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JEFworks-Lab / HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
http://jef.works/HoneyBADGER/
GNU General Public License v3.0
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Error: Failed to install 'HoneyBADGER' from GitHub #40

Closed yaskermezli closed 3 years ago

yaskermezli commented 3 years ago

Hi, I'm trying to install HoneyBADGER on my local machine (R4.0.2) and on cluster (R version 3.6.1 ) I had two kind of error, Firts on cluster (R version 3.6.1 ): sh: 1: /bin/gtar: not found sh: 1: /bin/gtar: not found Error: Failed to install 'HoneyBADGER' from GitHub: error in running command In addition: Warning messages: 1: In system(cmd) : error in running command 2: In utils::untar(tarfile, ...) : '/bin/gtar -xf '/tmp/RtmptXe1qc/file6039500f3705.tar.gz' -C '/tmp/RtmptXe1qc/remotes603946cf00e2'' returned error code 127 and the second (my local machine R4.0.2)

Downloading GitHub repo JEFworks/HoneyBADGER@HEAD Skipping 4 packages not available: TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationDbi, GenomicFeatures, GenomicRanges Installing 4 packages: coda, TxDb.Hsapiens.UCSC.hg19.knownGene, HiddenMarkov, rjags Installing packages into ‘/home/kermezly/R/x86_64-pc-linux-gnu-library/4.0’ (as ‘lib’ is unspecified) Erreur : Failed to install 'HoneyBADGER' from GitHub: (converti depuis l'avis) package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ is not available (for R version 4.0.2)

Any solution on your side ?

Thank you.

JEFworks commented 3 years ago

Dear Yasmina,

Thanks for trying out HoneyBADGER. It looks like the installation may have failed to install because these 4 other packages could not be installed:

TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationDbi, GenomicFeatures, GenomicRanges

These packages are available on Bioconductor and can be installed using BiocManager: https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html

Can you please install these 4 other packages manually and try again? Please let me know if that works.

Stay healthy and safe, Jean

Jean Fan, PhD Assistant Professor in Biomedical Engineering Center for Computational Biology Johns Hopkins University web: jef.workshttps://jef.works

On Oct 23, 2020, at 10:32 AM, Yasmina Kermezli notifications@github.com<mailto:notifications@github.com> wrote:

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Hi, I'm trying to install HoneyBADGER on my local machine (R4.0.2) and on cluster (R version 3.6.1 ) I had two kind of error, Firts on cluster (R version 3.6.1 ): sh: 1: /bin/gtar: not found sh: 1: /bin/gtar: not found Error: Failed to install 'HoneyBADGER' from GitHub: error in running command In addition: Warning messages: 1: In system(cmd) : error in running command 2: In utils::untar(tarfile, ...) : '/bin/gtar -xf '/tmp/RtmptXe1qc/file6039500f3705.tar.gz' -C '/tmp/RtmptXe1qc/remotes603946cf00e2'' returned error code 127 and the second (my local machine R4.0.2)

Downloading GitHub repo JEFworks/HoneyBADGER@HEAD Skipping 4 packages not available: TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationDbi, GenomicFeatures, GenomicRanges Installing 4 packages: coda, TxDb.Hsapiens.UCSC.hg19.knownGene, HiddenMarkov, rjags Installing packages into ‘/home/kermezly/R/x86_64-pc-linux-gnu-library/4.0’ (as ‘lib’ is unspecified) Erreur : Failed to install 'HoneyBADGER' from GitHub: (converti depuis l'avis) package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ is not available (for R version 4.0.2)

Any solution on your side ?

Thank you.

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yaskermezli commented 3 years ago

Hi JEF,

Thank you for your reply. it works on local after downloading dependencies... I will retry on the cluster.

Closing now.

Best.