No such index during test_4_workflow with v1.0.3 Conda builds

[mfansler]

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

************************************************************
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

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

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

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
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  - 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
  - harfbuzz=9.0.0=h098a298_1
  - icu=75.1=h120a0e1_0
  - isl=0.26=imath32_h2e86a7b_101
  - jq=1.7.1=h10d778d_0
  - krb5=1.21.3=h37d8d59_0
  - ld64_osx-64=951.9=h3c7722d_1
  - lerc=4.0.0=hb486fe8_0
  - libasprintf=0.22.5=hdfe23c8_3
  - libblas=3.9.0=25_osx64_openblas
  - libcblas=3.9.0=25_osx64_openblas
  - libclang-cpp19.1=19.1.3=default_hed3c1ff_0
  - libcurl=8.10.1=h58e7537_0
  - libcxx=19.1.3=hf95d169_0
  - libcxx-devel=19.1.3=h7c275be_0
  - libdeflate=1.22=h00291cd_0
  - libedit=3.1.20191231=h0678c8f_2
  - libev=4.33=h10d778d_2
  - libexpat=2.6.4=h240833e_0
  - libffi=3.4.2=h0d85af4_5
  - libgettextpo=0.22.5=hdfe23c8_3
  - libgfortran=5.0.0=13_2_0_h97931a8_3
  - libgfortran-devel_osx-64=13.2.0=h80d4556_3
  - libgfortran5=13.2.0=h2873a65_3
  - libgit2=1.8.4=hf50decd_0
  - libglib=2.82.2=hb6ef654_0
  - libiconv=1.17=hd75f5a5_2
  - libintl=0.22.5=hdfe23c8_3
  - libjpeg-turbo=3.0.0=h0dc2134_1
  - liblapack=3.9.0=25_osx64_openblas
  - libllvm19=19.1.3=h1e63acb_0
  - libmpdec=4.0.0=hfdf4475_0
  - libnghttp2=1.64.0=hc7306c3_0
  - libopenblas=0.3.28=openmp_hbf64a52_1
  - 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
  - r-bit64=4.5.2=r43h199b6f9_0
  - r-bitops=1.0_9=r43h199b6f9_0
  - r-blob=1.2.4=r43hc72bb7e_2
  - r-brew=1.0_10=r43hc72bb7e_1
  - r-brio=1.1.5=r43h6b9d099_1
  - r-bslib=0.8.0=r43hc72bb7e_0
  - r-cachem=1.1.0=r43h6b9d099_1
  - r-cairo=1.6_2=r43hf0ac09e_2
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  - r-clipr=0.8.0=r43hc72bb7e_3
  - r-clue=0.3_66=r43h79f565e_0
  - r-cluster=2.1.6=r43h9612530_1
  - r-codetools=0.2_20=r43hc72bb7e_1
  - r-colorspace=2.1_1=r43h6b9d099_0
  - r-commonmark=1.9.2=r43h199b6f9_0
  - r-cowplot=1.1.3=r43hc72bb7e_1
  - r-cpp11=0.5.0=r43hc72bb7e_0
  - r-crayon=1.5.3=r43hc72bb7e_1
  - r-credentials=2.0.2=r43hc72bb7e_0
  - r-crosstalk=1.2.1=r43hc72bb7e_1
  - r-curl=5.2.1=r43he8ffcfd_1
  - r-data.table=1.15.4=r43hd524c53_1
  - r-dbi=1.2.3=r43hc72bb7e_1
  - r-deldir=2.0_4=r43h9612530_1
  - r-desc=1.4.3=r43hc72bb7e_1
  - r-devtools=2.4.5=r43hc72bb7e_3
  - r-diffobj=0.3.5=r43h6b9d099_3
  - r-digest=0.6.37=r43h25d921d_0
  - r-doparallel=1.0.17=r43hc72bb7e_3
  - r-dotcall64=1.2=r43h7526d82_0
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  - r-dplyr=1.1.4=r43h25d921d_1
  - r-dqrng=0.3.2=r43h25d921d_1
  - r-dt=0.33=r43hc72bb7e_1
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  - r-evaluate=1.0.1=r43hc72bb7e_0
  - r-fansi=1.0.6=r43h6b9d099_1
  - r-farver=2.1.2=r43h25d921d_1
  - r-fastdummies=1.7.4=r43hc72bb7e_0
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  - r-fitdistrplus=1.2_1=r43hc72bb7e_0
  - r-fnn=1.1.4.1=r43hc83a2cd_0
  - r-fontawesome=0.5.2=r43hc72bb7e_1
  - r-foreach=1.5.2=r43hc72bb7e_3
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  - r-fs=1.6.5=r43hb79fae8_0
  - r-futile.logger=1.4.3=r43hc72bb7e_1006
  - r-futile.options=1.0.1=r43hc72bb7e_1005
  - r-future=1.34.0=r43h785f33e_0
  - r-future.apply=1.11.2=r43hc72bb7e_1
  - r-generics=0.1.3=r43hc72bb7e_3
  - r-gert=2.1.4=r43h8d37685_0
  - r-getoptlong=1.0.5=r43hc72bb7e_3
  - r-ggplot2=3.5.1=r43hc72bb7e_1
  - r-ggrepel=0.9.6=r43hc83a2cd_0
  - r-ggridges=0.5.6=r43hc72bb7e_1
  - r-gh=1.4.1=r43hc72bb7e_1
  - r-gitcreds=0.1.2=r43hc72bb7e_3
  - r-globaloptions=0.1.2=r43ha770c72_3
  - r-globals=0.16.3=r43hc72bb7e_1
  - r-glue=1.8.0=r43h199b6f9_0
  - r-goftest=1.2_3=r43h6b9d099_3
  - r-gplots=3.2.0=r43hc72bb7e_0
  - r-gridextra=2.3=r43hc72bb7e_1006
  - r-gtable=0.3.6=r43hc72bb7e_0
  - r-gtools=3.9.5=r43h6b9d099_1
  - r-harmony=1.2.1=r43haa2a3db_0
  - r-here=1.0.1=r43hc72bb7e_3
  - r-hexbin=1.28.5=r43hb3c2f18_0
  - r-highr=0.11=r43hc72bb7e_1
  - r-hms=1.1.3=r43hc72bb7e_2
  - r-htmltools=0.5.8.1=r43h25d921d_1
  - r-htmlwidgets=1.6.4=r43h785f33e_3
  - r-httpuv=1.6.15=r43h25d921d_1
  - r-httr=1.4.7=r43hc72bb7e_1
  - r-httr2=1.0.6=r43hc72bb7e_0
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  - r-igraph=2.0.3=r43h0b5c70c_1
  - r-ini=0.3.1=r43hc72bb7e_1006
  - r-irlba=2.3.5.1=r43h9cf22e7_3
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  - r-jsonlite=1.8.9=r43h199b6f9_0
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  - r-lambda.r=1.2.4=r43hc72bb7e_4
  - r-later=1.3.2=r43h25d921d_1
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  - r-matrixstats=1.4.1=r43h199b6f9_0
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  - r-mgcv=1.9_1=r43h374a70c_1
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  - r-pbapply=1.7_2=r43hc72bb7e_1
  - r-pillar=1.9.0=r43hc72bb7e_2
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  - r-pkgconfig=2.0.3=r43hc72bb7e_4
  - r-pkgdown=2.1.1=r43hc72bb7e_0
  - r-pkgload=1.4.0=r43hc72bb7e_0
  - r-plogr=0.2.0=r43hc72bb7e_1006
  - r-plotly=4.10.4=r43hc72bb7e_1
  - r-plyr=1.8.9=r43h25d921d_1
  - r-png=0.1_8=r43h9a19d2a_2
  - r-polyclip=1.10_7=r43h25d921d_0
  - r-powerlaw=0.80.0=r43hc72bb7e_1
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  - r-praise=1.0.0=r43hc72bb7e_1008
  - r-presto=1.0.0=r43h4a92bd6_1
  - r-prettyunits=1.2.0=r43hc72bb7e_1
  - r-processx=3.8.4=r43h6b9d099_1
  - r-profvis=0.4.0=r43h199b6f9_0
  - r-progress=1.2.3=r43hc72bb7e_1
  - r-progressr=0.15.0=r43hc72bb7e_0
  - r-promises=1.3.0=r43h25d921d_1
  - r-ps=1.8.1=r43h362b90a_0
  - r-purrr=1.0.2=r43h6b9d099_1
  - r-r.methodss3=1.8.2=r43hc72bb7e_3
  - r-r.oo=1.27.0=r43hc72bb7e_0
  - r-r.utils=2.12.3=r43hc72bb7e_1
  - r-r6=2.5.1=r43hc72bb7e_3
  - r-ragg=1.3.3=r43h3c7d252_0
  - r-rann=2.6.2=r43hc83a2cd_0
  - r-rappdirs=0.3.3=r43h6b9d099_3
  - r-rcmdcheck=1.4.0=r43h785f33e_3
  - r-rcolorbrewer=1.1_3=r43h785f33e_3
  - r-rcpp=1.0.13_1=r43h2711daa_0
  - r-rcppannoy=0.0.22=r43h25d921d_1
  - r-rcpparmadillo=14.0.2_1=r43h1e4f42f_0
  - r-rcppeigen=0.3.4.0.2=r43haa2a3db_0
  - r-rcpphnsw=0.6.0=r43h25d921d_1
  - r-rcppprogress=0.4.2=r43hc72bb7e_4
  - r-rcpptoml=0.2.2=r43h25d921d_2
  - r-rcurl=1.98_1.16=r43h761bb74_1
  - r-readr=2.1.5=r43h25d921d_1
  - r-rematch2=2.1.2=r43hc72bb7e_4
  - r-remotes=2.5.0=r43hc72bb7e_1
  - r-reshape2=1.4.4=r43h25d921d_4
  - r-restfulr=0.0.15=r43hfa19939_4
  - r-reticulate=1.40.0=r43h2711daa_0
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prefix: /Users/mfansler/miniforge3/envs/foo

Related Issues

#2130
#2168
#2210

[rcorces]

Hi @mfansler! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

[mfansler]

I am able to pass the tests by requiring ggplot2 <3.5. In the short-term, I would recommend that this package specify that as an upper bound.

Otherwise, for a more thorough fix, the violating code is here:

ArchR/R/VisualizeData.R

Line 888 in 65968a4

gl <- g$grobs[[legend]]

And for reference, here is the bisection in ggplot2 v3.4.4...v3.5.0.

[immanuelazn]

Should be fixed!