*Resubmission of 3.7.7, which was superseded in the CRAN queue before release. The package code is identical; only the version number and the submission comments differ.
*Fixed the "Rd files without \usage" NOTE reported by CRAN on
r-devel-linux-x86_64-debian-clang and -gcc. Eight roxygen blocks were
separated from the functions they document by an intervening top-level
globalVariables()/dontCheck() call, so roxygen2 attached the block to that
call and emitted no \usage section. Those calls now precede their roxygen
blocks, and the affected topics (CNVScopeserver, calcCNVKernelProbDist,
downsample_genomic_matrix, formSampleMatrixFromRawGDCData,
getBlockAverageMatrixFromBreakpoints, getInterchromosomalInteractivePlot,
importBreakpointBed, rebinGenomicInteractions) document their usage again.
*Documented the previously undocumented parallel and cnlabel arguments of
formSampleMatrixFromRawGDCData(), which the restored \usage sections revealed.
*Removed stray top-level test code from R/downsample_genomic_matrix.R that ran
at package build time.
*Moved biomaRt and GenomicInteractions from Imports to Suggests, with requireNamespace() guards at their points of use. This removes the BiocFileCache dependency chain (RSQLite, dbplyr) from the package's strong dependencies, fixing the intermittent Windows install failures ("there is no package called 'RSQLite'" / "'dbplyr'") caused when those transitive dependencies were unavailable on a CRAN build machine.
*Updated the maintainer email address to a working contact, as requested by CRAN.
*Removed the HiCseg dependency, which was archived from CRAN. getAsymmetricBlockIndices() now defaults to algorithm="jointSeg"; HiCseg is still used where it is installed.
*Updated NCI Policies on Server UI
*Minor change to ensure compatibility with multiple datasets.
*Require R-4.1.0 in order to make the package CRAN compliant (fixes a single rtracklayer check server install issue)
*Following CRAN guidance, removed a command to close all connections after opening a file.
*Bug fixes related to the suggested plotly dependency.
*Moved the plotly package to suggests because it has been temporarily orphaned.
*Made package check successfully without suggested dependencies.
*Made conditional BSgenome.Hsapiens.UCSC.hg19 to improve OSX installation.
*Made conditional InteractionSet to make OSX installation more seamless.
*We have now added smoothie::kernel2d smooth as an alternative smoother to spatialfil (now disabled) and now our package should once again be CRAN ready.
*With spatialfil removed from CRAN, we have disabled the spatialfil requirement to run the additional examples. *This algorithm is neat and we'll look at other ways to calculate interaction probability, but for the moment, we'll just disable things to keep the package on CRAN.
*Fixed the gene search in the shiny application *Added gene listing for row and column genes to the left of the plot. **These gene data table outputs are searchable and the size is adjustable. *Disabled automatic switching to the sample data tab on click so that users can properly use the new gene column feature. *CRAN fixes to keep the package publicly available
*Reduced imports to 20 and moved the remainder of packages into suggests. *Fixed whole genome map. *Optimized load time to plot a whole genome map (should be roughly a 50% reduction, according to profvis).
*Removed Biostrings dependency to clear NOTE (although packages that CNVScope depends on require it). The prior Biostrings issue has been fixed.
*Added an explicit dependency, Biostrings to keep CRAN check errors on debian from occurring. *Made a small fix to rebinGenomicInteractions, fixing a check at the end to handle a vector input **This will make the package compatible with R 4.0.
*Removed all blockseg references in code. It was a nice feature to have a third algorithm, but blockseg will not be on CRAN shortly.
*Removed blockseg as a strong dependency, per CRAN.
*Updated documentation (some new images have been added to show the effect of bin sizes and resolution). *Fixed a broken URL that was causing a CRAN note.
*Updated documentation for finely binned matrices (see the input matrix vignette). *Several sizes of NBL whole genome matrices are available within the package (1e5,2.5e5,1e6,1e7,1e8). **These are for package use only. The HD matrices are not speed-optimal for app use. **Functionality of basic package functions remains the same as 2.7.2.5. *passes CRAN checks again with flying colors (no notes, warnings, or errors).
*Added P-value filter *Added correlatoin options *Added additional app visualization options. *Added material on how to make higher resolution maps.
*Minor changes to package dependency CNVScopePublicData.
*Another minor cran fix to CNVScopeserver.
*Small changes to CNVScopeserver to fix a CRAN check.
*Small changes to dependencies (including pwr package) and vignettes.
*Minor fix to freadGDCfile documentation
*More information about BLCA, SKCM, and AML in additional examples vignette **Their processed files have been placed within the package **These are available only on the github site as the CRAN size limitations forbid it. *Added the ability to specify chrM and chrY in formSampleMatrixFromRawGDCData function.
Changes:
Changes: