bump
 

 skip libboost_fs.a for win build since it didn't work
 

 rm libprotobuf-lite.a to pass bioc size limit
 

 up x64/libprotobuf-lite.a
 

 up header for win
 

 up protobuf to 3.10 #8
 

 bump
 

 Merge branch 'cytoset' into trunk
 

 switch to boost::fs
 

 pkgdown updates
 

 Add cytolib and RcppParallel to imports for R CMD check
 

 fix typo
 

 fix typo
 

 Minor fix to ce_get_panels
 

 mv schema folder to inst
 

 update doc
 

 filter samples by panel when parsing cytobank_experiment  #73
 

 add attribute namespaces for modified tags
 

 pass dots to fcs parser. #68
 

 add CytoML XSD
 

 Merge branch 'trunk' of github.com:RGLab/CytoML into trunk
 

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 

 Merge branch 'trunk' into whitews-trunk
 

 Merge branch 'trunk' of https://github.com/rglab/cytoml into trunk
 

 export cytobank ML with attribute namespaces
 

 Fix diva_to_gatingset gate scaling issue
 

 update diva test case
 

 lower tolerance due to the lower digits
 

 fix test case related to flog
 

 bump
 

 use round to set precision for format_float
 

 format_float(gain)
 

 lower precision for format_float
 

 add test case for flog
 

 Strip name from value resulting from `format_float` calls
 

 add format_float to customize precision(increase default 15 to 17) for double to match up to pugixml behavior
 

 gate * to smart ptr
 

 Merge branch 'cytoset' of github.com:RGLab/CytoML into cytoset
 

 use non-header-only version of cytolib
 

 load flowCore in tests
 

 merge trunk
 

 bump
 

 run roxygen
 

 load ncdfFlow
 

 fix test case for Inverse function of flog
 

 getSampleGroups --> fj_ws_get_sample_groups
 

 fix diva_workspace class
 

 getCompensationMatrices --> gs_get_compensations
 

 getSampleGroups --> fj_ws_get_sample_groups
 

 Merge branch 'trunk' into cytoset
 

 merge cytoverse/trunk
 

 merge trunk
 

 fix tests
 

 Merge remote-tracking branch 'origin/cytoset' into cytoset
 

 fix #49
 

 Update DESCRIPTION 

 Update calls to ggcyto::transform_gate() to renamed ggcyto::rescale_gate()
 

 use cytoset in diva parser
 

 use S3 for getSamples
 

 update according to the latest changes in cytolib2
 

 updated
 

 export isValid functions
 

 add isValid functions
 

 using Roxygen 7.0.0, and version bump thanks to improved error message in readSingleGmt
 

 version bump
 

 Fixed direction in DESeq2
 

 Update JS
 

 Volcano graph
 

 ARCHS4: safe column adder
 

 Brief data fail-safe improved
 

 DESeq: finalisation
 

 ARCHS4: populate test h5 file
 

 ARCHS4: metadata population
 

 Limma test fix
 

 Update JS. DESeq2
 

 FGSEA: use BioC version
 

 Merge pull request #133 from ctlab/develop

New gpl loader. Example dataset  

 New GPL loader
 

 New GPL loader
 

 Update JS. Hide reproduce code
 

 fgsea database example with eval and symbols
 

 Added citation info
 

 Tutorial typo
 

 New tutorial
 

 Omit unannotated removes NA aswell
 

 AnnotationDB confusion fix
 

 Travis fix
 

 Update JS
 

 Update JS. Minor interface revamp
 

 HeatMap JSON view
 

 Add phantasus to opencpu preloaded packages?
 

 Use hotfixed GEOquery version. 

 verbose selfCheck
 

 Update JS
 

 Merge pull request #122 from ctlab/develop

Develop 

 Update JS. Chart warning message revised
 

 Update JS. Charts performance concerns
 

 Update JS. PCA plot enchancement. Linked dataset notice
 

 Add cairo package on OS X
 

 Named linked datasets
 

 Update JS. Old browser warnings + default library path
 

 update_21nov2018_SECOND_MASTER
 

 update_description_21_nov
 

 update master 20 november_pm
 

 19novemberpm
 

 update release
 

 perf.diablo supports progressBar on repeats
 

 update NEWS
 

 improve tune.spls tests
 

 improve parallel tune.splsda
 

 check warning fix
 

 perf DA to use FORK cluster for Unix-like
 

 improve parallel setup for perf DA
 

 add tune.spls tests
 

 perf.diablo supports auc

A simple average auc is calculated for all blocks
 

 ignore .Renviron
 

 perf.diablo now parallel on nrepeat
 

 perf.diablo if(!missing(cpus)) -> if(parallel)
 

 helper function to ignore $call in unit tests
 

 export cluster once - use .onUnix()

.onUnix() checks if the OS is Unix-like to create FORK clusters
 

 add some tests
 

 more readable t.test.process with improved condition handling

## comparing to the old code:

t.test.process_old = function(mat.error.rate, alpha = 0.01)
{
    # mat.error.rate has nrep rows and ncomp columns
    # we test successively whether adding a component improves the results

    max = ncol(mat.error.rate) #number max of components included
    pval = NULL
    opt = 1 #initialise the first optimal number of components
    for(opt in 1:max)
    {
        j=opt+1
        temp = try(t.test(mat.error.rate[,opt],mat.error.rate[,j],alternative="greater")$p.value, silent=TRUE) #t.test of "is adding X comp improves the overall results"
        if(is(temp, "try-error") || is.na(temp)) # temp can be NaN when error.keepX is constant
        {
            pval = 1
        } else {
            pval = temp
        }
        #print(opt)
        #print(j)
        #print(pval)

        while(pval> (alpha) & j<max)
        {
            j=j+1
            temp = try(t.test(mat.error.rate[,opt],mat.error.rate[,j],alternative="greater")$p.value, silent=TRUE) #t.test of "is adding X comp improves the overall results"
            if(is(temp, "try-error") || is.na(temp)) # temp can be NaN when error.keepX is constant
            {
                pval = 1
            } else {
                pval = temp
            }
            #print(opt)
            #print(j)
            #print(pval)
        }

        if( (pval> (alpha))) #if all pvalues were greater than alpha, then we do not increase opt and get out of the loop
            break
    }
    ncomp_opt = opt

    return(ncomp_opt)
}

expect_equal(t.test.process(data.frame(comp1=100:104, comp2=20:24, comp3=10:14)), t.test.process_old(data.frame(comp1=100:104, comp2=20:24, comp3=10:14)))

expect_equal(t.test.process(data.frame(comp1=100:114, comp2=20:24, comp3=50:54)), t.test.process_old(data.frame(comp1=100:114, comp2=20:24, comp3=50:54)))

expect_equal(t.test.process(data.frame(comp1=10:14, comp2=20:24, comp3=50:54)), t.test.process_old(data.frame(comp1=10:14, comp2=20:24, comp3=50:54)))
 

 ./gitignore
 

 .check_cpus to return cpus explicitly
 

 update NEWS
 

 Merge remote-tracking branch 'upstream/master'
 

 Fix mapIds issue
 

 check for empty delimiters in IDs
 

 Add updateObject() method for SplicingGraphs objects
 

 add reference
 

 Merge branch 'master' of git.bioconductor.org:packages/CellBench
 

 Removed extra line
 

 Search genes overlay fix
 

 added CRISPRscan efficacy prediction algorithm
 

 Extended the gitignore
 

 version bump
 

 second part of update to copyEnv

- forgot not to try to map C symbol
- forgot to return new environment in copyEnv
- :(
 

 implement copyEnv() in R

- avoids non-API INCREMENT_NAMED
- doesn't seem like this is used to copy very large environments?
 

 Merge branch 'postrelease'
 

 bug fixed
 

 rm .()
 

 xlim2 and ylim2
 

 roxygen2md
 

 ylim_ggtree
 

 update makefile
 

 Fix issue in `mapIds` returning empty character if unable to map

- Fix issue in `mapIds` that returned an empty character if the provided IDs
  could not be mapped (issue #104).
- Add documentation for the new gc_content column in tx table (issue #103).
 

 Add column gc_count to the transcript table (issue #103)
 

 Fixed failed test by updating example data.
 

 Updated README for new stable version.
 

 updated
 

 fixed conflict
 

 doc fixes: roxygen update, man pages, unitTests
 

 fix: .rbind for list with mixed data.frame/DataFrame
 

 chore: remove deprecated defaultMs{1,2}Settings
 

 Bumped version and date, reoxygenated.
 

 more doc fixes
 

 Merge branch 'master' of git.bioconductor.org:packages/GEOquery
 

 Merge branch 'master' of github.com:seandavi/GEOquery into RELEASE_3_8
 

 Merge pull request #96 from russHyde/scalar_bool_comparisons

fix a test that failed with strict boolean check-lengths 

 Do not freeze on empty files
 

 require readr >= 1.3.0 in DESCRIPTION
 

 with updated readr (1.3.0) fixes parsing errors

* Fixes #74
* Fixes #75
 

 vignette fixes
 

 fixes for updated MTseeker
 

 more documentation, more fixes, more correctness
 

 yet more fixes and coercion changes
 

 more tidying for BiocCheck and cleanup
 

 more fixes for documentation
 

 fix to examples in documentation
 

 more fixes! API is beginning to modernize
 

 bugfix
 

 Merge branch 'trunk' into devel
 

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 

 Update the way SingleCellExperiment is passed to computeSumFactors
 

 Remove merge conflict markers and bump version
 

 Fix indexing of introduction.
 

 description
 

 ViSEAGO 1.1 see NEWS for more informations