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ImmuneDynamics / Spectre

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
https://immunedynamics.github.io/spectre/
MIT License
57 stars 22 forks source link

cannot install on an ARM mac #181

Closed chintanparekh2301 closed 11 months ago

chintanparekh2301 commented 11 months ago

Hi Tried installing spectre on an M1 mac. The installation fails. Looks like theres an issue with the package "ALL" Here's the output Thanks Installing 49 packages: terra, RcppParallel, wk, units, s2, classInt, estimability, scatterplot3d, multcompView, leaps, flashClust, emmeans, ellipse, SQUAREM, lava, diagram, timechange, prodlim, tzdb, timeDate, lubridate, ipred, hardhat, gower, clock, rhdf5filters, ALL, sf, raster, stringfish, RApiSerialize, graphlayouts, tidygraph, FactoMineR, dendextend, recipes, pROC, ModelMetrics, rhdf5, exactextractr, qs, stars, tiff, ggraph, factoextra, ggpointdensity, caret, ggthemes, HDF5Array trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/terra_1.7-65.tgz' Content type 'application/x-gzip' length 97474072 bytes (93.0 MB)

downloaded 93.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/RcppParallel_5.1.7.tgz' Content type 'application/x-gzip' length 584884 bytes (571 KB)

downloaded 571 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/wk_0.9.1.tgz' Content type 'application/x-gzip' length 1967165 bytes (1.9 MB)

downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/units_0.8-5.tgz' Content type 'application/x-gzip' length 957884 bytes (935 KB)

downloaded 935 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/s2_1.1.5.tgz' Content type 'application/x-gzip' length 11907816 bytes (11.4 MB)

downloaded 11.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/classInt_0.4-10.tgz' Content type 'application/x-gzip' length 500344 bytes (488 KB)

downloaded 488 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/estimability_1.4.1.tgz' Content type 'application/x-gzip' length 40662 bytes (39 KB)

downloaded 39 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/scatterplot3d_0.3-44.tgz' Content type 'application/x-gzip' length 348793 bytes (340 KB)

downloaded 340 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/multcompView_0.1-9.tgz' Content type 'application/x-gzip' length 115755 bytes (113 KB)

downloaded 113 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/leaps_3.1.tgz' Content type 'application/x-gzip' length 102472 bytes (100 KB)

downloaded 100 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/flashClust_1.01-2.tgz' Content type 'application/x-gzip' length 25365 bytes (24 KB)

downloaded 24 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/emmeans_1.9.0.tgz' Content type 'application/x-gzip' length 2157888 bytes (2.1 MB)

downloaded 2.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ellipse_0.5.0.tgz' Content type 'application/x-gzip' length 218284 bytes (213 KB)

downloaded 213 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/SQUAREM_2021.1.tgz' Content type 'application/x-gzip' length 178436 bytes (174 KB)

downloaded 174 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/lava_1.7.3.tgz' Content type 'application/x-gzip' length 2570013 bytes (2.5 MB)

downloaded 2.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/diagram_1.6.5.tgz' Content type 'application/x-gzip' length 677608 bytes (661 KB)

downloaded 661 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/timechange_0.2.0.tgz' Content type 'application/x-gzip' length 884298 bytes (863 KB)

downloaded 863 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/prodlim_2023.08.28.tgz' Content type 'application/x-gzip' length 436616 bytes (426 KB)

downloaded 426 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/tzdb_0.4.0.tgz' Content type 'application/x-gzip' length 1240219 bytes (1.2 MB)

downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/timeDate_4032.109.tgz' Content type 'application/x-gzip' length 1427112 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/lubridate_1.9.3.tgz' Content type 'application/x-gzip' length 987159 bytes (964 KB)

downloaded 964 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ipred_0.9-14.tgz' Content type 'application/x-gzip' length 389018 bytes (379 KB)

downloaded 379 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/hardhat_1.3.0.tgz' Content type 'application/x-gzip' length 832025 bytes (812 KB)

downloaded 812 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/gower_1.0.1.tgz' Content type 'application/x-gzip' length 216565 bytes (211 KB)

downloaded 211 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/clock_0.7.0.tgz' Content type 'application/x-gzip' length 5068374 bytes (4.8 MB)

downloaded 4.8 MB

trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/rhdf5filters_1.10.1.tgz' Content type 'application/x-compressed-tar' length 753584 bytes (735 KB)

downloaded 735 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/sf_1.0-15.tgz' Content type 'application/x-gzip' length 86900092 bytes (82.9 MB)

downloaded 82.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/raster_3.6-26.tgz' Content type 'application/x-gzip' length 4831693 bytes (4.6 MB)

downloaded 4.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/stringfish_0.16.0.tgz' Content type 'application/x-gzip' length 1220476 bytes (1.2 MB)

downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/RApiSerialize_0.1.2.tgz' Content type 'application/x-gzip' length 22831 bytes (22 KB)

downloaded 22 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/graphlayouts_1.0.2.tgz' Content type 'application/x-gzip' length 4500329 bytes (4.3 MB)

downloaded 4.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/tidygraph_1.3.0.tgz' Content type 'application/x-gzip' length 634289 bytes (619 KB)

downloaded 619 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/FactoMineR_2.9.tgz' Content type 'application/x-gzip' length 3806176 bytes (3.6 MB)

downloaded 3.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/dendextend_1.17.1.tgz' Content type 'application/x-gzip' length 3906480 bytes (3.7 MB)

downloaded 3.7 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/recipes_1.0.9.tgz' Content type 'application/x-gzip' length 1599104 bytes (1.5 MB)

downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/pROC_1.18.5.tgz' Content type 'application/x-gzip' length 1127987 bytes (1.1 MB)

downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ModelMetrics_1.2.2.2.tgz' Content type 'application/x-gzip' length 560401 bytes (547 KB)

downloaded 547 KB

trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/rhdf5_2.42.1.tgz' Content type 'application/x-compressed-tar' length 2752800 bytes (2.6 MB)

downloaded 2.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/exactextractr_0.10.0.tgz' Content type 'application/x-gzip' length 2483545 bytes (2.4 MB)

downloaded 2.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/qs_0.25.7.tgz' Content type 'application/x-gzip' length 3798491 bytes (3.6 MB)

downloaded 3.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/stars_0.6-4.tgz' Content type 'application/x-gzip' length 4154657 bytes (4.0 MB)

downloaded 4.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/tiff_0.1-12.tgz' Content type 'application/x-gzip' length 1948558 bytes (1.9 MB)

downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ggraph_2.1.0.tgz' Content type 'application/x-gzip' length 4607099 bytes (4.4 MB)

downloaded 4.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/factoextra_1.0.7.tgz' Content type 'application/x-gzip' length 416918 bytes (407 KB)

downloaded 407 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ggpointdensity_0.1.0.tgz' Content type 'application/x-gzip' length 46128 bytes (45 KB)

downloaded 45 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/caret_6.0-94.tgz' Content type 'application/x-gzip' length 3587237 bytes (3.4 MB)

downloaded 3.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ggthemes_5.0.0.tgz' Content type 'application/x-gzip' length 443755 bytes (433 KB)

downloaded 433 KB

trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/HDF5Array_1.26.0.tgz' Content type 'application/x-compressed-tar' length 9985746 bytes (9.5 MB)

downloaded 9.5 MB

The downloaded binary packages are in /var/folders/1d/nnj_zbrn2_l3zl_yqqhs67t00000gn/T//RtmpwigHh2/downloaded_packages installing the source package ‘ALL’

trying URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALL_1.40.0.tar.gz' Content type 'application/gzip' length 11383132 bytes (10.9 MB)

downloaded 10.9 MB

Error in eval(quote({ : object '..version..' not found Calls: source ... local -> eval.parent -> eval -> eval -> eval -> eval Execution halted

The downloaded source packages are in ‘/private/var/folders/1d/nnj_zbrn2_l3zl_yqqhs67t00000gn/T/RtmpwigHh2/downloaded_packages’ ── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/1d/nnj_zbrn2_l3zl_yqqhs67t00000gn/T/RtmpwigHh2/remotesce2d59c96fec/ImmuneDynamics-Spectre-d0dd8d4/DESCRIPTION’ ... ─ preparing ‘Spectre’: ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘Spectre_1.1.0.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘Spectre/workflows/Spatial - advanced/Spectre advanced spatial/Adv spatial 3 - quantitative analysis.R’

Error in eval(quote({ : object '..version..' not found Calls: source ... local -> eval.parent -> eval -> eval -> eval -> eval Execution halted Warning messages: 1: In i.p(...) : installation of package ‘ALL’ had non-zero exit status 2: In i.p(...) : installation of package ‘/var/folders/1d/nnj_zbrn2_l3zl_yqqhs67t00000gn/T//RtmpwigHh2/filece2d7ee46839/Spectre_1.1.0.tar.gz’ had non-zero exit status

SamGG commented 11 months ago

Hi, Try to install ALL Bioconductor package on its own. If it succeeds, install Spectre.

BiocManager::install("ALL", update = FALSE)

The current release of Bioconductor is 3.18, you are using 3.16. @tomashhurst I don't know if it's a problem. Best. NB: please, click on Preview button before, all these big font characters make your message less clear to me.

tomashhurst commented 11 months ago

Hi @chintanparekh2301, I would try @SamGG 's suggestion and install 'ALL' separately in the first instance and see what happens. We are currently using Bioconductor 3.18 but I think 3.16 was working OK. See what happens after you install ALL separately and we can go from there.

chintanparekh2301 commented 11 months ago

thanks- worked! I updated OS to Sonoma, R to 4.3, bioconductor to 3.18, installed xcode 15, and then it worked

tomashhurst commented 11 months ago

Glad to hear it! Any further issues let us know. Good luck!