Merge recent changes to master to devel#108
Conversation
…ntical code is not erroring, testing to see if the other test will now run into bug
…ing used; the other did not have an impact in the output (coloring annotations)
One was in a function that was defunct, which was deleted; the other did not have an impact in the output (coloring annotations)
add Wiki section
Complete reformat of the celda package
Fix Bioconductor pheatmap import warning
Add installation instructions for R3.5 users and backward compatibility for results generated by older celda versions.
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R/celda_functions.R:94:1: style: Trailing whitespace is superfluous.
^~~~R/celda_functions.R:198:1: style: Trailing whitespace is superfluous.
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^~~~R/celda_functions.R:438:1: style: Trailing whitespace is superfluous.
^~~~R/celda_functions.R:448:1: style: Trailing whitespace is superfluous.
^~~~R/celda_G.R:428:49: style: Commas should always have a space after. nTSByC[prevY, ] <- nTSByC[prevY,] - counts[i, ]
^R/celda_G.R:432:47: style: Commas should always have a space after. nTSByC[y[i], ] <- nTSByC[y[i],] + counts[i, ]
^R/model_performance.R:28:1: style: Trailing whitespace is superfluous.
^~~~R/model_performance.R:35:1: style: Trailing whitespace is superfluous.
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^~~~R/RcppExports.R:4:1: style: Lines should not be more than 80 characters. cG_calcGibbsProbY_Simple <- function(counts, nGbyTS, nTSbyC, nbyTS, nbyG, y, L, index, gamma, beta, delta) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:5:1: style: Lines should not be more than 80 characters. .Call('_celda_cG_calcGibbsProbY_Simple', PACKAGE = 'celda', counts, nGbyTS, nTSbyC, nbyTS, nbyG, y, L, index, gamma, beta, delta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:5:11: style: Only use double-quotes. .Call('_celda_cG_calcGibbsProbY_Simple', PACKAGE = 'celda', counts, nGbyTS, nTSbyC, nbyTS, nbyG, y, L, index, gamma, beta, delta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:5:56: style: Only use double-quotes. .Call('_celda_cG_calcGibbsProbY_Simple', PACKAGE = 'celda', counts, nGbyTS, nTSbyC, nbyTS, nbyG, y, L, index, gamma, beta, delta)
^~~~~~~R/RcppExports.R:8:1: style: Lines should not be more than 80 characters. cG_CalcGibbsProbY <- function(index, counts, nTSbyC, nbyTS, nGbyTS, nbyG, y, L, nG, lg_beta, lg_gamma, lg_delta, delta) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:9:1: style: Lines should not be more than 80 characters. .Call('_celda_cG_CalcGibbsProbY', PACKAGE = 'celda', index, counts, nTSbyC, nbyTS, nGbyTS, nbyG, y, L, nG, lg_beta, lg_gamma, lg_delta, delta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:9:11: style: Only use double-quotes. .Call('_celda_cG_CalcGibbsProbY', PACKAGE = 'celda', index, counts, nTSbyC, nbyTS, nGbyTS, nbyG, y, L, nG, lg_beta, lg_gamma, lg_delta, delta)
^~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:9:49: style: Only use double-quotes. .Call('_celda_cG_CalcGibbsProbY', PACKAGE = 'celda', index, counts, nTSbyC, nbyTS, nGbyTS, nbyG, y, L, nG, lg_beta, lg_gamma, lg_delta, delta)
^~~~~~~R/RcppExports.R:13:3: style: Trailing whitespace is superfluous. #'
^R/RcppExports.R:18:11: style: Only use double-quotes. .Call('_celda_eigenMatMultInt', PACKAGE = 'celda', A, B)
^~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:18:47: style: Only use double-quotes. .Call('_celda_eigenMatMultInt', PACKAGE = 'celda', A, B)
^~~~~~~R/RcppExports.R:22:3: style: Trailing whitespace is superfluous. #'
^R/RcppExports.R:25:1: style: Lines should not be more than 80 characters. #' @return A numeric matrix where the columns have been normalized to proportions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:27:11: style: Only use double-quotes. .Call('_celda_fastNormProp', PACKAGE = 'celda', R_counts, R_alpha)
^~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:27:44: style: Only use double-quotes. .Call('_celda_fastNormProp', PACKAGE = 'celda', R_counts, R_alpha)
^~~~~~~R/RcppExports.R:31:3: style: Trailing whitespace is superfluous. #'
^R/RcppExports.R:34:1: style: Lines should not be more than 80 characters. #' @return A numeric matrix where the columns have been normalized to proportions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:36:11: style: Only use double-quotes. .Call('_celda_fastNormPropLog', PACKAGE = 'celda', R_counts, R_alpha)
^~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:36:47: style: Only use double-quotes. .Call('_celda_fastNormPropLog', PACKAGE = 'celda', R_counts, R_alpha)
^~~~~~~R/RcppExports.R:40:3: style: Trailing whitespace is superfluous. #'
^R/RcppExports.R:43:1: style: Lines should not be more than 80 characters. #' @return A numeric matrix where the columns have been normalized to proportions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:45:11: style: Only use double-quotes. .Call('_celda_fastNormPropSqrt', PACKAGE = 'celda', R_counts, R_alpha)
^~~~~~~~~~~~~~~~~~~~~~~~~R/RcppExports.R:45:48: style: Only use double-quotes. .Call('_celda_fastNormPropSqrt', PACKAGE = 'celda', R_counts, R_alpha)
^~~~~~~R/RcppExports.R:47:1: style: Trailing blank lines are superfluous.
^tests/testthat.R:1:22: style: Put spaces around all infix operators. Sys.setenv("R_TESTS" ="")
^~tests/testthat.R:4:1: style: Trailing blank lines are superfluous.
^tests/testthat/test-celda_C.R:180:13: style: Do not place spaces around code in parentheses or square brackets. to = ))
^tests/testthat/test-celda_CG.R:62:5: style: Opening curly braces should never go on their own line and should always be followed by a new line. {
^tests/testthat/test-celda_CG.R:156:1: style: Lines should not be more than 80 characters. # celdaCGresK5L10 <- subsetCeldaList(celdaCGres, params = list(K = 5, L = 10))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tests/testthat/test-celda_CG.R:241:13: style: Do not place spaces around code in parentheses or square brackets. to = ))
^tests/testthat/test-celda_CG.R:258:13: style: Do not place spaces around code in parentheses or square brackets. to = ))
^tests/testthat/test-celda_G.R:56:2: style: Trailing whitespace is superfluous. #
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^tests/testthat/test-celda_G.R:178:13: style: Do not place spaces around code in parentheses or square brackets. to = ))
^tests/testthat/test-celda_G.R:242:2: style: Trailing whitespace is superfluous. #
^tests/testthat/test-celda_G.R:248:2: style: Trailing whitespace is superfluous. #
^tests/testthat/test-celda_G.R:255:2: style: Trailing whitespace is superfluous. #
^tests/testthat/test-celda_G.R:350:2: style: Trailing whitespace is superfluous. #
^tests/testthat/test-recursiveSplit.R:5:2: style: Trailing whitespace is superfluous. #
^tests/testthat/test-recursiveSplit.R:30:2: style: Trailing whitespace is superfluous. #
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