                     Changes in version 2026-09-10                      

*Resubmission of 3.7.7, which was superseded in the CRAN queue before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.

                     Changes in version 2026-07-04                      

*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.

                     Changes in version 2026-07-03                      

*Updated the maintainer email address to a working contact, as requested
by CRAN.

                     Changes in version 2026-06-09                      

*Removed the HiCseg dependency, which was archived from CRAN.
getAsymmetricBlockIndices() now defaults to algorithm="jointSeg"; HiCseg
is still used where it is installed.

                     Changes in version 2022-08-12                      

*Updated NCI Policies on Server UI

                     Changes in version 2021-06-17                      

*Minor change to ensure compatibility with multiple datasets.

                     Changes in version 2021-05-19                      

*Require R-4.1.0 in order to make the package CRAN compliant (fixes a
single rtracklayer check server install issue)

                     Changes in version 2021-05-14                      

*Following CRAN guidance, removed a command to close all connections
after opening a file.

                     Changes in version 2021-01-07                      

*Bug fixes related to the suggested plotly dependency.

                     Changes in version 2021-01-05                      

*Moved the plotly package to suggests because it has been temporarily
orphaned.

                     Changes in version 2021-01-04                      

*Made package check successfully without suggested dependencies.

                     Changes in version 2020-12-15                      

*Made conditional BSgenome.Hsapiens.UCSC.hg19 to improve OSX
installation.

                     Changes in version 2020-12-14                      

*Made conditional InteractionSet to make OSX installation more seamless.

                     Changes in version 2020-11-28                      

*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.

                     Changes in version 2020-11-27                      

*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.

                      Changes in version 2020-8-14                      

*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

                      Changes in version 2020-7-2                       

*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).

                      Changes in version 2019-12-7                      

*Removed Biostrings dependency to clear NOTE (although packages that
CNVScope depends on require it). The prior Biostrings issue has been
fixed.

                      Changes in version 2019-12-5                      

*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.

                     Changes in version 2019-10-23                      

*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.

                     Changes in version 2019-10-18                      

*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.

                     Changes in version 2019-10-12                      

*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).

                     Changes in version 2019-09-21                      

*Added P-value filter *Added correlatoin options *Added additional app
visualization options. *Added material on how to make higher resolution
maps.

                     Changes in version 2019-07-19                      

*Minor changes to package dependency CNVScopePublicData.

                     Changes in version 2019-07-18                      

*Another minor cran fix to CNVScopeserver.

*Small changes to CNVScopeserver to fix a CRAN check.

                     Changes in version 2019-07-17                      

*Small changes to dependencies (including pwr package) and vignettes.

                     Changes in version 2019-07-16                      

*Minor fix to freadGDCfile documentation

                     Changes in version 2019-07-15                      

*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 in version 2019-07-09                      

Changes:

  - Fixed vignettes not properly linking to the package. CNVScope v2.4.4
    (Release date: 2019-07-09) ==============

Changes:

  - Added a power analysis vignette
  - Fixed issues with formSampleMatrixFromRawGDCData ** These issues
    arose from changing types with underlying Bioconductor dependencies
    from character to factor Rle.
  - Updated the build for R-base v3.6.1 *prior to this, this package now
    works with CNVScopePublicData, a large package containing *all that
    is requisite to run the server locally.
