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seqArchRplus
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- Repository: https://github.com/snikumbh/seqArchRplus
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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", , "[email protected]",
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
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
Hi @vjcitn I have improved the vignette. Can you please take a look now? Thanks.
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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
[email protected]:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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 https://github.com/tidyverse/dbplyr/issues/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.
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
Received a valid push on git.bioconductor.org; starting a build for commit id: 61caf154101acac04cc0f2b2692175ed2f6363e8
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
[email protected]:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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.
If it is a new version number on cran than it should update automatically. Can you bump the version and try again?
Received a valid push on git.bioconductor.org; starting a build for commit id: ddee1b266e5c4e10503b48fb87e49a5c11203d0b
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
[email protected]:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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.
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
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).
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
[email protected]:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I reinstalled Matrix, dbplyr, and Brobdingnag. I'm trying to kick off the spb so that we can see if it passed (but I'm botching it! pardon me). I'll retry.
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
[email protected]:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
We reinstalled on our builders and I reinstalled locally but all get the same ERROR.
Appreciate your efforts/help @lshep and @jwokaty !
FWIW, here's what I get on my end (debian machine) where it threw the exact same error 2 days ago, but has resolved now after the reinstallations. Full session info at the end.
I will investigate why it still fails on Ubuntu.
> BiocManager::install(version="devel", lib.loc = .libPaths()[1])
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://www.stats.bris.ac.uk/R/
Bioconductor version 3.16 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
>
> BiocManager::valid(lib.loc = .libPaths()[1])
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://www.stats.bris.ac.uk/R/
[1] TRUE
> BiocCheck::BiocCheck()
─ BiocCheckVersion: 1.33.20
─ BiocVersion: 3.16
─ Package: seqArchRplus
─ PackageVersion: 0.99.2
─ sourceDir: /mnt/biggley/home/sarvesh/authoredRpackages/seqArchRplus
─ installDir: /tmp/RtmpZXFBpE/file3cc83866e621ad
─ BiocCheckDir: ./seqArchRplus.BiocCheck
─ platform: unix
─ isTarBall: FALSE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking version number validity...
Package version 0.99.2; pre-release
* Checking R version dependency...
* Checking package size...
Skipped... only checked on source tarball
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of seqArchRplus...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There are 71 functions
greater than 50 lines.
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 7% of man pages
use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source...
* NOTE: Consider shorter lines; 19 lines (0%) are > 80 characters long.
* NOTE: Consider multiples of 4 spaces for line indents; 313 lines (5%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as described in the
BiocCheck vignette.
* Checking if package already exists in CRAN...
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://www.stats.bris.ac.uk/R/
* Checking for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list
(requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES
See the seqArchRplus.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
Here's the session info
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bookworm/sid
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
locale:
[1] LC_CTYPE=en_DK.UTF-8 LC_NUMERIC=C LC_TIME=en_DK.UTF-8
[4] LC_COLLATE=en_DK.UTF-8 LC_MONETARY=en_DK.UTF-8 LC_MESSAGES=en_DK.UTF-8
[7] LC_PAPER=en_DK.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 rtracklayer_1.57.0
[3] tidyr_1.2.1 ggplot2_3.3.6
[5] bit64_4.0.5 knitr_1.40
[7] DelayedArray_0.23.2 data.table_1.14.4
[9] KEGGREST_1.37.3 RCurl_1.98-1.9
[11] generics_0.1.3 BiocGenerics_0.43.4
[13] GenomicFeatures_1.49.7 cowplot_1.1.1
[15] RSQLite_2.2.18 shadowtext_0.1.2
[17] VGAM_1.1-7 commonmark_1.8.1
[19] bit_4.0.4 enrichplot_1.17.3
[21] xml2_1.3.3 SummarizedExperiment_1.27.3
[23] assertthat_0.2.1 viridis_0.6.2
[25] xfun_0.34 hms_1.1.2
[27] evaluate_0.17 fansi_1.0.3
[29] restfulr_0.0.15 progress_1.2.2
[31] caTools_1.18.2 dbplyr_2.2.1
[33] htmlwidgets_1.5.4 igraph_1.3.5
[35] DBI_1.1.3 seqArchR_1.1.3
[37] stringdist_0.9.8 stats4_4.2.1
[39] purrr_0.3.5 ellipsis_0.3.2
[41] backports_1.4.1 ggpubr_0.4.0
[43] ggnewscale_0.4.8 dplyr_1.0.10
[45] permute_0.9-7 biomaRt_2.53.3
[47] sparseMatrixStats_1.9.0 MatrixGenerics_1.9.1
[49] vctrs_0.4.2 Biobase_2.57.1
[51] abind_1.4-5 CAGEr_2.3.0
[53] cachem_1.0.6 withr_2.5.0
[55] ggforce_0.4.1 HDO.db_0.99.1
[57] BSgenome_1.65.2 vegan_2.6-4
[59] treeio_1.21.2 GenomicAlignments_1.33.1
[61] prettyunits_1.1.1 MultiAssayExperiment_1.23.11
[63] cluster_2.1.4 svglite_2.1.0
[65] DOSE_3.23.3 lazyeval_0.2.2
[67] ape_5.6-2 crayon_1.5.2
[69] pkgconfig_2.0.3 tweenr_2.0.2
[71] GenomeInfoDb_1.33.14 nlme_3.1-160
[73] rlang_1.0.6 lifecycle_1.0.3
[75] downloader_0.4 filelock_1.0.2
[77] BiocFileCache_2.5.2 seqPattern_1.29.0
[79] polyclip_1.10-0 matrixStats_0.62.0
[81] tiff_0.1-11 graph_1.75.0
[83] ggseqlogo_0.1 som_0.3-5.1
[85] Matrix_1.5-1 aplot_0.1.8
[87] carData_3.0-5 boot_1.3-28
[89] base64enc_0.1-3 png_0.1-7
[91] viridisLite_0.4.1 rjson_0.2.21
[93] bitops_1.0-7 gson_0.0.9
[95] KernSmooth_2.23-20 Biostrings_2.65.6
[97] blob_1.2.3 DelayedMatrixStats_1.19.2
[99] stringr_1.4.1 qvalue_2.29.0
[101] jpeg_0.1-9 rstatix_0.7.0
[103] gridGraphics_0.5-1 ggsignif_0.6.4
[105] S4Vectors_0.35.4 scales_1.2.1
[107] memoise_2.0.1 magrittr_2.0.3
[109] plyr_1.8.7 gplots_3.1.3
[111] zlibbioc_1.43.0 scatterpie_0.1.8
[113] compiler_4.2.1 factoextra_1.0.7
[115] BiocIO_1.7.1 RColorBrewer_1.1-3
[117] plotrix_3.8-2 Rsamtools_2.13.4
[119] cli_3.4.1 XVector_0.37.1
[121] patchwork_1.1.2 mgcv_1.8-40
[123] MASS_7.3-58.1 tidyselect_1.2.0
[125] forcats_0.5.2 stringi_1.7.8
[127] yaml_2.3.6 GOSemSim_2.23.1
[129] locfit_1.5-9.6 ggrepel_0.9.1
[131] biocViews_1.65.7 grid_4.2.1
[133] EBImage_4.39.0 fastmatch_1.1-3
[135] tools_4.2.1 parallel_4.2.1
[137] rstudioapi_0.14 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[139] gridExtra_2.3 farver_2.1.1
[141] heatmaps_1.21.0 ggraph_2.1.0
[143] BiocManager_1.30.18 digest_0.6.30
[145] operator.tools_1.6.3 Rcpp_1.0.9
[147] car_3.1-0 broom_1.0.1
[149] GenomicRanges_1.49.1 httr_1.4.4
[151] AnnotationDbi_1.59.1 colorspace_2.0-3
[153] XML_3.99-0.11 IRanges_2.31.2
[155] splines_4.2.1 RBGL_1.73.0
[157] BiocCheck_1.33.20 yulab.utils_0.0.5
[159] tidytree_0.4.1 graphlayouts_0.8.3
[161] ggplotify_0.1.0 systemfonts_1.0.4
[163] jsonlite_1.8.2 ggtree_3.5.3
[165] tidygraph_1.2.2 slickR_0.5.0
[167] ggfun_0.0.7 RUnit_0.4.32
[169] formula.tools_1.7.1 R6_2.5.1
[171] pillar_1.8.1 htmltools_0.5.3
[173] clusterProfiler_4.5.2 glue_1.6.2
[175] fastmap_1.1.0 BiocParallel_1.31.14
[177] fftwtools_0.9-11 codetools_0.2-18
[179] ChIPseeker_1.33.3 fgsea_1.23.4
[181] utf8_1.2.2 lattice_0.20-45
[183] tibble_3.1.8 curl_4.3.3
[185] gtools_3.9.3 GO.db_3.16.0
[187] rmarkdown_2.17 munsell_0.5.0
[189] GenomeInfoDbData_1.2.9 reshape2_1.4.4
[191] gtable_0.3.1
Received a valid push on git.bioconductor.org; starting a build for commit id: 3e881f736c3f55151664ccfb3686da49b05dfd1e
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
[email protected]:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 64533f4297148221d45f2b797f346764373c86cd
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: "WARNINGS". 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
[email protected]:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: a7807fbbaf13c75357bbe9f77813da4bb71acb4a
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
[email protected]:packages/seqArchRplus to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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