ResolvePackageNotFound Error for R packages when installing on Linux

thw17 · December 12, 2018, 10:03am

Hi,

I’m trying to install QIIME 2 on my cluster (Linux) using conda. When doing so, I run into a ResolvePackageNotFound error, which lists a large number of R packages (I’ll paste the full error at the end of this message because it is long).

I used the commands:

conda update conda

conda clean --all

wget https://data.qiime2.org/distro/core/qiime2-2018.11-py35-linux-conda.yml

conda env create -n qiime2-2018.11 --file qiime2-2018.11-py35-linux-conda.yml

My current conda version is “4.5.11” and my conda-build version is “3.0.31”. And the platform listed in “conda info” is “linux-64”.

Could you please help point me in the direction of what I might be doing wrong or what might be causing this error?

Thank you very much!

Best,
Tim

Full command and error message:

conda env create -n qiime2-2018.11 --file qiime2-2018.11-py35-linux-conda.yml

Using Anaconda API: https://api.anaconda.org

Solving environment: failed

ResolvePackageNotFound:

r-cli=1.0.0
r-crayon
r-base=3.4.1
_r-mutex=1[build=anacondar_1]
r-cli=1.0.0
r-assertthat
r-mgcv=1.8_24
r-matrix
r-base=3.4.1
_r-mutex=1[build=anacondar_1]
r-mgcv=1.8_24
r-matrix
r-lattice
r-mgcv=1.8_24
r-nlme[version=’>=3.1_64’]
r-rcppparallel=4.4.1
r-base[version=’>=3.4.1,<3.4.2.0a0’]
_r-mutex=1[build=anacondar_1]
r-rcppparallel=4.4.1
r-bh[version=’>=1.60.0_1’]
r=3.3.1
r-nlme=3.1_137
r-lattice
r-base[version=’>=3.4.1,<3.4.2.0a0’]
_r-mutex=1[build=anacondar_1]
r-gtable=0.2.0
r-base[version=’>=3.4.1,<3.4.2.0a0’]
_r-mutex=1[build=anacondar_1]
bioconductor-biobase=2.38.0
r-base=3.4.1
_r-mutex=1[build=anacondar_1]
bioconductor-biobase=2.38.0
bioconductor-biocgenerics[version=’>=0.3.2’]
r=3.3.1
bioconductor-xvector=0.18.0
r-base=3.4.1
_r-mutex=1[build=anacondar_1]
bioconductor-xvector=0.18.0
bioconductor-s4vectors[version=’>=0.15.14’]
bioconductor-biocgenerics[version=’>=0.26.0,<0.28.0’]
bioconductor-xvector=0.18.0
bioconductor-iranges[version=’>=2.9.18’]
bioconductor-xvector=0.18.0
bioconductor-zlibbioc
r=3.3.1
r-lazyeval=0.2.1
r-base[version=’>=3.4.1,<3.4.2.0a0’]
_r-mutex=1[build=anacondar_1]
r-plyr=1.8.4
r-base=3.4.1
_r-mutex=1[build=anacondar_1]
r-plyr=1.8.4
r-rcpp[version=’>=0.11.0’]
r-hwriter=1.3.2
r-base=3.3.2
_r-mutex=1[build=anacondar_1]
r-hwriter=1.3.2
r=3.3.1
bioconductor-biocgenerics=0.24.0
r-base=3.4.1
_r-mutex=1[build=anacondar_1]
r-stringi=1.2.4
r-base[version=’>=3.5.1,<3.5.2.0a0’]
_r-mutex=1[build=anacondar_1]
r-ggplot2=3.1.0
r-withr[version=’>=2.0.0’]
r-base[version=’>=3.5.1,<3.5.2.0a0’]
_r-mutex=1[build=anacondar_1]
r-ggplot2=3.1.0
r-tibble
r-cli
r-crayon
r-ggplot2=3.1.0
r-tibble
r-cli
r-assertthat
r-ggplot2=3.1.0
r-tibble
r-rlang
r-ggplot2=3.1.0
r-tibble
r-pillar[version=’>=1.1.0’]
r-utf8[version=’>=1.1.3’]
r-ggplot2=3.1.0
r-tibble
r-pillar[version=’>=1.1.0’]
r-fansi
r-ggplot2=3.1.0
r-tibble
r-lazyeval[version=’>=0.1.10’]
r-ggplot2=3.1.0
r-tibble
r-rcpp
r-ggplot2=3.1.0
r-mass
r-ggplot2=3.1.0
r-plyr[version=’>=1.7.1’]
r-ggplot2=3.1.0
r-gtable[version=’>=0.1.1’]
r-ggplot2=3.1.0
r-viridislite
r-ggplot2=3.1.0
r-reshape2
r-stringr
r-stringi[version=’>=1.1.6’]
r-ggplot2=3.1.0
r-reshape2
r-stringr
r-magrittr
r=3.3.1
r-ggplot2=3.1.0
r-reshape2
r-stringr
r-glue
r-ggplot2=3.1.0
r-scales[version=’>=0.5.0’]
r-rcolorbrewer
r-ggplot2=3.1.0
r-scales[version=’>=0.5.0’]
r-labeling
r-ggplot2=3.1.0
r-scales[version=’>=0.5.0’]
r-munsell[version=’>=0.2’]
r-colorspace
r-ggplot2=3.1.0
r-scales[version=’>=0.5.0’]
r-r6
r-ggplot2=3.1.0
r-scales[version=’>=0.5.0’]
r-dichromat
r-ggplot2=3.1.0
r-digest
r-ggplot2=3.1.0
r-mgcv
r-matrix
r-lattice
r-ggplot2=3.1.0
r-mgcv
r-nlme[version=’>=3.1_64’]
r-lattice=0.20_35
r-base[version=’>=3.4.1,<3.4.2.0a0’]
_r-mutex=1[build=anacondar_1]
bioconductor-genomeinfodb=1.14.0
bioconductor-s4vectors[version=’>=0.9.25’]
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bioconductor-genomeinfodb=1.14.0
bioconductor-s4vectors[version=’>=0.9.25’]
bioconductor-biocgenerics[version=’>=0.26.0,<0.28.0’]
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bioconductor-s4vectors[version=’>=0.9.25’]
r=3.3.1
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bioconductor-iranges[version=’>=1.99.26’]
bioconductor-genomeinfodb=1.14.0
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r-bitops
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r-base=3.4.1
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r-withr=2.1.2
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r-lambda.r=1.2.3
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bioconductor-genomicranges[version=’>=1.21.6’]
bioconductor-s4vectors[version=’>=0.9.47’]
bioconductor-biocgenerics[version=’>=0.26.0,<0.28.0’]
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bioconductor-genomicranges[version=’>=1.21.6’]
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bioconductor-biocparallel
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bioconductor-shortread=1.36.0
bioconductor-biocparallel
r-bh
bioconductor-shortread=1.36.0
bioconductor-biocparallel
r-futile.logger
r-futile.options
bioconductor-shortread=1.36.0
bioconductor-biocparallel
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bioconductor-shortread=1.36.0
bioconductor-biostrings[version=’>=2.37.1’]
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bioconductor-rsamtools[version=’>=1.21.4’]
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bioconductor-shortread=1.36.0
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bioconductor-shortread=1.36.0
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r-ggplot2[version=’>=2.1.0’]
r-mgcv
r-nlme[version=’>=3.1_64’]
q2-dada2=2018.11.0
bioconductor-dada2==1.6.0=r3.4.1_0
r-rcppparallel[version=’>=4.3.0’]
r-colorspace=1.3_2
r-base=3.3.2
_r-mutex=1[build=anacondar_1]
r-bitops=1.0_6
r-base[version=’>=3.5.1,<3.5.2.0a0’]
_r-mutex=1[build=anacondar_1]

thermokarst · December 13, 2018, 5:53pm

Hi @thw17!

Can you provide the full output from conda info?

This looks a lot like a network or firewall related issue to me. Are you attempting this install behind an institutional firewall?

thw17 · December 14, 2018, 8:13pm

Hi @thermokarst,

Thank you for the response! After some testing, I discovered that it was due to my local settings for default channels for Conda in my .condarc file (I’m a long-time conda user, and I had to manually set them a while ago to overcome some older channel priority issues for R packages as they migrated across various channels). Simply deleting the default channel override in .condarc completely solved my problem and I have successfully installed Qiime2.

Thank you!
Tim