
- r-plyr
- r-pscbs
- r-reshape
- r-rmarkdown
- r-rsqlite
- r-sleuth
- r-snow
- r-stringi
- r-viridis[version='>=0.5']
- r-wasabi
- r=3.5.1
- rapmap
- razers3=3.5.0
- readline
- rtg-tools
- s3gof3r
- sailfish
- salmon
- sambamba
- samblaster
- samtools=1.9
- scalpel
- seq2c[version='<2016']
- seqbuster
- seqcluster
- seqtk
- sickle-trim
- simple_sv_annotation
- singlecell-barcodes
- snap-aligner=1.0dev.97
- snpeff=4.3.1t
- solvebio
- spades
- staden_io_lib
- star=2.6.1d
- stringtie
- subread
- survivor
- tdrmapper
- tophat-recondition
- trim-galore
- ucsc-bedgraphtobigwig
- ucsc-bedtobigbed
- ucsc-bigbedinfo
- ucsc-bigbedsummary
- ucsc-bigbedtobed
- ucsc-bigwiginfo
- ucsc-bigwigsummary
- ucsc-bigwigtobedgraph
- ucsc-bigwigtowig
- ucsc-fatotwobit
- ucsc-gtftogenepred
- ucsc-liftover
- ucsc-wigtobigwig
- umis
- vardict-java
- vardict[version='<=2015']
- variantbam
- varscan
- vcfanno
- vcflib
- verifybamid2
- viennarna
- vqsr_cnn
- vt
- wham
- xorg-libxt
- xz
The following packages will be downloaded:
package | build
---------------------------|-----------------
r-janitor-2.0.1 | r35h6115d3f_0 235 KB conda-forge
r-snakecase-0.11.0 | r35h6115d3f_1 175 KB conda-forge
vardict-1.8.2 | pl526_0 102 KB bioconda
------------------------------------------------------------
Total: 513 KB
The following NEW packages will be INSTALLED:
arriba bioconda/linux-64::arriba-1.2.0-h248197f_1
bioconductor-anno~ bioconda/noarch::bioconductor-annotationfilter-1.6.0-r351_0
bioconductor-apeg~ bioconda/linux-64::bioconductor-apeglm-1.4.1-r351hf484d3e_0
bioconductor-biov~ bioconda/linux-64::bioconductor-biovizbase-1.30.1-r351h14c3975_0
bioconductor-bsge~ bioconda/noarch::bioconductor-bsgenome-1.50.0-r351_0
bioconductor-bsge~ bioconda/noarch::bioconductor-bsgenome.hsapiens.ucsc.hg19-1.4.0-r351_5
bioconductor-bsge~ bioconda/noarch::bioconductor-bsgenome.hsapiens.ucsc.hg38-1.4.1-r351_5
bioconductor-bubb~ bioconda/linux-64::bioconductor-bubbletree-2.6.0-0
bioconductor-cn.m~ bioconda/linux-64::bioconductor-cn.mops-1.28.0-r351hf484d3e_0
bioconductor-copy~ bioconda/noarch::bioconductor-copynumber-1.22.0-r351_0
bioconductor-degr~ bioconda/noarch::bioconductor-degreport-1.19.1-r351_0
bioconductor-dese~ bioconda/linux-64::bioconductor-deseq2-1.22.1-r351hf484d3e_0
bioconductor-dexs~ bioconda/noarch::bioconductor-dexseq-1.28.0-r351_0
bioconductor-ense~ bioconda/noarch::bioconductor-ensembldb-2.6.3-r351_0
bioconductor-exom~ bioconda/linux-64::bioconductor-exomecopy-1.28.0-r351h14c3975_0
bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.18.1-r351_0
bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.1-r351_0
bioconductor-geno~ bioconda/linux-64::bioconductor-genomicalignments-1.18.1-r351h14c3975_0
bioconductor-geno~ bioconda/noarch::bioconductor-genomicfeatures-1.34.1-r351_0
bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.34.0-r351h14c3975_0
bioconductor-olig~ bioconda/noarch::bioconductor-oligoclasses-1.44.0-r351_0
bioconductor-rsam~ bioconda/linux-64::bioconductor-rsamtools-1.34.0-r351hf484d3e_0
bioconductor-rtra~ bioconda/linux-64::bioconductor-rtracklayer-1.42.1-r351h9d9f1b6_1
bioconductor-snpc~ bioconda/noarch::bioconductor-snpchip-2.28.0-r351_0
bioconductor-summ~ bioconda/noarch::bioconductor-summarizedexperiment-1.12.0-r351_0
bioconductor-tita~ bioconda/linux-64::bioconductor-titancna-1.20.1-r351h14c3975_0
bioconductor-txim~ bioconda/noarch::bioconductor-tximport-1.12.1-r351_1
bioconductor-vari~ bioconda/linux-64::bioconductor-variantannotation-1.28.3-r351h14c3975_0
hmftools-amber bioconda/noarch::hmftools-amber-3.5-0
hmftools-cobalt bioconda/noarch::hmftools-cobalt-1.11-0
hmftools-purple bioconda/noarch::hmftools-purple-2.52-0
qualimap bioconda/noarch::qualimap-2.2.2d-1
r-basejump bioconda/linux-64::r-basejump-0.7.2-r351_1
r-bcbiobase bioconda/linux-64::r-bcbiobase-0.4.1-r351_3
r-bcbiornaseq bioconda/linux-64::r-bcbiornaseq-0.2.9-r351_0
r-janitor conda-forge/noarch::r-janitor-2.0.1-r35h6115d3f_0
r-optparse conda-forge/noarch::r-optparse-1.6.6-r35h6115d3f_0
r-pscbs bioconda/linux-64::r-pscbs-0.65.0-r351h6115d3f_0
r-snakecase conda-forge/noarch::r-snakecase-0.11.0-r35h6115d3f_1
r-tidyverse conda-forge/noarch::r-tidyverse-1.3.0-r35h6115d3f_1
The following packages will be DOWNGRADED:
pandoc 2.10.1-h516909a_0 --> 2.9.2.1-0
vardict 2019.06.04-pl526_0 --> 1.8.2-pl526_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
# Installing into conda environment bwakit: bwakit
## Package Plan ##
environment location: /apps1/local/share/bcbio/anaconda/envs/bwakit
added / updated specs:
- bwakit
- python=3
The following packages will be downloaded:
package | build
---------------------------|-----------------
bwakit-0.7.17.dev1 | 0 43.0 MB bioconda
c-ares-1.17.1 | h7f98852_1 109 KB conda-forge
fermi2-r170 | hed695b0_0 95 KB bioconda
htsbox-r315 | hed695b0_0 128 KB bioconda
htslib-1.11 | hd3b49d5_2 1.8 MB bioconda
libcurl-7.75.0 | hc4aaa36_0 328 KB conda-forge
libdeflate-1.7 | h27cfd23_5 55 KB
libssh2-1.9.0 | ha56f1ee_6 226 KB conda-forge
ropebwt2-r187 | hed695b0_4 79 KB bioconda
samblaster-0.1.20 | hc9558a2_0 24 KB bioconda
samtools-1.11 | h6270b1f_0 383 KB bioconda
seqtk-r82 | 1 76 KB bioconda
trimadap-r2 | hed695b0_0 33 KB bioconda
------------------------------------------------------------
Total: 46.3 MB
The following NEW packages will be INSTALLED:
bwa bioconda/linux-64::bwa-0.7.17-hed695b0_7
bwakit bioconda/noarch::bwakit-0.7.17.dev1-0
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.17.1-h7f98852_1
fermi2 bioconda/linux-64::fermi2-r170-hed695b0_0
htsbox bioconda/linux-64::htsbox-r315-hed695b0_0
htslib bioconda/linux-64::htslib-1.11-hd3b49d5_2
k8 bioconda/linux-64::k8-0.2.5-he513fc3_0
krb5 conda-forge/linux-64::krb5-1.17.2-h926e7f8_0
libcurl conda-forge/linux-64::libcurl-7.75.0-hc4aaa36_0
libdeflate pkgs/main/linux-64::libdeflate-1.7-h27cfd23_5
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2
libnghttp2 conda-forge/linux-64::libnghttp2-1.43.0-h812cca2_0
libssh2 conda-forge/linux-64::libssh2-1.9.0-ha56f1ee_6
make conda-forge/linux-64::make-4.3-hd18ef5c_1
perl conda-forge/linux-64::perl-5.32.0-h36c2ea0_0
ropebwt2 bioconda/linux-64::ropebwt2-r187-hed695b0_4
samblaster bioconda/linux-64::samblaster-0.1.20-hc9558a2_0
samtools bioconda/linux-64::samtools-1.11-h6270b1f_0
seqtk bioconda/linux-64::seqtk-r82-1
trimadap bioconda/linux-64::trimadap-r2-hed695b0_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
# Installing into conda environment dv: deepvariant
# All requested packages already installed.
# Installing into conda environment htslib1.10: mosdepth
# All requested packages already installed.
# Installing into conda environment htslib1.11: scramble
## Package Plan ##
environment location: /apps1/local/share/bcbio/anaconda/envs/htslib1.11
added / updated specs:
- python=3
- scramble
The following packages will be downloaded:
package | build
---------------------------|-----------------
blas-2.17 | openblas 11 KB conda-forge
blas-devel-3.8.0 | 17_openblas 10 KB conda-forge
blast-2.10.1 | pl526he19e7b1_3 20.6 MB bioconda
cairo-1.16.0 | h7979940_1007 1.5 MB conda-forge
curl-7.75.0 | h979ede3_0 147 KB conda-forge
entrez-direct-13.9 | pl526h375a9b1_1 5.2 MB bioconda
gcc_impl_linux-64-9.3.0 | h70c0ae5_18 43.1 MB conda-forge
gcc_linux-64-9.3.0 | hf25ea35_30 23 KB conda-forge
gettext-0.19.8.1 | h0b5b191_1005 3.6 MB conda-forge
gfortran_impl_linux-64-9.3.0| hc4a2995_18 10.1 MB conda-forge
gfortran_linux-64-9.3.0 | hdc58fab_30 22 KB conda-forge
gxx_impl_linux-64-9.3.0 | hd87eabc_18 10.7 MB conda-forge
gxx_linux-64-9.3.0 | h3fbe746_30 23 KB conda-forge
harfbuzz-2.7.4 | h5cf4720_0 1.9 MB conda-forge
icu-68.1 | h2531618_0 11.8 MB
libgcc-devel_linux-64-9.3.0| h7864c58_18 4.0 MB conda-forge
libglib-2.66.7 | h3e27bee_1 3.0 MB conda-forge
liblapacke-3.8.0 | 17_openblas 11 KB conda-forge
libopenblas-0.3.10 |pthreads_hb3c22a3_5 7.8 MB conda-forge
libstdcxx-devel_linux-64-9.3.0| hb016644_18 13.9 MB conda-forge
libxml2-2.9.10 | h72842e0_3 1.3 MB conda-forge
openblas-0.3.10 |pthreads_h43bd3aa_5 8.3 MB conda-forge
pango-1.42.4 | h80147aa_5 533 KB conda-forge
pcre2-10.36 | h032f7d1_1 1.1 MB conda-forge
perl-5.26.2 | h36c2ea0_1008 15.4 MB conda-forge
perl-archive-tar-2.32 | pl526_0 31 KB bioconda
perl-io-zlib-1.10 | pl526_2 9 KB bioconda
pixman-0.40.0 | h36c2ea0_0 627 KB conda-forge
r-base-4.0.3 | h8ff2632_7 23.7 MB conda-forge
r-glue-1.4.2 | r40hcfec24a_0 141 KB conda-forge
r-magrittr-2.0.1 | r40hcfec24a_1 211 KB conda-forge
r-rblast-0.99.1 | r40_3 40 KB bioconda
r-stringi-1.5.3 | r40hcabe038_1 803 KB conda-forge
scramble-1.0.1 | h516909a_0 1.2 MB bioconda
xorg-libsm-1.2.3 | hd9c2040_1000 26 KB conda-forge
xorg-libx11-1.7.0 | h36c2ea0_0 943 KB conda-forge
xorg-libxext-1.3.4 | h7f98852_1 54 KB conda-forge
xorg-libxrender-0.9.10 | h7f98852_1003 32 KB conda-forge
xorg-libxt-1.2.1 | h7f98852_2 375 KB conda-forge
zstd-1.4.9 | ha95c52a_0 431 KB conda-forge
------------------------------------------------------------
Total: 192.6 MB
The following NEW packages will be INSTALLED:
_r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1
binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.35.1-h193b22a_2
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.35-h67ddf6f_30
bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.36.0-r40_0
bioconductor-bioc~ bioconda/linux-64::bioconductor-biocparallel-1.24.0-r40h5f743cb_0
bioconductor-bios~ bioconda/linux-64::bioconductor-biostrings-2.58.0-r40h037d062_0
bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.26.0-r40_0
bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.4-r40_0
bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.42.0-r40h037d062_0
bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.24.0-r40h037d062_0
bioconductor-rhts~ bioconda/linux-64::bioconductor-rhtslib-1.22.0-r40h037d062_0
bioconductor-rsam~ bioconda/linux-64::bioconductor-rsamtools-2.6.0-r40h5f743cb_0
bioconductor-s4ve~ bioconda/linux-64::bioconductor-s4vectors-0.28.0-r40h037d062_0
bioconductor-xvec~ bioconda/linux-64::bioconductor-xvector-0.30.0-r40h037d062_0
bioconductor-zlib~ bioconda/linux-64::bioconductor-zlibbioc-1.36.0-r40h037d062_0
blast bioconda/linux-64::blast-2.10.1-pl526he19e7b1_3
bwidget conda-forge/linux-64::bwidget-1.9.14-0
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.17.1-h7f98852_1
cairo conda-forge/linux-64::cairo-1.16.0-h7979940_1007
curl conda-forge/linux-64::curl-7.75.0-h979ede3_0
entrez-direct bioconda/linux-64::entrez-direct-13.9-pl526h375a9b1_1
expat pkgs/main/linux-64::expat-2.2.10-he6710b0_2
fontconfig conda-forge/linux-64::fontconfig-2.13.1-hba837de_1004
freetype conda-forge/linux-64::freetype-2.10.4-h0708190_1
fribidi conda-forge/linux-64::fribidi-1.0.10-h516909a_0
gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-9.3.0-h70c0ae5_18
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-9.3.0-hf25ea35_30
gettext conda-forge/linux-64::gettext-0.19.8.1-h0b5b191_1005
gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-9.3.0-hc4a2995_18
gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-9.3.0-hdc58fab_30
graphite2 pkgs/main/linux-64::graphite2-1.3.14-h23475e2_0
gsl conda-forge/linux-64::gsl-2.6-he838d99_2
gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-9.3.0-hd87eabc_18
gxx_linux-64 conda-forge/linux-64::gxx_linux-64-9.3.0-h3fbe746_30
harfbuzz conda-forge/linux-64::harfbuzz-2.7.4-h5cf4720_0
htslib bioconda/linux-64::htslib-1.11-hd3b49d5_2
icu pkgs/main/linux-64::icu-68.1-h2531618_0
jpeg conda-forge/linux-64::jpeg-9d-h516909a_0
kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-h77966d4_13
krb5 conda-forge/linux-64::krb5-1.17.2-h926e7f8_0
libcurl conda-forge/linux-64::libcurl-7.75.0-hc4aaa36_0
libdeflate pkgs/main/linux-64::libdeflate-1.7-h27cfd23_5
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libgcc-devel_linu~ conda-forge/linux-64::libgcc-devel_linux-64-9.3.0-h7864c58_18
libgfortran4 conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_18
libglib conda-forge/linux-64::libglib-2.66.7-h3e27bee_1
libgomp conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18
libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0
libnghttp2 conda-forge/linux-64::libnghttp2-1.43.0-h812cca2_0
libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_2
libssh2 conda-forge/linux-64::libssh2-1.9.0-ha56f1ee_6
libstdcxx-devel_l~ conda-forge/linux-64::libstdcxx-devel_linux-64-9.3.0-hb016644_18
libtiff conda-forge/linux-64::libtiff-4.2.0-hdc55705_0
libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
libwebp-base pkgs/main/linux-64::libwebp-base-1.2.0-h27cfd23_0
libxcb pkgs/main/linux-64::libxcb-1.14-h7b6447c_0
libxml2 conda-forge/linux-64::libxml2-2.9.10-h72842e0_3
lz4-c pkgs/main/linux-64::lz4-c-1.9.3-h2531618_0
make conda-forge/linux-64::make-4.3-hd18ef5c_1
pango conda-forge/linux-64::pango-1.42.4-h80147aa_5
pcre pkgs/main/linux-64::pcre-8.44-he6710b0_0
pcre2 conda-forge/linux-64::pcre2-10.36-h032f7d1_1
perl conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008
perl-app-cpanminus bioconda/linux-64::perl-app-cpanminus-1.7044-pl526_1
perl-archive-tar bioconda/linux-64::perl-archive-tar-2.32-pl526_0
perl-base bioconda/linux-64::perl-base-2.23-pl526_1
perl-business-isbn bioconda/linux-64::perl-business-isbn-3.004-pl526_0
perl-business-isb~ bioconda/linux-64::perl-business-isbn-data-20140910.003-pl526_0
perl-carp bioconda/linux-64::perl-carp-1.38-pl526_3
perl-common-sense bioconda/linux-64::perl-common-sense-3.74-pl526_2
perl-compress-raw~ bioconda/linux-64::perl-compress-raw-bzip2-2.087-pl526he1b5a44_0
perl-compress-raw~ bioconda/linux-64::perl-compress-raw-zlib-2.087-pl526hc9558a2_0
perl-constant bioconda/linux-64::perl-constant-1.33-pl526_1
perl-data-dumper bioconda/linux-64::perl-data-dumper-2.173-pl526_0
perl-digest-hmac bioconda/linux-64::perl-digest-hmac-1.03-pl526_3
perl-digest-md5 bioconda/linux-64::perl-digest-md5-2.55-pl526_0
perl-encode bioconda/linux-64::perl-encode-2.88-pl526_1
perl-encode-locale bioconda/linux-64::perl-encode-locale-1.05-pl526_6
perl-exporter bioconda/linux-64::perl-exporter-5.72-pl526_1
perl-exporter-tiny bioconda/linux-64::perl-exporter-tiny-1.002001-pl526_0
perl-extutils-mak~ bioconda/linux-64::perl-extutils-makemaker-7.36-pl526_1
perl-file-listing bioconda/linux-64::perl-file-listing-6.04-pl526_1
perl-file-path bioconda/linux-64::perl-file-path-2.16-pl526_0
perl-file-temp bioconda/linux-64::perl-file-temp-0.2304-pl526_2
perl-html-parser bioconda/linux-64::perl-html-parser-3.72-pl526h6bb024c_5
perl-html-tagset bioconda/linux-64::perl-html-tagset-3.20-pl526_3
perl-html-tree bioconda/linux-64::perl-html-tree-5.07-pl526_1
perl-http-cookies bioconda/linux-64::perl-http-cookies-6.04-pl526_0
perl-http-daemon bioconda/linux-64::perl-http-daemon-6.01-pl526_1
perl-http-date bioconda/linux-64::perl-http-date-6.02-pl526_3
perl-http-message bioconda/linux-64::perl-http-message-6.18-pl526_0
perl-http-negotia~ bioconda/linux-64::perl-http-negotiate-6.01-pl526_3
perl-io-compress bioconda/linux-64::perl-io-compress-2.087-pl526he1b5a44_0
perl-io-html bioconda/linux-64::perl-io-html-1.001-pl526_2
perl-io-socket-ssl bioconda/linux-64::perl-io-socket-ssl-2.066-pl526_0
perl-io-zlib bioconda/linux-64::perl-io-zlib-1.10-pl526_2
perl-json bioconda/linux-64::perl-json-4.02-pl526_0
perl-json-xs bioconda/linux-64::perl-json-xs-2.34-pl526h6bb024c_3
perl-libwww-perl bioconda/noarch::perl-libwww-perl-6.39-pl526_0
perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-0.428-pl526_1
perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.428-pl526_0
perl-lwp-mediatyp~ bioconda/linux-64::perl-lwp-mediatypes-6.04-pl526_0
perl-lwp-protocol~ bioconda/linux-64::perl-lwp-protocol-https-6.07-pl526_4
perl-mime-base64 bioconda/linux-64::perl-mime-base64-3.15-pl526_1
perl-mozilla-ca bioconda/linux-64::perl-mozilla-ca-20180117-pl526_1
perl-net-http bioconda/noarch::perl-net-http-6.19-pl526_0
perl-net-ssleay bioconda/linux-64::perl-net-ssleay-1.88-pl526h90d6eec_0
perl-ntlm bioconda/linux-64::perl-ntlm-1.09-pl526_4
perl-parent bioconda/linux-64::perl-parent-0.236-pl526_1
perl-pathtools bioconda/linux-64::perl-pathtools-3.75-pl526h14c3975_1
perl-scalar-list-~ bioconda/linux-64::perl-scalar-list-utils-1.52-pl526h516909a_0
perl-socket bioconda/linux-64::perl-socket-2.027-pl526_1
perl-storable bioconda/linux-64::perl-storable-3.15-pl526h14c3975_0
perl-test-require~ bioconda/linux-64::perl-test-requiresinternet-0.05-pl526_0
perl-time-local bioconda/linux-64::perl-time-local-1.28-pl526_1
perl-try-tiny bioconda/linux-64::perl-try-tiny-0.30-pl526_1
perl-types-serial~ bioconda/linux-64::perl-types-serialiser-1.0-pl526_2
perl-uri bioconda/linux-64::perl-uri-1.76-pl526_0
perl-www-robotrul~ bioconda/linux-64::perl-www-robotrules-6.02-pl526_3
perl-xml-namespac~ bioconda/linux-64::perl-xml-namespacesupport-1.12-pl526_0
perl-xml-parser conda-forge/linux-64::perl-xml-parser-2.44_01-pl526ha1d75be_1002
perl-xml-sax bioconda/noarch::perl-xml-sax-1.02-pl526_0
perl-xml-sax-base bioconda/linux-64::perl-xml-sax-base-1.09-pl526_0
perl-xml-sax-expat bioconda/linux-64::perl-xml-sax-expat-0.51-pl526_3
perl-xml-simple bioconda/linux-64::perl-xml-simple-2.25-pl526_1
perl-xsloader bioconda/linux-64::perl-xsloader-0.24-pl526_0
pixman conda-forge/linux-64::pixman-0.40.0-h36c2ea0_0
r-base conda-forge/linux-64::r-base-4.0.3-h8ff2632_7
r-bh conda-forge/noarch::r-bh-1.75.0_0-r40hc72bb7e_0
r-bitops conda-forge/linux-64::r-bitops-1.0_6-r40hcdcec82_1004
r-crayon conda-forge/noarch::r-crayon-1.4.1-r40hc72bb7e_0
r-formatr conda-forge/noarch::r-formatr-1.7-r40h6115d3f_2
r-futile.logger conda-forge/noarch::r-futile.logger-1.4.3-r40h6115d3f_1003
r-futile.options conda-forge/noarch::r-futile.options-1.0.1-r40h6115d3f_1002
r-getopt conda-forge/noarch::r-getopt-1.20.3-r40_2
r-glue conda-forge/linux-64::r-glue-1.4.2-r40hcfec24a_0
r-lambda.r conda-forge/noarch::r-lambda.r-1.2.4-r40h6115d3f_1
r-magrittr conda-forge/linux-64::r-magrittr-2.0.1-r40hcfec24a_1
r-optparse conda-forge/noarch::r-optparse-1.6.6-r40h6115d3f_1
r-rblast bioconda/linux-64::r-rblast-0.99.1-r40_3
r-rcurl conda-forge/linux-64::r-rcurl-1.98_1.2-r40hcdcec82_1
r-snow conda-forge/noarch::r-snow-0.4_3-r40h6115d3f_1002
r-stringi conda-forge/linux-64::r-stringi-1.5.3-r40hcabe038_1
r-stringr conda-forge/noarch::r-stringr-1.4.0-r40h6115d3f_2
scramble bioconda/linux-64::scramble-1.0.1-h516909a_0
sed conda-forge/linux-64::sed-4.8-he412f7d_0
sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-h77966d4_13
tktable conda-forge/linux-64::tktable-2.10-hb7b940f_3
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-hd9c2040_1000
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.7.0-h36c2ea0_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h7f98852_1003
xorg-libxt conda-forge/linux-64::xorg-libxt-1.2.1-h7f98852_2
xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
xorg-xproto pkgs/main/linux-64::xorg-xproto-7.0.31-h27cfd23_1007
zstd conda-forge/linux-64::zstd-1.4.9-ha95c52a_0
The following packages will be DOWNGRADED:
blas 2.108-openblas --> 2.17-openblas
blas-devel 3.9.0-8_openblas --> 3.8.0-17_openblas
libblas 3.9.0-8_openblas --> 3.8.0-17_openblas
libcblas 3.9.0-8_openblas --> 3.8.0-17_openblas
libgfortran-ng 9.3.0-hff62375_18 --> 7.5.0-h14aa051_18
liblapack 3.9.0-8_openblas --> 3.8.0-17_openblas
liblapacke 3.9.0-8_openblas --> 3.8.0-17_openblas
libopenblas 0.3.12-pthreads_h4812303_1 --> 0.3.10-pthreads_hb3c22a3_5
openblas 0.3.12-pthreads_h04b7a96_1 --> 0.3.10-pthreads_h43bd3aa_5
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
# Installing into conda environment python2: bismark, cpat, cutadapt=1.16, dkfz-bias-filter, gemini, gvcf-regions, hap.py, htseq=0.9.1, lumpy-sv, manta, metasv, mirge, phylowgs, platypus-variant, sentieon, smcounter2, smoove, strelka, svtools, svtyper, theta2, tophat, vawk, vcf2db
# All requested packages already installed.
# Installing into conda environment python3: atropos, crossmap
# All requested packages already installed.
# Installing into conda environment r36: ataqv, bioconductor-degreport, bioconductor-deseq2, bioconductor-genomeinfodb, bioconductor-genomeinfodbdata, bioconductor-org.hs.eg.db, bioconductor-purecn>=1.18.0, bioconductor-rtracklayer, bioconductor-txdb.hsapiens.ucsc.hg19.knowngene, bioconductor-txdb.hsapiens.ucsc.hg38.knowngene, bioconductor-tximport, r-janitor, r-optparse, r-pscbs, r-tidyverse
## Package Plan ##
environment location: /apps1/local/share/bcbio/anaconda/envs/r36
added / updated specs:
- ataqv
- bioconductor-degreport
- bioconductor-deseq2
- bioconductor-genomeinfodb
- bioconductor-genomeinfodbdata
- bioconductor-org.hs.eg.db
- bioconductor-purecn[version='>=1.18.0']
- bioconductor-rtracklayer
- bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
- bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
- bioconductor-tximport
- python=3
- r-janitor
- r-optparse
- r-pscbs
- r-tidyverse
The following packages will be downloaded:
package | build
---------------------------|-----------------
bioconductor-all-1.32.0 | r40_0 7 KB bioconda
bioconductor-annotate-1.68.0| r40_0 2.1 MB bioconda
bioconductor-complexheatmap-2.6.2| r40_0 3.0 MB bioconda
bioconductor-consensusclusterplus-1.54.0| r40_0 342 KB bioconda
bioconductor-degreport-1.26.0| r40_0 3.0 MB bioconda
bioconductor-deseq2-1.30.0 | r40h5f743cb_0 2.7 MB bioconda
bioconductor-edger-3.32.0 | r40h5f743cb_0 2.4 MB bioconda
bioconductor-genefilter-1.72.0| r40hc6cf775_0 1.8 MB bioconda
bioconductor-geneplotter-1.68.0| r40_0 1.5 MB bioconda
bioconductor-limma-3.46.0 | r40h037d062_0 2.8 MB bioconda
bioconductor-tximport-1.18.0| r40_0 364 KB bioconda
pandoc-2.12 | h7f98852_0 12.4 MB conda-forge
r-base64enc-0.1_3 | r40hcdcec82_1004 43 KB conda-forge
r-broom-0.7.5 | r40hc72bb7e_0 1.7 MB conda-forge
r-cairo-1.5_12.2 | r40hcdcec82_0 94 KB conda-forge
r-cellranger-1.1.0 | r40h6115d3f_1003 108 KB conda-forge
r-circlize-0.4.12 | r40hc72bb7e_0 3.2 MB conda-forge
r-clipr-0.7.1 | r40h142f84f_0 65 KB conda-forge
r-clue-0.3_57 | r40h516909a_2 1.0 MB conda-forge
r-cluster-2.1.0 | r40h31ca83e_4 553 KB conda-forge
r-cowplot-1.1.1 | r40hc72bb7e_0 1.3 MB conda-forge
r-cpp11-0.2.6 | r40hc72bb7e_0 154 KB conda-forge
r-forcats-0.5.1 | r40hc72bb7e_0 377 KB conda-forge
r-fs-1.5.0 | r40h0357c0b_0 515 KB conda-forge
r-getoptlong-1.0.5 | r40hc72bb7e_0 1.0 MB conda-forge
r-ggdendro-0.1.22 | r40h6115d3f_0 195 KB conda-forge
r-ggrepel-0.8.2 | r40h0357c0b_1 653 KB conda-forge
r-globaloptions-0.1.2 | r40_0 472 KB conda-forge
r-haven-2.3.1 | r40hde08347_0 373 KB conda-forge
r-highr-0.8 | r40h6115d3f_2 58 KB conda-forge
r-htmltools-0.5.0 | r40h0357c0b_0 233 KB conda-forge
r-janitor-2.1.0 | r40hc72bb7e_0 243 KB conda-forge
r-knitr-1.31 | r40hc72bb7e_0 1.3 MB conda-forge
r-lasso2-1.2_21.1 | r40h0eb13af_0 280 KB conda-forge
r-locfit-1.5_9.4 | r40hcdcec82_1 560 KB conda-forge
r-logging-0.10_108 | r40_2 177 KB conda-forge
r-lubridate-1.7.9.2 | r40he524a50_0 1.1 MB conda-forge
r-markdown-1.1 | r40hcdcec82_1 143 KB conda-forge
r-mnormt-1.5_7 | r40h31ca83e_2 113 KB conda-forge
r-modelr-0.1.8 | r40h6115d3f_0 218 KB conda-forge
r-nozzle.r1-1.1_1 | r40_1003 374 KB conda-forge
r-png-0.1_7 | r40hcdcec82_1004 58 KB conda-forge
r-psych-2.0.12 | r40hc72bb7e_0 4.6 MB conda-forge
r-rcpparmadillo-0.10.1.2.0 | r40hfbb317b_0 1.2 MB conda-forge
r-readr-1.4.0 | r40h1b71b39_0 861 KB conda-forge
r-readxl-1.3.1 | r40hde08347_4 859 KB conda-forge
r-rematch-1.0.1 | r40h6115d3f_1003 19 KB conda-forge
r-reprex-1.0.0 | r40hc72bb7e_0 483 KB conda-forge
r-reshape-0.8.8 | r40hcdcec82_2 175 KB conda-forge
r-reshape2-1.4.4 | r40h0357c0b_1 135 KB conda-forge
r-rjson-0.2.20 | r40h0357c0b_1002 146 KB conda-forge
r-rmarkdown-2.7 | r40hc72bb7e_0 3.1 MB conda-forge
r-rvest-0.3.6 | r40h6115d3f_0 1.5 MB conda-forge
r-selectr-0.4_2 | r40h6115d3f_1 449 KB conda-forge
r-shape-1.4.5 | r40_0 795 KB conda-forge
r-snakecase-0.11.0 | r40h6115d3f_2 176 KB conda-forge
r-survival-3.2_7 | r40hcdcec82_0 7.6 MB conda-forge
r-tidyr-1.1.2 | r40h0357c0b_0 806 KB conda-forge
r-tidyverse-1.3.0 | r40h6115d3f_2 452 KB conda-forge
r-tinytex-0.30 | r40hc72bb7e_0 123 KB conda-forge
r-xfun-0.19 | r40h9e2df91_0 293 KB conda-forge
r-xtable-1.8_4 | r40h6115d3f_3 697 KB conda-forge
r-yaml-2.2.1 | r40hcdcec82_1 117 KB conda-forge
xorg-libxt-1.2.0 | h516909a_0 374 KB conda-forge
------------------------------------------------------------
Total: 73.5 MB
The following NEW packages will be INSTALLED:
bioconductor-all bioconda/noarch::bioconductor-all-1.32.0-r40_0
bioconductor-anno~ bioconda/noarch::bioconductor-annotate-1.68.0-r40_0
bioconductor-comp~ bioconda/noarch::bioconductor-complexheatmap-2.6.2-r40_0
bioconductor-cons~ bioconda/noarch::bioconductor-consensusclusterplus-1.54.0-r40_0
bioconductor-degr~ bioconda/noarch::bioconductor-degreport-1.26.0-r40_0
bioconductor-dese~ bioconda/linux-64::bioconductor-deseq2-1.30.0-r40h5f743cb_0
bioconductor-edger bioconda/linux-64::bioconductor-edger-3.32.0-r40h5f743cb_0
bioconductor-gene~ bioconda/linux-64::bioconductor-genefilter-1.72.0-r40hc6cf775_0
bioconductor-gene~ bioconda/noarch::bioconductor-geneplotter-1.68.0-r40_0
bioconductor-limma bioconda/linux-64::bioconductor-limma-3.46.0-r40h037d062_0
bioconductor-txim~ bioconda/noarch::bioconductor-tximport-1.18.0-r40_0
pandoc conda-forge/linux-64::pandoc-2.12-h7f98852_0
r-base64enc conda-forge/linux-64::r-base64enc-0.1_3-r40hcdcec82_1004
r-broom conda-forge/noarch::r-broom-0.7.5-r40hc72bb7e_0
r-cairo conda-forge/linux-64::r-cairo-1.5_12.2-r40hcdcec82_0
r-cellranger conda-forge/noarch::r-cellranger-1.1.0-r40h6115d3f_1003
r-circlize conda-forge/noarch::r-circlize-0.4.12-r40hc72bb7e_0
r-clipr conda-forge/noarch::r-clipr-0.7.1-r40h142f84f_0
r-clue conda-forge/linux-64::r-clue-0.3_57-r40h516909a_2
r-cluster conda-forge/linux-64::r-cluster-2.1.0-r40h31ca83e_4
r-cowplot conda-forge/noarch::r-cowplot-1.1.1-r40hc72bb7e_0
r-cpp11 conda-forge/noarch::r-cpp11-0.2.6-r40hc72bb7e_0
r-forcats conda-forge/noarch::r-forcats-0.5.1-r40hc72bb7e_0
r-fs conda-forge/linux-64::r-fs-1.5.0-r40h0357c0b_0
r-getoptlong conda-forge/noarch::r-getoptlong-1.0.5-r40hc72bb7e_0
r-ggdendro conda-forge/noarch::r-ggdendro-0.1.22-r40h6115d3f_0
r-ggrepel conda-forge/linux-64::r-ggrepel-0.8.2-r40h0357c0b_1
r-globaloptions conda-forge/noarch::r-globaloptions-0.1.2-r40_0
r-haven conda-forge/linux-64::r-haven-2.3.1-r40hde08347_0
r-highr conda-forge/noarch::r-highr-0.8-r40h6115d3f_2
r-htmltools conda-forge/linux-64::r-htmltools-0.5.0-r40h0357c0b_0
r-janitor conda-forge/noarch::r-janitor-2.1.0-r40hc72bb7e_0
r-knitr conda-forge/noarch::r-knitr-1.31-r40hc72bb7e_0
r-lasso2 conda-forge/linux-64::r-lasso2-1.2_21.1-r40h0eb13af_0
r-locfit conda-forge/linux-64::r-locfit-1.5_9.4-r40hcdcec82_1
r-logging conda-forge/noarch::r-logging-0.10_108-r40_2
r-lubridate conda-forge/linux-64::r-lubridate-1.7.9.2-r40he524a50_0
r-markdown conda-forge/linux-64::r-markdown-1.1-r40hcdcec82_1
r-mnormt conda-forge/linux-64::r-mnormt-1.5_7-r40h31ca83e_2
r-modelr conda-forge/noarch::r-modelr-0.1.8-r40h6115d3f_0
r-nozzle.r1 conda-forge/noarch::r-nozzle.r1-1.1_1-r40_1003
r-plyr conda-forge/linux-64::r-plyr-1.8.6-r40h0357c0b_1
r-png conda-forge/linux-64::r-png-0.1_7-r40hcdcec82_1004
r-psych conda-forge/noarch::r-psych-2.0.12-r40hc72bb7e_0
r-rcpparmadillo conda-forge/linux-64::r-rcpparmadillo-0.10.1.2.0-r40hfbb317b_0
r-readr conda-forge/linux-64::r-readr-1.4.0-r40h1b71b39_0
r-readxl conda-forge/linux-64::r-readxl-1.3.1-r40hde08347_4
r-rematch conda-forge/noarch::r-rematch-1.0.1-r40h6115d3f_1003
r-reprex conda-forge/noarch::r-reprex-1.0.0-r40hc72bb7e_0
r-reshape conda-forge/linux-64::r-reshape-0.8.8-r40hcdcec82_2
r-reshape2 conda-forge/linux-64::r-reshape2-1.4.4-r40h0357c0b_1
r-rjson conda-forge/linux-64::r-rjson-0.2.20-r40h0357c0b_1002
r-rmarkdown conda-forge/noarch::r-rmarkdown-2.7-r40hc72bb7e_0
r-rvest conda-forge/noarch::r-rvest-0.3.6-r40h6115d3f_0
r-selectr conda-forge/noarch::r-selectr-0.4_2-r40h6115d3f_1
r-shape conda-forge/noarch::r-shape-1.4.5-r40_0
r-snakecase conda-forge/noarch::r-snakecase-0.11.0-r40h6115d3f_2
r-survival conda-forge/linux-64::r-survival-3.2_7-r40hcdcec82_0
r-tidyr conda-forge/linux-64::r-tidyr-1.1.2-r40h0357c0b_0
r-tidyverse conda-forge/noarch::r-tidyverse-1.3.0-r40h6115d3f_2
r-tinytex conda-forge/noarch::r-tinytex-0.30-r40hc72bb7e_0
r-xfun conda-forge/linux-64::r-xfun-0.19-r40h9e2df91_0
r-xtable conda-forge/noarch::r-xtable-1.8_4-r40h6115d3f_3
r-yaml conda-forge/linux-64::r-yaml-2.2.1-r40hcdcec82_1
xorg-libxt conda-forge/linux-64::xorg-libxt-1.2.0-h516909a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
# Installing into conda environment samtools0: ericscript
# All requested packages already installed.
Creating manifest of installed packages in /apps1/local/share/bcbio/manifest
Third party tools upgrade complete.
Upgrade completed successfully.
But still the bcbio run failed because dplyr version is too low. Can you check this for me too? Thank you.
Running bcbio version: 1.2.7
global config: /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbio_system.yaml
run info config: /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/config/K0008-K0011_RNA_updated.yaml
[2021-03-09T21:53Z] System YAML configuration: /apps1/local/share/bcbio/galaxy/bcbio_system.yaml.
[2021-03-09T21:53Z] Locale set to C.UTF-8.
[2021-03-09T21:53Z] Resource requests: picard; memory: 3.00; cores: 16
[2021-03-09T21:53Z] Configuring 8 jobs to run, using 1 cores each with 3.00g of memory reserved for each job
[2021-03-09T21:53Z] Timing: organize samples
[2021-03-09T21:53Z] multiprocessing: organize_samples
[2021-03-09T21:53Z] Using input YAML configuration: /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/config/K0008-K0011_RNA_updated.yaml
[2021-03-09T21:53Z] Checking sample YAML configuration: /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/config/K0008-K0011_RNA_updated.yaml
[2021-03-09T21:53Z] Retreiving program versions from /apps1/local/share/bcbio/manifest/python-packages.yaml.
[2021-03-09T21:53Z] Retreiving program versions from /apps1/local/share/bcbio/manifest/r-packages.yaml.
[2021-03-09T21:53Z] Testing minimum versions of installed programs
[2021-03-09T21:53Z] multiprocessing: prepare_sample
[2021-03-09T21:53Z] Preparing K0006-BF1-RNAseq
[2021-03-09T21:53Z] Preparing K0011-BF1-RNAseq
[2021-03-09T21:53Z] Preparing K0011-AF1-RNAseq
[2021-03-09T21:53Z] Preparing K0009-AF1-RNAseq
[2021-03-09T21:53Z] Preparing K0008-AF1-RNAseq
[2021-03-09T21:53Z] Preparing K0006-AF1-RNAseq
[2021-03-09T21:53Z] Preparing K0008-AF1-LMDRNAseq
[2021-03-09T21:53Z] Preparing K0010-AF1-RNAseq
[2021-03-09T21:53Z] Resource requests: picard, samtools, star; memory: 3.00, 3.00, 3.00; cores: 16, 16, 16
[2021-03-09T21:53Z] Configuring 6 jobs to run, using 16 cores each with 48.1g of memory reserved for each job
[2021-03-09T21:53Z] Timing: alignment
[2021-03-09T21:53Z] multiprocessing: disambiguate_split
[2021-03-09T21:53Z] multiprocessing: process_alignment
[2021-03-09T21:53Z] Resource requests: cufflinks, samtools; memory: 3.00, 3.00; cores: 16, 16
[2021-03-09T21:53Z] Configuring 6 jobs to run, using 16 cores each with 48.1g of memory reserved for each job
[2021-03-09T21:53Z] Timing: disambiguation
[2021-03-09T21:53Z] Timing: transcript assembly
[2021-03-09T21:53Z] Timing: estimate expression (threaded)
[2021-03-09T21:53Z] multiprocessing: generate_transcript_counts
[2021-03-09T21:53Z] multiprocessing: run_kallisto_index
[2021-03-09T21:53Z] multiprocessing: run_kallisto_rnaseq
[2021-03-09T21:53Z] multiprocessing: run_salmon_index
[2021-03-09T21:53Z] multiprocessing: run_salmon_reads
[2021-03-09T21:53Z] multiprocessing: detect_fusions
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
with h5py.File(h5) as f:
[2021-03-09T21:53Z] Resource requests: dexseq, express; memory: 10.00, 8.00; cores: 1, 1
[2021-03-09T21:53Z] Configuring 8 jobs to run, using 1 cores each with 10.00g of memory reserved for each job
[2021-03-09T21:53Z] Timing: estimate expression (single threaded)
[2021-03-09T21:53Z] Loading tximport.
[2021-03-09T21:53Z] Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
[2021-03-09T21:53Z] namespace ‘dplyr’ 1.0.2 is already loaded, but >= 1.0.3 is required
[2021-03-09T21:53Z] Execution halted
[2021-03-09T21:53Z] Uncaught exception occurred
Traceback (most recent call last):
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command '/apps1/local/share/bcbio/anaconda/envs/r36/bin/Rscript --vanilla -e library(tidyverse);salmon_files = list.files("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/salmon", pattern="quant.sf", recursive=TRUE, full.names=TRUE);tx2gene = readr::read_csv("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/inputs/transcriptome/tx2gene.csv", col_names=c("transcript", "gene")); samples = basename(dirname(salmon_files));names(salmon_files) = samples;txi = tximport::tximport(salmon_files, type="salmon", tx2gene=tx2gene, countsFromAbundance="lengthScaledTPM", dropInfReps=TRUE);readr::write_csv(round(txi$counts) %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmpd1qg0wnz/tximport-counts.csv");readr::write_csv(txi$abundance %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmps3yflioo/tximport-tpm.csv");
Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace ‘dplyr’ 1.0.2 is already loaded, but >= 1.0.3 is required
Execution halted
' returned non-zero exit status 1.
Traceback (most recent call last):
File "/apps1/local/bin/bcbio_nextgen.py", line 245, in <module>
main(**kwargs)
File "/apps1/local/bin/bcbio_nextgen.py", line 46, in main
run_main(**kwargs)
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
fc_dir, run_info_yaml)
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 264, in rnaseqpipeline
samples = rnaseq.combine_files(samples)
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/rnaseq.py", line 489, in combine_files
tximport = load_tximport(data)
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/rnaseq.py", line 556, in load_tximport
do.run([rcmd, "--vanilla", "-e", render_string], f"Loading tximport.")
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command '/apps1/local/share/bcbio/anaconda/envs/r36/bin/Rscript --vanilla -e library(tidyverse);salmon_files = list.files("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/salmon", pattern="quant.sf", recursive=TRUE, full.names=TRUE);tx2gene = readr::read_csv("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/inputs/transcriptome/tx2gene.csv", col_names=c("transcript", "gene")); samples = basename(dirname(salmon_files));names(salmon_files) = samples;txi = tximport::tximport(salmon_files, type="salmon", tx2gene=tx2gene, countsFromAbundance="lengthScaledTPM", dropInfReps=TRUE);readr::write_csv(round(txi$counts) %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmpd1qg0wnz/tximport-counts.csv");readr::write_csv(txi$abundance %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmps3yflioo/tximport-tpm.csv");
Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace ‘dplyr’ 1.0.2 is already loaded, but >= 1.0.3 is required
Execution halted
' returned non-zero exit status 1.
Я бы тоже добавил это в комментарии, но он не работает в этом формате. Я очень надеюсь, что фактический комментарий будет иметь решение, поэтому этот вопрос может быть отмечен как дубликат.
Выходные данные действительно давали инструкции, но все это сжималось и несколько предчувствовало (что несколько уместно, учитывая близость к Хэллоуину).
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
говорит, что вам нужно знать, какой дистрибутив linux у вас есть, и установить пакет ОС libcurl для него, прежде чем пытаться установить tidyverse.
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
* deb: libxml2-dev (Debian, Ubuntu, etc)
* rpm: libxml2-devel (Fedora, CentOS, RHEL)
* csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
говорит, что вам нужно знать, какой дистрибутив linux у вас есть, и установить пакет ОС libxml2 для него, прежде чем пытаться установить tidyverse.
Пока вы на нем, убедитесь, что у вас установлен пакет ОС openssl.