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VallejosGroup / BASiCSWorkflow

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Build issue on Mac #40

Closed nilseling closed 2 years ago

nilseling commented 3 years ago

Hi @Alanocallaghan

thanks so much for setting this up - really great stuff!

I get the following issue when running it on my mac using sudo make. I also get the same issue when running it in Rstudio within the container.

nils@DQBM-NBM-NIEL BASiCSWorkflow % make     
docker run -v /Users/nils/Github/BASiCSWorkflow:/home/rstudio/mycode \
        -w /home/rstudio/mycode \
        alanocallaghan/bocker:0.1.0 \
        /bin/bash \
        -c 'Rscript -e "rmarkdown::render(\"Workflow.Rmd\")"'
Unable to find image 'alanocallaghan/bocker:0.1.0' locally
0.1.0: Pulling from alanocallaghan/bocker
Digest: sha256:b99e0218ff2f52d01182f6dd1e51aa841cc3fe550e7b18850b7f626d5e545e06
Status: Downloaded newer image for alanocallaghan/bocker:0.1.0
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.12' is out-of-date; the current release version '3.13'
  is available with R version '4.1'; see https://bioconductor.org/install

processing file: Workflow.Rmd
  |.                                                                     |   1%
  ordinary text without R code

  |..                                                                    |   2%
label: setup_knitr (with options) 
List of 2
 $ include: logi FALSE
 $ cache  : logi FALSE

  |..                                                                    |   3%
   inline R code fragments

  |...                                                                   |   4%
label: overview (with options) 
List of 4
 $ out.width : symbol out_width
 $ out.height: symbol out_height
 $ fig.cap   : chr "Graphical overview for the scRNA-seq analysis workflow described in this manuscript. Starting from a matrix of "| __truncated__
 $ echo      : logi FALSE

  |....                                                                  |   5%
  ordinary text without R code

  |.....                                                                 |   7%
label: unnamed-chunk-1
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

  |.....                                                                 |   8%
   inline R code fragments

  |......                                                                |   9%
label: unnamed-chunk-2
  |.......                                                               |  10%
   inline R code fragments

  |........                                                              |  11%
label: unnamed-chunk-3
    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
  |........                                                              |  12%
   inline R code fragments

  |.........                                                             |  13%
label: naive-data
trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4888/E-MTAB-4888.processed.1.zip'
Content type 'application/zip' length 7200152 bytes (6.9 MB)
==================================================
downloaded 6.9 MB

  |..........                                                            |  14%
   inline R code fragments

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label: selecting-serum-cells
trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4888/E-MTAB-4888.additional.1.zip'
Content type 'application/zip' length 33455 bytes (32 KB)
==================================================
downloaded 32 KB

  |............                                                          |  16%
  ordinary text without R code

  |............                                                          |  18%
label: CD4-SCE-object
  |.............                                                         |  19%
   inline R code fragments

  |..............                                                        |  20%
label: naive-activated-CD4-SCE-object
  |...............                                                       |  21%
   inline R code fragments

  |...............                                                       |  22%
label: obtain-gene-symbols
  |................                                                      |  23%
  ordinary text without R code

  |.................                                                     |  24%
label: unnamed-chunk-4
  |..................                                                    |  25%
   inline R code fragments

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label: unnamed-chunk-5
  |...................                                                   |  27%
  ordinary text without R code

  |....................                                                  |  29%
label: PerCellQC (with options) 
List of 1
 $ fig.cap: chr "Cell-level QC metrics. The total number of endogenous read-counts (excludes non-mapped and intronic reads) is p"| __truncated__

  |.....................                                                 |  30%
  ordinary text without R code

  |......................                                                |  31%
label: experimental-condition-batch (with options) 
List of 1
 $ fig.cap: chr "Cell-level QC metrics according to cell-level metadata. The total number of endogenous reads (excludes non-mapp"| __truncated__

  |......................                                                |  32%
   inline R code fragments

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label: pca-visualisation-stimulus-batch (with options) 
List of 1
 $ fig.cap: chr "First two principal components of log-transformed expression counts after scran normalisation. Colour indicates"| __truncated__

  |........................                                              |  34%
   inline R code fragments

  |.........................                                             |  35%
label: gene-selection (with options) 
List of 1
 $ fig.cap: chr "Average read-count for each gene is plotted against the number of cells in which that gene was detected. Dashed"| __truncated__

  |.........................                                             |  36%
  ordinary text without R code

  |..........................                                            |  37%
label: spike-ins-present
  |...........................                                           |  38%
   inline R code fragments

  |............................                                          |  40%
label: SCE-separation
  |............................                                          |  41%
   inline R code fragments

  |.............................                                         |  42%
label: BatchInfo
  |..............................                                        |  43%
   inline R code fragments

  |...............................                                       |  44%
label: spike-in_download
trying URL 'https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095046.txt'
Content type 'text/plain' length 4086 bytes
==================================================
downloaded 4086 bytes

  |................................                                      |  45%
  ordinary text without R code

  |................................                                      |  46%
label: ercc-mul
  |.................................                                     |  47%
  ordinary text without R code

  |..................................                                    |  48%
label: spike-info
  |...................................                                   |  49%
   inline R code fragments

  |...................................                                   |  51%
label: MCMC-run (with options) 
List of 1
 $ eval: logi FALSE

  |....................................                                  |  52%
  ordinary text without R code

  |.....................................                                 |  53%
label: download-chain-naive
trying URL 'https://zenodo.org/record/5243265/files/chain_naive.Rds'
Content type 'application/octet-stream' length 119109227 bytes (113.6 MB)
==================================================
downloaded 113.6 MB

trying URL 'https://zenodo.org/record/5243265/files/chain_active.Rds'
Content type 'application/octet-stream' length 117080996 bytes (111.7 MB)
==================================================
downloaded 111.7 MB

  |......................................                                |  54%
  ordinary text without R code

  |......................................                                |  55%
label: displayChainBASiCS
  |.......................................                               |  56%
   inline R code fragments

  |........................................                              |  57%
label: convergence-naive (with options) 
List of 1
 $ fig.cap: chr "Trace plot, marginal histogram, and autocorrelation function of the posterior distribution of the mean expressi"| __truncated__

  |.........................................                             |  58%
   inline R code fragments

  |..........................................                            |  59%
label: mcmc-diag (with options) 
List of 1
 $ fig.cap: chr "MCMC diagnostics for gene-specific mean expression parameters; naive CD4+ T cells. A: Geweke Z-score for mean e"| __truncated__

Loading required package: viridisLite
  |..........................................                            |  60%
   inline R code fragments

  |...........................................                           |  62%
label: dispersion-vs-mean (with options) 
List of 3
 $ fig.width : num 6
 $ fig.height: num 6
 $ fig.cap   : chr "Comparison of gene-specific transcriptional variability estimates and mean expression estimates obtained for ea"| __truncated__

  |............................................                          |  63%
   inline R code fragments

  |.............................................                         |  64%
label: plot-vg-naive (with options) 
List of 1
 $ fig.cap: chr "HVG and LVG detection using BASiCS. For each gene, BASiCS posterior estimates (posterior medians) associated to"| __truncated__

For LVG detection task:
the posterior probability threshold chosen via EFDR calibrationis too low. Probability threshold automatically set equal to'ProbThreshold'.
  |.............................................                         |  65%
   inline R code fragments

  |..............................................                        |  66%
label: plot-example-vg-naive (with options) 
List of 1
 $ fig.cap: chr "BASiCS denoised counts for example HVG and LVG with similar overall levels of expression."

  |...............................................                       |  67%
   inline R code fragments

  |................................................                      |  68%
label: mean-expression-testing
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.5987
(ratio Naive vs Active).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

For Differential mean task:
the posterior probability threshold chosen via EFDR calibrationis too low. Probability threshold automatically set equal to'ProbThresholdM'.
  |................................................                      |  69%
   inline R code fragments

  |.................................................                     |  70%
label: visualise-DE-mean-plot (with options) 
List of 3
 $ fig.height: num 8
 $ fig.width : num 6
 $ fig.cap   : chr "Upper panel presents the MA plot associated to the differential mean expression test between naive and active c"| __truncated__

  |..................................................                    |  71%
  ordinary text without R code

  |...................................................                   |  73%
label: offset-denoised
  |....................................................                  |  74%
   inline R code fragments

  |....................................................                  |  75%
label: heatmap-diffexp (with options) 
List of 3
 $ fig.width : num 7
 $ fig.height: num 6
 $ fig.cap   : chr "Heatmap displays normalised expression values (log10(x + 1) scale) for naive and active cells. Genes are strati"| __truncated__

Loading required package: grid
========================================
ComplexHeatmap version 2.6.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

========================================
circlize version 0.4.11
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

  |.....................................................                 |  76%
   inline R code fragments

  |......................................................                |  77%
label: diff-res-plot (with options) 
List of 3
 $ fig.height: num 8
 $ fig.width : num 6
 $ fig.cap   : chr "Upper panel presents the MA plot associated to the differential residual over-dispersion test between naive and"| __truncated__

  |.......................................................               |  78%
  ordinary text without R code

  |.......................................................               |  79%
label: combine-results
Quitting from lines 1496-1505 (Workflow.Rmd) 
Error in ggplot(table_combined_de) : object 'table_combined_de' not found
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> ggplot
In addition: Warning messages:
1: Removed 18 rows containing missing values (geom_point). 
2: Removed 127 rows containing missing values (geom_point). 
3: Removed 127 rows containing missing values (geom_point). 

Execution halted
make: *** [Workflow.pdf] Error 1

Here is also my sessionInfo (of course only the systems part applies here):

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7       fansi_0.5.0      crayon_1.4.1     utf8_1.2.2       digest_0.6.28    later_1.3.0      R6_2.5.1         lifecycle_1.0.1 
 [9] magrittr_2.0.1   evaluate_0.14    pillar_1.6.3     rlang_0.4.11     fs_1.5.0         promises_1.2.0.1 vctrs_0.3.8      ellipsis_0.3.2  
[17] rmarkdown_2.11   tools_4.1.0      compiler_4.1.0   httpuv_1.6.3     xfun_0.26        fastmap_1.1.0    pkgconfig_2.0.3  htmltools_0.5.2 
[25] knitr_1.36       tibble_3.1.5
catavallejos commented 3 years ago

fixed (I think) by 42ee080

catavallejos commented 3 years ago

@nilseling could you please check if everything builds ok for you and send me the pdf? I can then compare to what Alan gets in Linux

nilseling commented 3 years ago

Hey,

the workflow now builds - I'll send you the pdf. But the Supplements fail with:

docker run -v /Users/nils/Github/BASiCSWorkflow:/home/rstudio/mycode \
        -w /home/rstudio/mycode \
        alanocallaghan/bocker:0.1.0 \
        /bin/bash \
        -c 'Rscript -e "rmarkdown::render(\"Supplements.Rmd\")"'
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.12' is out-of-date; the current release version '3.13'
  is available with R version '4.1'; see https://bioconductor.org/install

processing file: Supplements.Rmd
  |.                                                                     |   1%
  ordinary text without R code

  |..                                                                    |   3%
label: setup_knitr (with options) 
List of 2
 $ include: logi FALSE
 $ cache  : logi FALSE

  |...                                                                   |   4%
  ordinary text without R code

  |....                                                                  |   6%
label: load-chain-naive
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
  |.....                                                                 |   7%
  ordinary text without R code

  |......                                                                |   9%
label: trace-naive

Quitting from lines 176-183 (Supplements.Rmd) 
Error in x@parameters[[Parameter]][, Column] : subscript out of bounds
Calls: <Anonymous> ... eval -> eval -> plot -> plot -> .local -> data.frame
Execution halted
make: *** [Supplements.pdf] Error 1
alanocallaghan commented 2 years ago

Should all be fixed now