seqArchRplus

[snikumbh]

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[bioc-issue-bot]

Hi @snikumbh

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Type: Package
Package: seqArchRplus
Title: Downstream analyses of promoter sequence architectures and HTML
    report generation
Version: 0.99.0
Authors@R: 
    person("Sarvesh", "Nikumbh", , "sarvesh.nikumbh@gmail.com", 
    role = c("aut", "cre", "cph"),
    comment = c(ORCID = "0000-0003-3163-4447"))
Description: seqArchRplus enables downstream analyses of promoter
    sequence architectures/clusters identified by seqArchR (or any other 
    tool/method). With additional available information such as the TPM values 
    and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus 
    can order the input promoter clusters by their shape (IQWs), and write the 
    cluster information as browser/IGV track files. Provided visualizations 
    are of two kind: per sample/stage and per cluster visualizations. Those of 
    the first kind include: plot panels for each sample showing per cluster 
    shape, TPM and other score distributions, sequence logos, and peak 
    annotations. The second include per cluster chromosome-wise and strand 
    distributions, motif occurrence heatmaps and GO term enrichments. 
    Additionally, seqArchRplus can also generate HTML reports for easy viewing 
    and comparison of promoter architectures between samples/stages (future).
License: GPL-3 | file LICENSE
URL: https://snikumbh.github.io/seqArchRplus/,
    https://github.com/snikumbh/seqArchRplus
BugReports: https://github.com/snikumbh/seqArchRplus/issues
Depends:
    R (>= 4.2.1),
    GenomicRanges,
    IRanges,
    S4Vectors
Imports: 
    BiocParallel,
    Biostrings,
    BSgenome,
    ChIPseeker,
    cli,
    clusterProfiler,
    cowplot,
    factoextra,
    forcats,
    GenomeInfoDb,
    ggplot2,
    graphics,
    grDevices,
    gridExtra,
    heatmaps,
    methods,
    RColorBrewer,
    scales,
    seqArchR,
    seqPattern,
    stats,
    utils
Suggests:
    BSgenome.Dmelanogaster.UCSC.dm6,
    BiocStyle,
    CAGEr (>= 2.0.2),
    covr,
    knitr (>= 1.22),
    org.Dm.eg.db,
    pdftools,
    rmarkdown (>= 1.12),
    slickR,
    svglite,
    testthat (>= 3.0.2),
    TxDb.Dmelanogaster.UCSC.dm6.ensGene,
    vdiffr (>= 0.3.0),
    xfun
VignetteBuilder: 
    knitr
biocViews: Annotation, Visualization, ReportWriting, GO, MotifAnnotation, 
    Clustering
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.2

[vjcitn]

Thanks for submitting this package. I rendered the vignette and I find that it is not sufficiently demonstrative of what the package does. There is

## Using dummy sample names. Please replace with your sample names here

sample_names <- paste0("sample", 1:3)

sn <- "sample1"
use_aggl <- "complete"
use_dist <- "euclid"

use_dir <- tempdir()

seqArchR_result <- readRDS(system.file("extdata", "seqArchR_result.rds",
      package = "seqArchRplus", mustWork = TRUE))

## get seqArchR clusters custom curated
seqArchR_clusts <- seqArchRplus::curate_clusters(
    sname = sn,
    use_aggl = use_aggl, use_dist = use_dist,
    seqArchR_result = seqArchR_result, iter = 5,
    pos_lab = NULL, regularize = FALSE, topn = 50,
    use_cutk = 2, final = FALSE, dir_path = use_dir
)
#> 
#> ── seqArchR result clusters curation ───────────────────────────────────────────
#> 
#> ── Sample: sample1 ──
#> 
#> ! Creating directory: /tmp/Rtmp1Yk1Qj/sample1_results
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
#> "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
#> "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
#> "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.

and so on. Please compile the vignette and look at it as something that a newcomer should be able to consume with interest and some aesthetic satisfaction. This would mean that you suppress certain messages in your methods, have good show methods for data structures of significance, and display some of the visualizations that you describe. Let us know your plans @vjcitn

[snikumbh]

Thanks for the comment/suggestion. Will work on it and reply here.

[snikumbh]

Hi @vjcitn
I have improved the vignette. Can you please take a look now? Thanks.

[snikumbh]

Hi @vjcitn
Pinging to bump this up.

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[snikumbh]

Hi @lshep,
The error reported is

Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class ident; class definition removed from dbplyr
Execution halted

which going by info at
tidyverse/dbplyr#779 is caused by Brobdingnag, and resolved with version 1.2-8 which unfortunately doesn't seem to be on CRAN yet due to some platform specific issues (see here).

What do you suggest in this regard?
How can I know what package dependency is causing this problem here for seqArchRplus?

R CMD check has actually passed fine, and this error did not show up with BiocCheck when run locally.

Thanks.

[lshep]

Bioconductor will only use whatever version is available through CRAN. If it is not available via CRAN Bioconductor will not have access as we do not use remotes or download specific versions of packages. For what its worth I can reproduce this locally on my computer so I suggest making sure you are using the right version of R and all updated packages by check BiocManager::valid() or BiocManager::install()` Please also be sure to be using Bioc devel

Bioconductor version 3.16 (BiocManager 1.30.18), R 4.2.1 Patched (2022-09-28
  r82935)
> library(BiocCheck)
> BiocCheck("seqArchRplus)
+ 
> BiocCheck("seqArchRplus")
─ BiocCheckVersion: 1.33.20
─ BiocVersion: 3.16
─ Package: seqArchRplus
─ PackageVersion: 0.99.0
─ sourceDir: /home/shepherd/PkgReviews/seqArchRplus
─ installDir: /tmp/Rtmpsv0gyI/file13523d7f3859
─ BiocCheckDir: ./seqArchRplus.BiocCheck
─ platform: unix
─ isTarBall: FALSE

* Installing package...
* Checking package dependencies...

Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class "ident"; class definition removed from 'dbplyr'
> sessionInfo()
R version 4.2.1 Patched (2022-09-28 r82935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /home/shepherd/R-Installs/bin/R-4-2-branch/lib/libRblas.so
LAPACK: /home/shepherd/R-Installs/bin/R-4-2-branch/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocCheck_1.33.20   praise_1.0.0        BiocManager_1.30.18

loaded via a namespace (and not attached):
  [1] shadowtext_0.1.2            fastmatch_1.1-3            
  [3] plyr_1.8.7                  igraph_1.3.5               
  [5] lazyeval_0.2.2              splines_4.2.1              
  [7] BiocParallel_1.31.13        GenomeInfoDb_1.33.10       
  [9] ggplot2_3.3.6               digest_0.6.30              
 [11] yulab.utils_0.0.5           GOSemSim_2.23.1            
 [13] viridis_0.6.2               GO.db_3.16.0               
 [15] fansi_1.0.3                 magrittr_2.0.3             
 [17] memoise_2.0.1               BSgenome_1.65.2            
 [19] Biostrings_2.65.6           graphlayouts_0.8.2         
 [21] seqArchR_1.1.2              matrixStats_0.62.0         
 [23] enrichplot_1.17.3           prettyunits_1.1.1          
 [25] colorspace_2.0-3            blob_1.2.3                 
 [27] ggrepel_0.9.1               xfun_0.33                  
 [29] dplyr_1.0.10                crayon_1.5.2               
 [31] RCurl_1.98-1.9              jsonlite_1.8.2             
 [33] graph_1.75.0                scatterpie_0.1.8           
 [35] ape_5.6-2                   glue_1.6.2                 
 [37] polyclip_1.10-0             gtable_0.3.1               
 [39] zlibbioc_1.43.0             XVector_0.37.1             
 [41] DelayedArray_0.23.2         BiocGenerics_0.43.4        
 [43] scales_1.2.1                DOSE_3.23.3                
 [45] DBI_1.1.3                   Rcpp_1.0.9                 
 [47] plotrix_3.8-2               progress_1.2.2             
 [49] viridisLite_0.4.1           gridGraphics_0.5-1         
 [51] tidytree_0.4.1              bit_4.0.4                  
 [53] stats4_4.2.1                httr_1.4.4                 
 [55] fgsea_1.23.4                RColorBrewer_1.1-3         
 [57] ellipsis_0.3.2              pkgconfig_2.0.3            
 [59] XML_3.99-0.11               farver_2.1.1               
 [61] ggseqlogo_0.1               utf8_1.2.2                 
 [63] ggplotify_0.1.0             tidyselect_1.2.0           
 [65] rlang_1.0.6                 reshape2_1.4.4             
 [67] AnnotationDbi_1.59.1        munsell_0.5.0              
 [69] biocViews_1.65.7            tools_4.2.1                
 [71] cachem_1.0.6                downloader_0.4             
 [73] cli_3.4.1                   generics_0.1.3             
 [75] RSQLite_2.2.18              gson_0.0.9                 
 [77] stringr_1.4.1               fastmap_1.1.0              
 [79] yaml_2.3.6                  ggtree_3.5.3               
 [81] knitr_1.40                  bit64_4.0.5                
 [83] tidygraph_1.2.2             purrr_0.3.5                
 [85] KEGGREST_1.37.3             ggraph_2.1.0               
 [87] RBGL_1.73.0                 nlme_3.1-160               
 [89] aplot_0.1.8                 compiler_4.2.1             
 [91] png_0.1-7                   treeio_1.21.2              
 [93] tibble_3.1.8                tweenr_2.0.2               
 [95] stringi_1.7.8               forcats_0.5.2              
 [97] lattice_0.20-45             Matrix_1.5-1               
 [99] vctrs_0.4.2                 stringdist_0.9.8           
[101] pillar_1.8.1                lifecycle_1.0.3            
[103] RUnit_0.4.32                data.table_1.14.4          
[105] cowplot_1.1.1               bitops_1.0-7               
[107] patchwork_1.1.2             rtracklayer_1.57.0         
[109] GenomicRanges_1.49.1        qvalue_2.29.0              
[111] R6_2.5.1                    BiocIO_1.7.1               
[113] KernSmooth_2.23-20          gridExtra_2.3              
[115] IRanges_2.31.2              codetools_0.2-18           
[117] MASS_7.3-58.1               assertthat_0.2.1           
[119] SummarizedExperiment_1.27.3 rjson_0.2.21               
[121] withr_2.5.0                 GenomicAlignments_1.33.1   
[123] Rsamtools_2.13.4            S4Vectors_0.35.4           
[125] GenomeInfoDbData_1.2.9      hms_1.1.2                  
[127] parallel_4.2.1              clusterProfiler_4.5.2      
[129] grid_4.2.1                  ggfun_0.0.7                
[131] tidyr_1.2.1                 HDO.db_0.99.1              
[133] MatrixGenerics_1.9.1        ggnewscale_0.4.8           
[135] ggforce_0.4.1               seqPattern_1.29.0          
[137] Biobase_2.57.1              restfulr_0.0.15            

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 61caf154101acac04cc0f2b2692175ed2f6363e8

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[snikumbh]

Hi @lshep
Sorry, I took some time to setup bioc-devel on linux at my end so that I could see if things have been fixed after the Brobdingnag package was updated and is now again available on CRAN.

Could I please ask you to install the updated version of Brobdingnag 1.2-9 from CRAN on the builders? Thanks in advance.

I just re-installed Brobdingnag and the error is no more there.

I will then bump and push again to trigger a build.

[lshep]

If it is a new version number on cran than it should update automatically. Can you bump the version and try again?

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ddee1b266e5c4e10503b48fb87e49a5c11203d0b

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[snikumbh]

OK, still the error.
I think it will require reinstalling dbplyr (same version should be fine) along with Brobdingnag (newer version 1.2-9, now on cran), and perhaps even Matrix (this I am not completely sure)?

One way to check directly would be to
library(dbplyr)
after all (re-)instllations, which should not give the same error that it did before.

[lshep]

I think you might need to declare Brobdingnag in your dependency list? I still get the same ERROR as before after installing the new version locally but when I am checking my sessionInfo I do not see Brobdingnag loaded

> library(BiocCheck)
> BiocCheck("seqArchRplus")
─ BiocCheckVersion: 1.33.20
─ BiocVersion: 3.16
─ Package: seqArchRplus
─ PackageVersion: 0.99.0
─ sourceDir: /home/shepherd/PkgReviews/seqArchRplus
─ installDir: /tmp/RtmpII1QPr/file3b3260369e01
─ BiocCheckDir: ./seqArchRplus.BiocCheck
─ platform: unix
─ isTarBall: FALSE

* Installing package...
* Checking package dependencies...

Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class "ident"; class definition removed from 'dbplyr'
> sessionInfo()
R version 4.2.1 Patched (2022-09-28 r82935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /home/shepherd/R-Installs/bin/R-4-2-branch/lib/libRblas.so
LAPACK: /home/shepherd/R-Installs/bin/R-4-2-branch/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocCheck_1.33.20   praise_1.0.0        BiocManager_1.30.18

loaded via a namespace (and not attached):
  [1] shadowtext_0.1.2            fastmatch_1.1-3            
  [3] plyr_1.8.7                  igraph_1.3.5               
  [5] lazyeval_0.2.2              splines_4.2.1              
  [7] BiocParallel_1.31.13        GenomeInfoDb_1.33.10       
  [9] ggplot2_3.3.6               digest_0.6.30              
 [11] yulab.utils_0.0.5           GOSemSim_2.23.1            
 [13] viridis_0.6.2               GO.db_3.16.0               
 [15] fansi_1.0.3                 magrittr_2.0.3             
 [17] memoise_2.0.1               BSgenome_1.65.2            
 [19] Biostrings_2.65.6           graphlayouts_0.8.2         
 [21] seqArchR_1.1.2              matrixStats_0.62.0         
 [23] enrichplot_1.17.3           prettyunits_1.1.1          
 [25] colorspace_2.0-3            blob_1.2.3                 
 [27] ggrepel_0.9.1               xfun_0.33                  
 [29] dplyr_1.0.10                crayon_1.5.2               
 [31] RCurl_1.98-1.9              jsonlite_1.8.2             
 [33] graph_1.75.0                scatterpie_0.1.8           
 [35] ape_5.6-2                   glue_1.6.2                 
 [37] polyclip_1.10-0             gtable_0.3.1               
 [39] zlibbioc_1.43.0             XVector_0.37.1             
 [41] DelayedArray_0.23.2         BiocGenerics_0.43.4        
 [43] scales_1.2.1                DOSE_3.23.3                
 [45] DBI_1.1.3                   Rcpp_1.0.9                 
 [47] plotrix_3.8-2               progress_1.2.2             
 [49] viridisLite_0.4.1           gridGraphics_0.5-1         
 [51] tidytree_0.4.1              bit_4.0.4                  
 [53] stats4_4.2.1                httr_1.4.4                 
 [55] fgsea_1.23.4                RColorBrewer_1.1-3         
 [57] ellipsis_0.3.2              pkgconfig_2.0.3            
 [59] XML_3.99-0.11               farver_2.1.1               
 [61] ggseqlogo_0.1               utf8_1.2.2                 
 [63] ggplotify_0.1.0             tidyselect_1.2.0           
 [65] rlang_1.0.6                 reshape2_1.4.4             
 [67] AnnotationDbi_1.59.1        munsell_0.5.0              
 [69] biocViews_1.65.7            tools_4.2.1                
 [71] cachem_1.0.6                downloader_0.4             
 [73] cli_3.4.1                   generics_0.1.3             
 [75] RSQLite_2.2.18              gson_0.0.9                 
 [77] stringr_1.4.1               fastmap_1.1.0              
 [79] yaml_2.3.6                  ggtree_3.5.3               
 [81] knitr_1.40                  bit64_4.0.5                
 [83] tidygraph_1.2.2             purrr_0.3.5                
 [85] KEGGREST_1.37.3             ggraph_2.1.0               
 [87] RBGL_1.73.0                 nlme_3.1-160               
 [89] aplot_0.1.8                 compiler_4.2.1             
 [91] png_0.1-7                   treeio_1.21.2              
 [93] tibble_3.1.8                tweenr_2.0.2               
 [95] stringi_1.7.8               forcats_0.5.2              
 [97] lattice_0.20-45             Matrix_1.5-1               
 [99] vctrs_0.4.2                 stringdist_0.9.8           
[101] pillar_1.8.1                lifecycle_1.0.3            
[103] RUnit_0.4.32                data.table_1.14.4          
[105] cowplot_1.1.1               bitops_1.0-7               
[107] patchwork_1.1.2             rtracklayer_1.57.0         
[109] GenomicRanges_1.49.1        qvalue_2.29.0              
[111] R6_2.5.1                    BiocIO_1.7.1               
[113] KernSmooth_2.23-20          gridExtra_2.3              
[115] IRanges_2.31.2              codetools_0.2-18           
[117] MASS_7.3-58.1               assertthat_0.2.1           
[119] SummarizedExperiment_1.27.3 rjson_0.2.21               
[121] withr_2.5.0                 GenomicAlignments_1.33.1   
[123] Rsamtools_2.13.4            S4Vectors_0.35.4           
[125] GenomeInfoDbData_1.2.9      hms_1.1.2                  
[127] parallel_4.2.1              clusterProfiler_4.5.2      
[129] grid_4.2.1                  ggfun_0.0.7                
[131] tidyr_1.2.1                 HDO.db_0.99.1              
[133] MatrixGenerics_1.9.1        ggnewscale_0.4.8           
[135] ggforce_0.4.1               seqPattern_1.29.0          
[137] Biobase_2.57.1              restfulr_0.0.15            


> library(Brobdingnag)
Loading required package: Matrix

Attaching package: 'Brobdingnag'

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

    diag, t

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

    diag, t

However I am doubtful that that would work too:

> library(BiocCheck)
> BiocCheck("seqArchRplus")
─ BiocCheckVersion: 1.33.20
─ BiocVersion: 3.16
─ Package: seqArchRplus
─ PackageVersion: 0.99.0
─ sourceDir: /home/shepherd/PkgReviews/seqArchRplus
─ installDir: /tmp/RtmprU5rz7/file3d3f2d6f7ee1
─ BiocCheckDir: ./seqArchRplus.BiocCheck
─ platform: unix
─ isTarBall: FALSE

* Installing package...
* Checking package dependencies...

Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class "ident"; class definition removed from 'dbplyr'
> 
> library(dbplyr)
Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: package or namespace load failed for 'dbplyr':
 .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class "ident"; class definition removed from 'dbplyr'
> library(Brobdingnag)
Loading required package: Matrix

Attaching package: 'Brobdingnag'

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

    diag, t

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

    diag, t

> library(dbplyr)
Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: package or namespace load failed for 'dbplyr':
 .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class "ident"; class definition removed from 'dbplyr'
> sessionInfo()
R version 4.2.1 Patched (2022-09-28 r82935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /home/shepherd/R-Installs/bin/R-4-2-branch/lib/libRblas.so
LAPACK: /home/shepherd/R-Installs/bin/R-4-2-branch/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] Brobdingnag_1.2-9   Matrix_1.5-1        BiocCheck_1.33.20  
[4] praise_1.0.0        BiocManager_1.30.18

loaded via a namespace (and not attached):
  [1] shadowtext_0.1.2            fastmatch_1.1-3            
  [3] plyr_1.8.7                  igraph_1.3.5               
  [5] lazyeval_0.2.2              splines_4.2.1              
  [7] BiocParallel_1.31.13        GenomeInfoDb_1.33.10       
  [9] ggplot2_3.3.6               digest_0.6.30              
 [11] yulab.utils_0.0.5           GOSemSim_2.23.1            
 [13] viridis_0.6.2               GO.db_3.16.0               
 [15] fansi_1.0.3                 magrittr_2.0.3             
 [17] memoise_2.0.1               BSgenome_1.65.2            
 [19] Biostrings_2.65.6           graphlayouts_0.8.2         
 [21] seqArchR_1.1.2              matrixStats_0.62.0         
 [23] enrichplot_1.17.3           prettyunits_1.1.1          
 [25] colorspace_2.0-3            blob_1.2.3                 
 [27] ggrepel_0.9.1               xfun_0.33                  
 [29] dplyr_1.0.10                crayon_1.5.2               
 [31] RCurl_1.98-1.9              jsonlite_1.8.2             
 [33] graph_1.75.0                scatterpie_0.1.8           
 [35] ape_5.6-2                   glue_1.6.2                 
 [37] polyclip_1.10-0             gtable_0.3.1               
 [39] zlibbioc_1.43.0             XVector_0.37.1             
 [41] DelayedArray_0.23.2         BiocGenerics_0.43.4        
 [43] scales_1.2.1                DOSE_3.23.3                
 [45] DBI_1.1.3                   Rcpp_1.0.9                 
 [47] plotrix_3.8-2               progress_1.2.2             
 [49] viridisLite_0.4.1           gridGraphics_0.5-1         
 [51] tidytree_0.4.1              bit_4.0.4                  
 [53] stats4_4.2.1                httr_1.4.4                 
 [55] fgsea_1.23.4                RColorBrewer_1.1-3         
 [57] ellipsis_0.3.2              pkgconfig_2.0.3            
 [59] XML_3.99-0.11               farver_2.1.1               
 [61] ggseqlogo_0.1               utf8_1.2.2                 
 [63] ggplotify_0.1.0             tidyselect_1.2.0           
 [65] rlang_1.0.6                 reshape2_1.4.4             
 [67] AnnotationDbi_1.59.1        munsell_0.5.0              
 [69] biocViews_1.65.7            tools_4.2.1                
 [71] cachem_1.0.6                downloader_0.4             
 [73] cli_3.4.1                   generics_0.1.3             
 [75] RSQLite_2.2.18              gson_0.0.9                 
 [77] stringr_1.4.1               fastmap_1.1.0              
 [79] yaml_2.3.6                  ggtree_3.5.3               
 [81] knitr_1.40                  bit64_4.0.5                
 [83] tidygraph_1.2.2             purrr_0.3.5                
 [85] KEGGREST_1.37.3             ggraph_2.1.0               
 [87] RBGL_1.73.0                 nlme_3.1-160               
 [89] aplot_0.1.8                 compiler_4.2.1             
 [91] png_0.1-7                   treeio_1.21.2              
 [93] tibble_3.1.8                tweenr_2.0.2               
 [95] stringi_1.7.8               forcats_0.5.2              
 [97] lattice_0.20-45             vctrs_0.4.2                
 [99] stringdist_0.9.8            pillar_1.8.1               
[101] lifecycle_1.0.3             RUnit_0.4.32               
[103] data.table_1.14.4           cowplot_1.1.1              
[105] bitops_1.0-7                patchwork_1.1.2            
[107] rtracklayer_1.57.0          GenomicRanges_1.49.1       
[109] qvalue_2.29.0               R6_2.5.1                   
[111] BiocIO_1.7.1                KernSmooth_2.23-20         
[113] gridExtra_2.3               IRanges_2.31.2             
[115] codetools_0.2-18            MASS_7.3-58.1              
[117] assertthat_0.2.1            SummarizedExperiment_1.27.3
[119] rjson_0.2.21                withr_2.5.0                
[121] GenomicAlignments_1.33.1    Rsamtools_2.13.4           
[123] S4Vectors_0.35.4            GenomeInfoDbData_1.2.9     
[125] hms_1.1.2                   parallel_4.2.1             
[127] clusterProfiler_4.5.2       grid_4.2.1                 
[129] ggfun_0.0.7                 tidyr_1.2.1                
[131] HDO.db_0.99.1               MatrixGenerics_1.9.1       
[133] ggnewscale_0.4.8            ggforce_0.4.1              
[135] seqPattern_1.29.0           Biobase_2.57.1             
[137] restfulr_0.0.15            

[snikumbh]

I was not sure about re-installing Matrix, so I tried to look for my command history. Here it is

I re-installed all three (Matrix, Brobdingnag, and dbplyr), and the error went away.

Interestingly, even dbplyr does not directly depend on Brobdingnag (it perhaps does indirectly via the tidyverse, but I may be wrong).

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ABNORMAL".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: a7807fbbaf13c75357bbe9f77813da4bb71acb4a

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[snikumbh]

Hi @lshep

The package looks good to go. Thanks for your patience all along.
I also understand that the release week will be busy, so no hurry.

Best,
Sarvesh

[snikumbh]

Hi @lshep
Just wanted to ask when you will have time to review this package, so that I can plan around it.

Thanks. Appreciate all your help.

[lshep]

Sorry for the delay - I'll try to get to a review before the end of hte week

[lshep]

Please remove or populate the currently empty README.md

I am unable to run the code in the vignette. When I work through the code that is shown to a rendered vignette I get the following ERROR in section 3.1.2

> 
sn <- "RAL28_10_to_12h"
use_aggl <- "complete"
use_dist <- "euclid"

## get seqArchR clusters custom curated
seqArchR_curated_clusts <- curate_clusters(sname = sn,
                                use_aggl = use_aggl, use_dist = use_dist,
                                seqArchR_result = seqArchR_result, iter = 5,
                                pos_lab = NULL, regularize = TRUE, topn = 50,
                                use_cutk = 2, final = FALSE, dir_path = NULL
                            )

── seqArchR result clusters curation ───────────────────────────────────────────

── Sample: RAL28_10_to_12h ──

Error in seqArchR::plot_arch_for_clusters(seqs = seqArchR::seqs_str(seqArchR_result),  : 
  Expecting either a DNAStringSet object or a character vector

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 0559ac65699b8f203da49b98782943f027e3f0a6

[snikumbh]

OK. This error in running line 312 is anticipated (and reproduced) if/when line number 226 is not run (previous chunk) which is not shown to the user.

I have changed the vignette to include that part into the chunk that is visible to the user with a clear note in the comment.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[snikumbh]

Done. I have made the necessary changes (moved that code to the visible chunk). Removed the empty README.md as well.

[snikumbh]

Hi @lshep
Just a ping to bump this up

[lshep]

Yes I will try to review shortly sorry for the delay.

[lshep]

Minor comment:

R ships with the GPL-3 license so there is no need to include it as a seperate file. Please update the package DESCRIPTION to just GPL-3

[snikumbh]

Noted, thanks.
If you don't mind, I will make all the updates at once after I receive the bulk feedback on the package.

Best,
Sarvesh

[lshep]

Sorry I was short yesterday. I think the rest of the package looks good and would be willing to accept with the licensing change.

[snikumbh]

OK, great. On it then! Thanks.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 06af1a14d08005e486e0d032785648b3e00a9864

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[snikumbh]

Hi @lshep, all done! Thanks.

[snikumbh]

Ping :)

[snikumbh]

Hi @lshep
I am looking forward to seeing this as accepted if all the steps are now complete. Please let me know. Appreciate all your help along the way.

Best wishes,
Sarvesh

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

[lshep]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/snikumbh.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("seqArchRplus"). The package 'landing page' will be created at

https://bioconductor.org/packages/seqArchRplus

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.