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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
56 stars 21 forks source link

cannot install on an ARM mac #181

Closed chintanparekh2301 closed 8 months ago

chintanparekh2301 commented 8 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 8 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 8 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 8 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 8 months ago

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