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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Installation Failed #73

Open diyang1354 opened 5 years ago

diyang1354 commented 5 years ago

I tried to install it with the command: devtools::install_github('dviraran/SingleR') but library(SingleR) returns there is no such library, how to fix it? thx!

diyang1354 commented 5 years ago

devtools::install_github('dviraran/SingleR') Downloading GitHub repo dviraran/SingleR@master These packages have more recent versions available. Which would you like to update?

1: All 2: CRAN packages only 3: None 4: formatR (1.6 -> 1.7 ) [CRAN] 5: mime (0.6 -> 0.7 ) [CRAN] 6: openssl (1.3 -> 1.4 ) [CRAN] 7: pillar (1.4.0 -> 1.4.1 ) [CRAN] 8: tibble (2.1.1 -> 2.1.3 ) [CRAN] 9: XML (3.98-1.19 -> 3.98-1.20) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel 1: 1 digest (NA -> 0.6.19 ) [CRAN] doFuture (NA -> 0.8.0 ) [CRAN] doParallel (NA -> 1.0.14 ) [CRAN] edgeR (NA -> 3.24.3 ) [CRAN] foreach (NA -> 1.4.4 ) [CRAN] formatR (1.6 -> 1.7 ) [CRAN] future (NA -> 1.13.0 ) [CRAN] ggsci (NA -> 2.9 ) [CRAN] globals (NA -> 0.12.4 ) [CRAN] graph (NA -> 1.60.0 ) [CRAN] GSEABase (NA -> 1.44.0 ) [CRAN] GSVA (NA -> 1.30.0 ) [CRAN] hexbin (NA -> 1.27.3 ) [CRAN] iterators (NA -> 1.0.10 ) [CRAN] listenv (NA -> 0.7.0 ) [CRAN] mime (0.6 -> 0.7 ) [CRAN] openssl (1.3 -> 1.4 ) [CRAN] outliers (NA -> 0.14 ) [CRAN] pbmcapply (NA -> 1.4.1 ) [CRAN] pillar (1.4.0 -> 1.4.1 ) [CRAN] plotly (NA -> 4.9.0 ) [CRAN] reshape (NA -> 0.8.8 ) [CRAN] shinythemes (NA -> 1.1.2 ) [CRAN] singscore (NA -> 1.2.2 ) [CRAN] tibble (2.1.1 -> 2.1.3 ) [CRAN] XML (3.98-1.19 -> 3.98-1.20) [CRAN] Skipping 16 packages ahead of CRAN: annotate, AnnotationDbi, Biobase, BiocGenerics, BiocParallel, DelayedArray, geneplotter, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, IRanges, limma, S4Vectors, SummarizedExperiment, XVector, zlibbioc Installing 26 packages: digest, doFuture, doParallel, edgeR, foreach, formatR, future, ggsci, globals, graph, GSEABase, GSVA, hexbin, iterators, listenv, mime, openssl, outliers, pbmcapply, pillar, plotly, reshape, shinythemes, singscore, tibble, XML Installing packages into 'C:/Users/admin/Documents/R/win-library/3.6' (as 'lib' is unspecified)

There are binary versions available but the source versions are later: binary source needs_compilation formatR 1.6 1.7 FALSE mime 0.6 0.7 TRUE

Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/digest_0.6.19.zip' Content type 'application/zip' length 211459 bytes (206 KB) downloaded 206 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/doFuture_0.8.0.zip' Content type 'application/zip' length 76213 bytes (74 KB) downloaded 74 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/doParallel_1.0.14.zip' Content type 'application/zip' length 199961 bytes (195 KB) downloaded 195 KB

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.6/edgeR_3.24.3.zip' Content type 'application/zip' length 2941920 bytes (2.8 MB) downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/foreach_1.4.4.zip' Content type 'application/zip' length 420026 bytes (410 KB) downloaded 410 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/future_1.13.0.zip' Content type 'application/zip' length 622426 bytes (607 KB) downloaded 607 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/ggsci_2.9.zip' Content type 'application/zip' length 2978482 bytes (2.8 MB) downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/globals_0.12.4.zip' Content type 'application/zip' length 76178 bytes (74 KB) downloaded 74 KB

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.6/graph_1.60.0.zip' Content type 'application/zip' length 1758466 bytes (1.7 MB) downloaded 1.7 MB

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.6/GSEABase_1.44.0.zip' Content type 'application/zip' length 1025649 bytes (1001 KB) downloaded 1001 KB

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.6/GSVA_1.30.0.zip' Content type 'application/zip' length 1331766 bytes (1.3 MB) downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/hexbin_1.27.3.zip' Content type 'application/zip' length 935967 bytes (914 KB) downloaded 914 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/iterators_1.0.10.zip' Content type 'application/zip' length 341790 bytes (333 KB) downloaded 333 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/listenv_0.7.0.zip' Content type 'application/zip' length 102718 bytes (100 KB) downloaded 100 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/mime_0.6.zip' Content type 'application/zip' length 48137 bytes (47 KB) downloaded 47 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/openssl_1.4.zip' Content type 'application/zip' length 3967162 bytes (3.8 MB) downloaded 3.8 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/outliers_0.14.zip' Content type 'application/zip' length 84962 bytes (82 KB) downloaded 82 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/pbmcapply_1.4.1.zip' Content type 'application/zip' length 53474 bytes (52 KB) downloaded 52 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/pillar_1.4.1.zip' Content type 'application/zip' length 182615 bytes (178 KB) downloaded 178 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/plotly_4.9.0.zip' Content type 'application/zip' length 2848898 bytes (2.7 MB) downloaded 2.7 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/reshape_0.8.8.zip' Content type 'application/zip' length 171050 bytes (167 KB) downloaded 167 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/shinythemes_1.1.2.zip' Content type 'application/zip' length 990275 bytes (967 KB) downloaded 967 KB

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.6/singscore_1.2.2.zip' Content type 'application/zip' length 2579469 bytes (2.5 MB) downloaded 2.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tibble_2.1.3.zip' Content type 'application/zip' length 337326 bytes (329 KB) downloaded 329 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/XML_3.98-1.20.zip' Content type 'application/zip' length 4610084 bytes (4.4 MB) downloaded 4.4 MB

package 'digest' successfully unpacked and MD5 sums checked Error: (converted from warning) cannot remove prior installation of package 'digest'

dviraran commented 5 years ago

Hi,

I don't know which of SingleR dependencies is uses digest, but you should try to figure out why installing digest fails. Not really a SingleR issue.

Best, Dvir

diyang1354 commented 5 years ago

Hi Dvir, Thank you, but I've tried again and returned a failure again as the following:

Downloading GitHub repo dviraran/SingleR@master dviraran-SingleR-4bb890a/vignettes/SingleR_specifications.pdf: truncated gzip input tar.exe: Error exit delayed from previous errors. Error: Does not appear to be an R package (no DESCRIPTION) In addition: Warning messages: 1: In utils::untar(tarfile, ...) : 'tar.exe -xf "C:\Users\admin\AppData\Local\Temp\RtmpCS6ezc\file33dc56bf601f.tar.gz" -C "C:/Users/admin/AppData/Local/Temp/RtmpCS6ezc/remotes33dc67b9225c"' returned error code 1 2: In system(cmd, intern = TRUE) : running command 'tar.exe -tf "C:\Users\admin\AppData\Local\Temp\RtmpCS6ezc\file33dc56bf601f.tar.gz"' had status 1

dviraran commented 5 years ago

I really don't know why this is happening to you. I just installed SingleR and it worked smoothly.

diyang1354 commented 5 years ago

fixed! It seems to be the internet issue.