No such index during `test_4_workflow` with v1.0.3 Conda builds

Description

Running the test_4_workflow.R testthat test fails on both Linux and OSX during the addIterativeLSI call with the error:

<simpleError in g$grobs[[legend]]: no such index at level 2>

Logs

Testthat testing

On Bioconda, one can view the build and test logs in the CI.

Local testing

ArchR log ArchR-addIterativeLSI-162231e937ce-Date-2024-11-16_Time-11-32-05.668778.log

Relevant Section

```r ************************************************************ 2024-11-16 11:32:10.007772 : ERROR Found in .saveIteration for LogFile = ArchRLogs/ArchR-addIterativeLSI-162231e937ce-Date-2024-11-16_Time-11-32-05.668778.log 2024-11-16 11:32:10.008531 : errorList, Class = list errorList$: length = 1 1 function (name) 2 .Internal(args(name)) errorList$matSVD: nRows = 127, nCols = 5 LSI1 LSI2 LSI3 LSI4 LSI5 PBSmall#B.43 61.20232 -7.339108 1.498346 -0.4849603 3.282681 PBSmall#T.24 61.31319 -10.017733 -9.136004 -6.1153782 1.629309 PBSmall#T.6 59.15276 -15.960483 -7.146590 16.2898198 -21.101676 PBSmall#T.38 59.31868 -13.347877 -13.008407 -7.0132095 -18.478613 PBSmall#T.18 56.53750 -11.750483 -9.249800 -14.1898937 -2.631180 errorList$clusters: length = 127 [1] "C4" "C4" "C3" "C5" "C4" "C3" errorList$nPlot: length = 1 [1] 10000 errorList$ArchRProj: length = 1 errorList$scaleDims: length = 1 [1] TRUE errorList$corCutOff: length = 1 [1] 0.75 errorList$dimsToUse: length = 5 [1] 1 2 3 4 5 errorList$j: length = 1 [1] 1 errorList$threads: length = 1 [1] 8 errorList$outDir: length = 1 [1] "/Users/mfansler/scratch/r-archr/Test/IterativeLSI" errorList$logFile: length = 1 [1] "ArchRLogs/ArchR-addIterativeLSI-162231e937ce-Date-2024-11-16_Time-11-32-05.668778.log" ************************************************************ ```

Reproduction

Local environment is on osx-64 using artifact from Bioconda builds. Note the artifact must be downloaded and installed from local filesystem. Additional requirements added were r-cairo and macs2.

Run the code found in test_4_workflow.R.

env.yaml

```yaml name: foo channels: - file:///Users/mfansler/Downloads/packages - conda-forge - bioconda dependencies: - _r-mutex=1.0.1=anacondar_1 - argcomplete=3.5.1=pyhd8ed1ab_0 - bioconductor-annotate=1.80.0=r43hdfd78af_0 - bioconductor-annotationdbi=1.64.1=r43hdfd78af_0 - bioconductor-biobase=2.62.0=r43h4c50009_2 - bioconductor-biocgenerics=0.48.1=r43hdfd78af_2 - bioconductor-biocio=1.12.0=r43hdfd78af_0 - bioconductor-biocparallel=1.36.0=r43hc0ef7c4_2 - bioconductor-biostrings=2.70.1=r43h4c50009_2 - bioconductor-bsgenome=1.70.1=r43hdfd78af_0 - bioconductor-bsgenome.hsapiens.ucsc.hg19=1.4.3=r43hdfd78af_8 - bioconductor-chromvar=1.24.0=r43hc0ef7c4_0 - bioconductor-cner=1.38.0=r43h4c50009_1 - bioconductor-complexheatmap=2.18.0=r43hdfd78af_0 - bioconductor-data-packages=20231203=hdfd78af_0 - bioconductor-delayedarray=0.28.0=r43h4c50009_2 - bioconductor-dirichletmultinomial=1.44.0=r43hd4be0b2_1 - bioconductor-genomeinfodb=1.38.1=r43hdfd78af_1 - bioconductor-genomeinfodbdata=1.2.11=r43hdfd78af_1 - bioconductor-genomicalignments=1.38.0=r43h4c50009_1 - bioconductor-genomicranges=1.54.1=r43h4c50009_2 - bioconductor-go.db=3.18.0=r43hdfd78af_0 - bioconductor-iranges=2.36.0=r43h4c50009_2 - bioconductor-keggrest=1.42.0=r43hdfd78af_0 - bioconductor-matrixgenerics=1.14.0=r43hdfd78af_3 - bioconductor-motifmatchr=1.24.0=r43hc0ef7c4_1 - bioconductor-rhdf5=2.46.1=r43hc0ef7c4_1 - bioconductor-rhdf5filters=1.14.1=r43hc0ef7c4_1 - bioconductor-rhdf5lib=1.24.0=r43h4c50009_2 - bioconductor-rhtslib=2.4.0=r43h4c50009_2 - bioconductor-rsamtools=2.18.0=r43hc0ef7c4_2 - bioconductor-rtracklayer=1.62.0=r43h4c50009_1 - bioconductor-s4arrays=1.2.0=r43h4c50009_2 - bioconductor-s4vectors=0.40.2=r43h4c50009_2 - bioconductor-seqlogo=1.68.0=r43hdfd78af_0 - bioconductor-sparsearray=1.2.2=r43h4c50009_2 - bioconductor-sparsematrixstats=1.14.0=r43hc0ef7c4_1 - bioconductor-summarizedexperiment=1.32.0=r43hdfd78af_0 - bioconductor-tfbstools=1.40.0=r43h4c50009_1 - bioconductor-xvector=0.42.0=r43h4c50009_2 - bioconductor-zlibbioc=1.48.0=r43h4c50009_2 - bwidget=1.9.14=h694c41f_1 - bzip2=1.0.8=hfdf4475_7 - c-ares=1.34.3=hf13058a_0 - ca-certificates=2024.8.30=h8857fd0_0 - cairo=1.18.0=h37bd5c4_3 - cctools_osx-64=1010.6=hd0ff2cf_1 - clang=19.1.3=default_h4bb2e93_0 - clang-19=19.1.3=default_hed3c1ff_0 - clang_impl_osx-64=19.1.3=h1fa0277_21 - clang_osx-64=19.1.3=hb91bd55_21 - clangxx=19.1.3=default_h4bb2e93_0 - clangxx_impl_osx-64=19.1.3=h5b10c28_21 - clangxx_osx-64=19.1.3=hb91bd55_21 - compiler-rt=19.1.3=hf2491d2_0 - compiler-rt_osx-64=19.1.3=h9518668_0 - curl=8.10.1=h58e7537_0 - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 - font-ttf-inconsolata=3.000=h77eed37_0 - font-ttf-source-code-pro=2.038=h77eed37_0 - font-ttf-ubuntu=0.83=h77eed37_3 - fontconfig=2.15.0=h37eeddb_1 - fonts-conda-ecosystem=1=0 - fonts-conda-forge=1=0 - freetype=2.12.1=h60636b9_2 - fribidi=1.0.10=hbcb3906_0 - gfortran_impl_osx-64=13.2.0=h2bc304d_3 - gfortran_osx-64=13.2.0=h18f7dce_1 - glpk=5.0=h3cb5acd_0 - gmp=6.3.0=hf036a51_2 - graphite2=1.3.13=h73e2aa4_1003 - gsl=2.7=h93259b0_0 - 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libpng=1.6.44=h4b8f8c9_0 - libsqlite=3.47.0=h2f8c449_1 - libssh2=1.11.0=hd019ec5_0 - libtiff=4.7.0=h583c2ba_1 - libuv=1.49.2=hd79239c_0 - libwebp-base=1.4.0=h10d778d_0 - libxml2=2.13.5=h495214b_0 - libzlib=1.3.1=hd23fc13_2 - llvm-openmp=19.1.3=hf78d878_0 - llvm-tools=19.1.3=h062cec2_0 - llvm-tools-19=19.1.3=h65ece69_0 - macs2=2.2.9.1=py311hb338bc1_1 - make=4.4.1=h00291cd_2 - mpc=1.3.1=h9d8efa1_1 - mpfr=4.2.1=haed47dc_3 - ncurses=6.5=hf036a51_1 - numpy=1.26.4=py311hc43a94b_0 - oniguruma=6.9.9=h10d778d_0 - openssl=3.4.0=hd471939_0 - pandoc=3.5=h694c41f_0 - pango=1.54.0=h115fe74_2 - pcre2=10.44=h7634a1b_2 - pip=24.3.1=pyh8b19718_0 - pixman=0.43.4=h73e2aa4_0 - python=3.11.10=ha513fb2_3_cpython - python_abi=3.11=5_cp311 - pyyaml=6.0.2=py311h3336109_1 - r-abind=1.4_5=r43hc72bb7e_1006 - r-archr=1.0.3=r43h4a92bd6_0 - r-askpass=1.2.1=r43h199b6f9_0 - r-assertthat=0.2.1=r43hc72bb7e_5 - r-base=4.3.3=hc011bdf_15 - r-base64enc=0.1_3=r43h6b9d099_1007 - r-bh=1.84.0_0=r43hc72bb7e_1 - r-bit=4.5.0=r43h199b6f9_0 - 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r-restfulr=0.0.15=r43hfa19939_4 - r-reticulate=1.40.0=r43h2711daa_0 - r-rhpcblasctl=0.23_42=r43hc5191ce_2 - r-rjson=0.2.23=r43hc83a2cd_0 - r-rlang=1.1.4=r43h25d921d_1 - r-rmarkdown=2.29=r43hc72bb7e_0 - r-rocr=1.0_11=r43hbe3e9c8_4 - r-roxygen2=7.3.2=r43h25d921d_1 - r-rprojroot=2.0.4=r43hc72bb7e_1 - r-rspectra=0.16_2=r43hec4e08c_0 - r-rsqlite=2.3.7=r43hb79fae8_1 - r-rstudioapi=0.17.1=r43hc72bb7e_0 - r-rtsne=0.17=r43h3eeea24_1 - r-rversions=2.1.2=r43hc72bb7e_3 - r-sass=0.4.9=r43h25d921d_1 - r-scales=1.3.0=r43hc72bb7e_1 - r-scattermore=1.2=r43h25d921d_3 - r-sctransform=0.4.1=r43hec4e08c_1 - r-sessioninfo=1.2.2=r43hc72bb7e_3 - r-seurat=5.1.0=r43h25d921d_1 - r-seuratobject=5.0.2=r43h25d921d_1 - r-shape=1.4.6.1=r43ha770c72_1 - r-shiny=1.9.1=r43h785f33e_0 - r-sitmo=2.0.2=r43hccab667_3 - r-snow=0.4_4=r43hc72bb7e_3 - r-sourcetools=0.1.7_1=r43h25d921d_2 - r-sp=2.1_4=r43h6b9d099_1 - r-spam=2.11_0=r43hb891a21_0 - r-spatstat.data=3.1_4=r43hc72bb7e_0 - r-spatstat.explore=3.2_6=r43h6b9d099_1 - r-spatstat.geom=3.2_9=r43h6b9d099_1 - r-spatstat.random=3.2_3=r43h25d921d_1 - r-spatstat.sparse=3.1_0=r43h6b9d099_1 - r-spatstat.utils=3.1_1=r43h79f565e_0 - r-stringi=1.8.4=r43hf60abff_3 - r-stringr=1.5.1=r43h785f33e_1 - r-survival=3.7_0=r43h6b9d099_1 - r-sys=3.4.3=r43h199b6f9_0 - r-systemfonts=1.1.0=r43h24f689b_1 - r-tensor=1.5=r43hc72bb7e_1006 - r-testthat=3.2.1.1=r43h25d921d_1 - r-textshaping=0.4.0=r43hcf60599_2 - r-tfmpvalue=0.0.9=r43h25d921d_2 - r-tibble=3.2.1=r43h6b9d099_3 - r-tidyr=1.3.1=r43h25d921d_1 - r-tidyselect=1.2.1=r43hc72bb7e_1 - r-tinytex=0.54=r43hc72bb7e_0 - r-tzdb=0.4.0=r43h25d921d_2 - r-urlchecker=1.0.1=r43hc72bb7e_3 - r-usethis=3.0.0=r43hc72bb7e_0 - r-utf8=1.2.4=r43h6b9d099_1 - r-uwot=0.1.16=r43h25d921d_1 - r-vctrs=0.6.5=r43h25d921d_1 - r-viridislite=0.4.2=r43hc72bb7e_2 - r-vroom=1.6.5=r43h25d921d_1 - r-waldo=0.6.1=r43hc72bb7e_0 - r-whisker=0.4.1=r43hc72bb7e_2 - r-withr=3.0.2=r43hc72bb7e_0 - r-xfun=0.48=r43hc83a2cd_0 - r-xml=3.99_0.17=r43h695470d_1 - r-xml2=1.3.6=r43h0ea9301_2 - r-xopen=1.0.1=r43hc72bb7e_1 - r-xtable=1.8_4=r43hc72bb7e_6 - r-yaml=2.3.10=r43h6b9d099_0 - r-zip=2.3.1=r43h6b9d099_1 - r-zoo=1.8_12=r43h6b9d099_2 - readline=8.2=h9e318b2_1 - setuptools=75.5.0=pyhff2d567_0 - sigtool=0.1.3=h88f4db0_0 - tapi=1300.6.5=h390ca13_0 - tk=8.6.13=h1abcd95_1 - tktable=2.10=hba9d6f1_6 - toml=0.10.2=pyhd8ed1ab_0 - tomlkit=0.13.2=pyha770c72_0 - tzdata=2024b=hc8b5060_0 - wheel=0.45.0=pyhd8ed1ab_0 - xmltodict=0.14.2=pyhd8ed1ab_0 - xz=5.2.6=h775f41a_0 - yaml=0.2.5=h0d85af4_2 - yq=3.4.3=pyhd8ed1ab_0 - zlib=1.3.1=hd23fc13_2 - zstd=1.5.6=h915ae27_0 prefix: /Users/mfansler/miniforge3/envs/foo ```

GreenleafLab / ArchR