remotes:install_github error

[ghost]

Installing the package does not work. I have had multiple different issues now:

ERROR: lazy loading failed for package ‘Biostrings’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings’
Error: Failed to install 'gwasglue' from GitHub:
  Failed to install 'gwasvcf' from GitHub:
  Failed to install 'Biostrings' from Bioc:
  (converted from warning) installation of package ‘/var/folders/15/564m2q6n7bvdtl7jn8clyxzr0000gn/T//RtmpN2F7eX/file1189c736aeb34/Biostrings_2.56.0.tar.gz’ had non-zero exit status

#10 680.8 ** byte-compile and prepare package for lazy loading
#10 683.5 Error: package or namespace load failed for ‘IRanges’:
#10 683.5  (converted from warning) multiple methods tables found for ‘mstack’
#10 683.5 Error: package ‘IRanges’ could not be loaded
#10 683.5 Execution halted
#10 683.5 ERROR: lazy loading failed for package ‘DelayedArray’
#10 683.5 * removing ‘/usr/local/lib/R/site-library/DelayedArray’
#10 683.9 Error: Failed to install 'gwasglue' from GitHub:
#10 683.9   Failed to install 'gwasvcf' from GitHub:
#10 683.9   Failed to install 'SummarizedExperiment' from Bioc:
#10 683.9   (converted from warning) installation of package ‘DelayedArray’ had non-zero exit status
#10 683.9 Execution halted
#10 ERROR: executor failed running [/bin/sh -c Rscript -e 'devtools::install_github(c("mrcieu/TwoSampleMR", "mrcieu/gwasglue"))']: runc did not terminate sucessfully

[song-ying-chao]

i have the similar problem，have you successfully install gwasglue?

[remlapmot]

Could you tell us which operating system and which version of R you are using?

[remlapmot]

(trying again, actually installing the correct package) It is working on Ubuntu Linux with R 4.2.2. (You will see different output depending upon which dependency packages are not installed on your system.)

remotes::install_github('MRCIEU/gwasglue')
#> Downloading GitHub repo MRCIEU/gwasglue@HEAD
#> MRPRESSO    (1.0     -> cece763b4...) [GitHub]
#> ieugwasr    (0.1.5   -> 33e4629f4...) [GitHub]
#> TwoSampleMR (0.5.6   -> f5935b55d...) [GitHub]
#> RadialMR    (1.0     -> d63d3fc82...) [GitHub]
#> MRMix       (0.1.0   -> 56afdb2bc...) [GitHub]
#> susieR      (0.12.35 -> da24d5fba...) [GitHub]
#> Downloading GitHub repo rondolab/MR-PRESSO@HEAD
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpQxHG2s/remotes23b665749baa/rondolab-MR-PRESSO-cece763/DESCRIPTION’ ... OK
#> * preparing ‘MRPRESSO’:
#> * checking DESCRIPTION meta-information ... OK
#> * installing the package to process help pages
#> * saving partial Rd database
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * looking to see if a ‘data/datalist’ file should be added
#> * building ‘MRPRESSO_1.0.tar.gz’
#> Installing package into '/home/tom/R/x86_64-pc-linux-gnu-library/4.2'
#> (as 'lib' is unspecified)
#> Downloading GitHub repo mrcieu/ieugwasr@HEAD
#> 
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpQxHG2s/remotes23b638a2d8ed/MRCIEU-ieugwasr-33e4629/DESCRIPTION’ ... OK
#> * preparing ‘ieugwasr’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘ieugwasr_0.1.5.tar.gz’
#> Installing package into '/home/tom/R/x86_64-pc-linux-gnu-library/4.2'
#> (as 'lib' is unspecified)
#> Downloading GitHub repo mrcieu/TwoSampleMR@HEAD
#> MRMix    (0.1.0 -> 56afdb2bc...) [GitHub]
#> RadialMR (1.0   -> d63d3fc82...) [GitHub]
#> Downloading GitHub repo gqi/MRMix@HEAD
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpQxHG2s/remotes23b648862c76/gqi-MRMix-56afdb2/DESCRIPTION’ ... OK
#> * preparing ‘MRMix’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘MRMix_0.1.0.tar.gz’
#> Installing package into '/home/tom/R/x86_64-pc-linux-gnu-library/4.2'
#> (as 'lib' is unspecified)
#> Downloading GitHub repo WSpiller/RadialMR@HEAD
#> 
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpQxHG2s/remotes23b653aeede/WSpiller-RadialMR-d63d3fc/DESCRIPTION’ ... OK
#> * preparing ‘RadialMR’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘RadialMR_1.0.tar.gz’
#> Installing package into '/home/tom/R/x86_64-pc-linux-gnu-library/4.2'
#> (as 'lib' is unspecified)
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpQxHG2s/remotes23b628485bb1/MRCIEU-TwoSampleMR-f5935b5/DESCRIPTION’ ... OK
#> * preparing ‘TwoSampleMR’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘TwoSampleMR_0.5.6.tar.gz’
#> Installing package into '/home/tom/R/x86_64-pc-linux-gnu-library/4.2'
#> (as 'lib' is unspecified)
#> Skipping install of 'RadialMR' from a github remote, the SHA1 (d63d3fc8) has not changed since last install.
#>   Use `force = TRUE` to force installation
#> Skipping install of 'MRMix' from a github remote, the SHA1 (56afdb2b) has not changed since last install.
#>   Use `force = TRUE` to force installation
#> Downloading GitHub repo stephenslab/susieR@HEAD
#> 
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpQxHG2s/remotes23b65be62509/stephenslab-susieR-da24d5f/DESCRIPTION’ ... OK
#> * preparing ‘susieR’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘susieR_0.12.35.tar.gz’
#> Installing package into '/home/tom/R/x86_64-pc-linux-gnu-library/4.2'
#> (as 'lib' is unspecified)
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpQxHG2s/remotes23b626a652a8/MRCIEU-gwasglue-c2d5660/DESCRIPTION’ ... OK
#> * preparing ‘gwasglue’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> Omitted ‘LazyData’ from DESCRIPTION
#> * building ‘gwasglue_0.0.0.9000.tar.gz’
#> Installing package into '/home/tom/R/x86_64-pc-linux-gnu-library/4.2'
#> (as 'lib' is unspecified)

^{Created on 2023-03-08 with reprex v2.0.2}