Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-11 12:04 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 255/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BufferedMatrix 1.73.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: BufferedMatrix |
Version: 1.73.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.73.0.tar.gz |
StartedAt: 2025-10-10 20:25:41 -0400 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 20:26:32 -0400 (Fri, 10 Oct 2025) |
EllapsedTime: 50.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BufferedMatrix.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.73.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK * this is package ‘BufferedMatrix’ version ‘1.73.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BufferedMatrix’ can be installed ... WARNING Found the following significant warnings: doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] See ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.1.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup? 209 | $x^{power}$ elementwise of the matrix | ^ prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘Rcodetesting.R’ Running ‘c_code_level_tests.R’ Running ‘objectTesting.R’ Running ‘rawCalltesting.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’ for details.
BufferedMatrix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BufferedMatrix’ ... ** this is package ‘BufferedMatrix’ version ‘1.73.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] if (!(Matrix->readonly) & setting){ ^ ~ doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first if (!(Matrix->readonly) & setting){ ^ ( ) doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning if (!(Matrix->readonly) & setting){ ^ ( ) doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function] static int sort_double(const double *a1,const double *a2){ ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’ Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’ Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’ Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’ Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’ Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1)) Attaching package: 'BufferedMatrix' The following objects are masked from 'package:base': colMeans, colSums, rowMeans, rowSums Checking dimensions Rows: 5 Cols: 5 Buffer Rows: 1 Buffer Cols: 1 Assigning Values 0.000000 1.000000 2.000000 3.000000 4.000000 1.000000 2.000000 3.000000 4.000000 5.000000 2.000000 3.000000 4.000000 5.000000 6.000000 3.000000 4.000000 5.000000 6.000000 7.000000 4.000000 5.000000 6.000000 7.000000 8.000000 Adding Additional Column Checking dimensions Rows: 5 Cols: 6 Buffer Rows: 1 Buffer Cols: 1 0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 Reassigning values 1.000000 6.000000 11.000000 16.000000 21.000000 26.000000 2.000000 7.000000 12.000000 17.000000 22.000000 27.000000 3.000000 8.000000 13.000000 18.000000 23.000000 28.000000 4.000000 9.000000 14.000000 19.000000 24.000000 29.000000 5.000000 10.000000 15.000000 20.000000 25.000000 30.000000 Resizing Buffers Checking dimensions Rows: 5 Cols: 6 Buffer Rows: 3 Buffer Cols: 3 1.000000 6.000000 11.000000 16.000000 21.000000 26.000000 2.000000 7.000000 12.000000 17.000000 22.000000 27.000000 3.000000 8.000000 13.000000 18.000000 23.000000 28.000000 4.000000 9.000000 14.000000 19.000000 24.000000 29.000000 5.000000 10.000000 15.000000 20.000000 25.000000 30.000000 Activating Row Buffer In row mode: 1 1.000000 6.000000 11.000000 16.000000 21.000000 26.000000 2.000000 7.000000 12.000000 17.000000 22.000000 27.000000 3.000000 8.000000 13.000000 18.000000 23.000000 28.000000 4.000000 9.000000 14.000000 19.000000 24.000000 29.000000 5.000000 10.000000 15.000000 20.000000 25.000000 30.000000 Squaring Last Column 1.000000 6.000000 11.000000 16.000000 21.000000 676.000000 2.000000 7.000000 12.000000 17.000000 22.000000 729.000000 3.000000 8.000000 13.000000 18.000000 23.000000 784.000000 4.000000 9.000000 14.000000 19.000000 24.000000 841.000000 5.000000 10.000000 15.000000 20.000000 25.000000 900.000000 Square rooting Last Row, then turing off Row Buffer In row mode: 0 Checking on value that should be not be in column buffer2.236068 1.000000 6.000000 11.000000 16.000000 21.000000 676.000000 2.000000 7.000000 12.000000 17.000000 22.000000 729.000000 3.000000 8.000000 13.000000 18.000000 23.000000 784.000000 4.000000 9.000000 14.000000 19.000000 24.000000 841.000000 2.236068 3.162278 3.872983 4.472136 5.000000 30.000000 Single Indexing. Assign each value its square 1.000000 36.000000 121.000000 256.000000 441.000000 676.000000 4.000000 49.000000 144.000000 289.000000 484.000000 729.000000 9.000000 64.000000 169.000000 324.000000 529.000000 784.000000 16.000000 81.000000 196.000000 361.000000 576.000000 841.000000 25.000000 100.000000 225.000000 400.000000 625.000000 900.000000 Resizing Buffers Smaller Checking dimensions Rows: 5 Cols: 6 Buffer Rows: 1 Buffer Cols: 1 1.000000 36.000000 121.000000 256.000000 441.000000 676.000000 4.000000 49.000000 144.000000 289.000000 484.000000 729.000000 9.000000 64.000000 169.000000 324.000000 529.000000 784.000000 16.000000 81.000000 196.000000 361.000000 576.000000 841.000000 25.000000 100.000000 225.000000 400.000000 625.000000 900.000000 Activating Row Mode. Resizing Buffers Checking dimensions Rows: 5 Cols: 6 Buffer Rows: 1 Buffer Cols: 1 Activating ReadOnly Mode. The results of assignment is: 0 Printing matrix reversed. 900.000000 625.000000 400.000000 225.000000 100.000000 25.000000 841.000000 576.000000 361.000000 196.000000 81.000000 16.000000 784.000000 529.000000 324.000000 169.000000 64.000000 9.000000 729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000 676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000 [[1]] [1] 0 > > proc.time() user system elapsed 0.374 0.166 0.554
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths()); Attaching package: 'BufferedMatrix' The following objects are masked from 'package:base': colMeans, colSums, rowMeans, rowSums > > > ### this is used to control how many repetitions in something below > ### higher values result in more checks. > nreps <-100 ##20000 > > > ## test creation and some simple assignments and subsetting operations > > ## first on single elements > tmp <- createBufferedMatrix(1000,10) > > tmp[10,5] [1] 0 > tmp[10,5] <- 10 > tmp[10,5] [1] 10 > tmp[10,5] <- 12.445 > tmp[10,5] [1] 12.445 > > > > ## now testing accessing multiple elements > tmp2 <- createBufferedMatrix(10,20) > > > tmp2[3,1] <- 51.34 > tmp2[9,2] <- 9.87654 > tmp2[,1:2] [,1] [,2] [1,] 0.00 0.00000 [2,] 0.00 0.00000 [3,] 51.34 0.00000 [4,] 0.00 0.00000 [5,] 0.00 0.00000 [6,] 0.00 0.00000 [7,] 0.00 0.00000 [8,] 0.00 0.00000 [9,] 0.00 9.87654 [10,] 0.00 0.00000 > tmp2[,-(3:20)] [,1] [,2] [1,] 0.00 0.00000 [2,] 0.00 0.00000 [3,] 51.34 0.00000 [4,] 0.00 0.00000 [5,] 0.00 0.00000 [6,] 0.00 0.00000 [7,] 0.00 0.00000 [8,] 0.00 0.00000 [9,] 0.00 9.87654 [10,] 0.00 0.00000 > tmp2[3,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0 [,14] [,15] [,16] [,17] [,18] [,19] [,20] [1,] 0 0 0 0 0 0 0 > tmp2[-3,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 [2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 [3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 [4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 [5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 [6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 [7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 [8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0 [9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 [,14] [,15] [,16] [,17] [,18] [,19] [,20] [1,] 0 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 0 [8,] 0 0 0 0 0 0 0 [9,] 0 0 0 0 0 0 0 > tmp2[2,1:3] [,1] [,2] [,3] [1,] 0 0 0 > tmp2[3:9,1:3] [,1] [,2] [,3] [1,] 51.34 0.00000 0 [2,] 0.00 0.00000 0 [3,] 0.00 0.00000 0 [4,] 0.00 0.00000 0 [5,] 0.00 0.00000 0 [6,] 0.00 0.00000 0 [7,] 0.00 9.87654 0 > tmp2[-4,-4] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0 [2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0 [3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0 [4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0 [5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0 [6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0 [7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0 [8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0 [9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0 [,14] [,15] [,16] [,17] [,18] [,19] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 [8,] 0 0 0 0 0 0 [9,] 0 0 0 0 0 0 > > ## now testing accessing/assigning multiple elements > tmp3 <- createBufferedMatrix(10,10) > > for (i in 1:10){ + for (j in 1:10){ + tmp3[i,j] <- (j-1)*10 + i + } + } > > tmp3[2:4,2:4] [,1] [,2] [,3] [1,] 12 22 32 [2,] 13 23 33 [3,] 14 24 34 > tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [1,] 11 21 31 11 21 31 91 1 11 1 11 21 31 [2,] 12 22 32 12 22 32 92 2 12 2 12 22 32 [3,] 13 23 33 13 23 33 93 3 13 3 13 23 33 [4,] 14 24 34 14 24 34 94 4 14 4 14 24 34 [5,] 15 25 35 15 25 35 95 5 15 5 15 25 35 [6,] 16 26 36 16 26 36 96 6 16 6 16 26 36 [7,] 17 27 37 17 27 37 97 7 17 7 17 27 37 [8,] 18 28 38 18 28 38 98 8 18 8 18 28 38 [9,] 19 29 39 19 29 39 99 9 19 9 19 29 39 [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [1,] 41 51 61 71 81 91 91 81 71 61 51 41 [2,] 42 52 62 72 82 92 92 82 72 62 52 42 [3,] 43 53 63 73 83 93 93 83 73 63 53 43 [4,] 44 54 64 74 84 94 94 84 74 64 54 44 [5,] 45 55 65 75 85 95 95 85 75 65 55 45 [6,] 46 56 66 76 86 96 96 86 76 66 56 46 [7,] 47 57 67 77 87 97 97 87 77 67 57 47 [8,] 48 58 68 78 88 98 98 88 78 68 58 48 [9,] 49 59 69 79 89 99 99 89 79 69 59 49 [,26] [,27] [,28] [,29] [1,] 31 21 11 1 [2,] 32 22 12 2 [3,] 33 23 13 3 [4,] 34 24 14 4 [5,] 35 25 15 5 [6,] 36 26 16 6 [7,] 37 27 17 7 [8,] 38 28 18 8 [9,] 39 29 19 9 > tmp3[-c(1:5),-c(6:10)] [,1] [,2] [,3] [,4] [,5] [1,] 6 16 26 36 46 [2,] 7 17 27 37 47 [3,] 8 18 28 38 48 [4,] 9 19 29 39 49 [5,] 10 20 30 40 50 > > ## assignment of whole columns > tmp3[,1] <- c(1:10*100.0) > tmp3[,1:2] <- tmp3[,1:2]*100 > tmp3[,1:2] <- tmp3[,2:1] > tmp3[,1:2] [,1] [,2] [1,] 1100 1e+04 [2,] 1200 2e+04 [3,] 1300 3e+04 [4,] 1400 4e+04 [5,] 1500 5e+04 [6,] 1600 6e+04 [7,] 1700 7e+04 [8,] 1800 8e+04 [9,] 1900 9e+04 [10,] 2000 1e+05 > > > tmp3[,-1] <- tmp3[,1:9] > tmp3[,1:10] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 1100 1100 1e+04 21 31 41 51 61 71 81 [2,] 1200 1200 2e+04 22 32 42 52 62 72 82 [3,] 1300 1300 3e+04 23 33 43 53 63 73 83 [4,] 1400 1400 4e+04 24 34 44 54 64 74 84 [5,] 1500 1500 5e+04 25 35 45 55 65 75 85 [6,] 1600 1600 6e+04 26 36 46 56 66 76 86 [7,] 1700 1700 7e+04 27 37 47 57 67 77 87 [8,] 1800 1800 8e+04 28 38 48 58 68 78 88 [9,] 1900 1900 9e+04 29 39 49 59 69 79 89 [10,] 2000 2000 1e+05 30 40 50 60 70 80 90 > > tmp3[,1:2] <- rep(1,10) > tmp3[,1:2] <- rep(1,20) > tmp3[,1:2] <- matrix(c(1:5),1,5) > > tmp3[,-c(1:8)] <- matrix(c(1:5),1,5) > > tmp3[1,] <- 1:10 > tmp3[1,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 1 2 3 4 5 6 7 8 9 10 > tmp3[-1,] <- c(1,2) > tmp3[1:10,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 1 2 3 4 5 6 7 8 9 10 [2,] 1 2 1 2 1 2 1 2 1 2 [3,] 2 1 2 1 2 1 2 1 2 1 [4,] 1 2 1 2 1 2 1 2 1 2 [5,] 2 1 2 1 2 1 2 1 2 1 [6,] 1 2 1 2 1 2 1 2 1 2 [7,] 2 1 2 1 2 1 2 1 2 1 [8,] 1 2 1 2 1 2 1 2 1 2 [9,] 2 1 2 1 2 1 2 1 2 1 [10,] 1 2 1 2 1 2 1 2 1 2 > tmp3[-c(1:8),] <- matrix(c(1:5),1,5) > tmp3[1:10,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 1 2 3 4 5 6 7 8 9 10 [2,] 1 2 1 2 1 2 1 2 1 2 [3,] 2 1 2 1 2 1 2 1 2 1 [4,] 1 2 1 2 1 2 1 2 1 2 [5,] 2 1 2 1 2 1 2 1 2 1 [6,] 1 2 1 2 1 2 1 2 1 2 [7,] 2 1 2 1 2 1 2 1 2 1 [8,] 1 2 1 2 1 2 1 2 1 2 [9,] 1 3 5 2 4 1 3 5 2 4 [10,] 2 4 1 3 5 2 4 1 3 5 > > > tmp3[1:2,1:2] <- 5555.04 > tmp3[-(1:2),1:2] <- 1234.56789 > > > > ## testing accessors for the directory and prefix > directory(tmp3) [1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests" > prefix(tmp3) [1] "BM" > > ## testing if we can remove these objects > rm(tmp, tmp2, tmp3) > gc() used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) Ncells 480848 25.7 1056620 56.5 NA 634462 33.9 Vcells 891079 6.8 8388608 64.0 98304 2108714 16.1 > > > > > ## > ## checking reads > ## > > tmp2 <- createBufferedMatrix(10,20) > > test.sample <- rnorm(10*20) > > tmp2[1:10,1:20] <- test.sample > > test.matrix <- matrix(test.sample,10,20) > > ## testing reads > for (rep in 1:nreps){ + which.row <- sample(1:10,1) + which.col <- sample(1:20,1) + if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){ + cat("incorrect agreement") + break; + } + } > > > for (rep in 1:nreps){ + which.row <- sample(1:10,1) + if (!all(tmp2[which.row,] == test.matrix[which.row,])){ + cat("incorrect agreement") + break; + } + } > > > for (rep in 1:nreps){ + which.col <- sample(1:20,1) + if (!all(tmp2[,which.col] == test.matrix[,which.col])){ + cat("incorrect agreement") + break; + } + } > > > > for (rep in 1:nreps){ + which.col <- sample(1:10,5,replace=TRUE) + if (!all(tmp2[,which.col] == test.matrix[,which.col])){ + cat("incorrect agreement") + break; + } + } > > > date() [1] "Fri Oct 10 20:26:06 2025" > for (rep in 1:nreps){ + which.row <- sample(1:10,5,replace=TRUE) + if (!all(tmp2[which.row,] == test.matrix[which.row,])){ + cat("incorrect agreement") + break; + } + } > date() [1] "Fri Oct 10 20:26:06 2025" > > > for (rep in 1:nreps){ + which.row <- sample(1:10,5,replace=TRUE) + which.col <- sample(1:10,5,replace=TRUE) + if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){ + cat("incorrect agreement") + break; + } + } > > > > > > RowMode(tmp2) <pointer: 0x6000012ac000> > > > > for (rep in 1:nreps){ + which.row <- sample(1:10,1) + which.col <- sample(1:20,1) + if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){ + cat("incorrect agreement") + break; + } + } > > > for (rep in 1:nreps){ + which.row <- sample(1:10,1) + if (!all(tmp2[which.row,] == test.matrix[which.row,])){ + cat("incorrect agreement") + break; + } + } > > > for (rep in 1:nreps){ + which.col <- sample(1:20,1) + if (!all(tmp2[,which.col] == test.matrix[,which.col])){ + cat("incorrect agreement") + break; + } + } > > > > for (rep in 1:nreps){ + which.col <- sample(1:20,5,replace=TRUE) + if (!all(tmp2[,which.col] == test.matrix[,which.col])){ + cat("incorrect agreement") + break; + } + } > > > > for (rep in 1:nreps){ + which.row <- sample(1:10,5,replace=TRUE) + if (!all(tmp2[which.row,] == test.matrix[which.row,])){ + cat("incorrect agreement") + break; + } + } > > > date() [1] "Fri Oct 10 20:26:10 2025" > for (rep in 1:nreps){ + which.row <- sample(1:10,5,replace=TRUE) + which.col <- sample(1:20,5,replace=TRUE) + if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){ + cat("incorrect agreement") + break; + } + } > date() [1] "Fri Oct 10 20:26:12 2025" > > ColMode(tmp2) <pointer: 0x6000012ac000> > > > > ### Now testing assignments > > for (rep in 1:nreps){ + which.row <- sample(1:10,1) + + new.data <- rnorm(20) + tmp2[which.row,] <- new.data + test.matrix[which.row,] <- new.data + if (rep > 1){ + if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){ + cat("incorrect agreement") + break; + } + } + prev.row <- which.row + + } > > > > > > for (rep in 1:nreps){ + which.col <- sample(1:20,1) + new.data <- rnorm(10) + tmp2[,which.col] <- new.data + test.matrix[,which.col]<- new.data + + if (rep > 1){ + if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){ + cat("incorrect agreement") + break; + } + } + prev.col <- which.col + } > > > > > > for (rep in 1:nreps){ + which.col <- sample(1:20,5,replace=TRUE) + new.data <- matrix(rnorm(50),5,10) + tmp2[,which.col] <- new.data + test.matrix[,which.col]<- new.data + + if (rep > 1){ + if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){ + cat("incorrect agreement") + break; + } + } + prev.col <- which.col + } > > > > for (rep in 1:nreps){ + which.row <- sample(1:10,5,replace=TRUE) + new.data <- matrix(rnorm(50),5,10) + tmp2[which.row,] <- new.data + test.matrix[which.row,]<- new.data + + if (rep > 1){ + if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){ + cat("incorrect agreement") + break; + } + } + prev.row <- which.row + } > > > > > > for (rep in 1:nreps){ + which.row <- sample(1:10,5,replace=TRUE) + which.col <- sample(1:20,5,replace=TRUE) + new.data <- matrix(rnorm(25),5,5) + tmp2[which.row,which.col] <- new.data + test.matrix[which.row,which.col]<- new.data + + if (rep > 1){ + if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){ + cat("incorrect agreement") + break; + } + } + prev.row <- which.row + prev.col <- which.col + } > > > > > ### > ### > ### testing some more functions > ### > > > > ## duplication function > tmp5 <- duplicate(tmp2) > > # making sure really did copy everything. > tmp5[1,1] <- tmp5[1,1] +100.00 > > if (tmp5[1,1] == tmp2[1,1]){ + stop("Problem with duplication") + } > > > > > ### testing elementwise applying of functions > > tmp5[1:4,1:4] [,1] [,2] [,3] [,4] [1,] 100.054492161 -2.2055563 1.02042638 -0.4326305 [2,] -0.001394229 0.6393145 0.65209975 0.4051067 [3,] 1.090442903 -1.2408841 0.08846564 -1.8860308 [4,] -0.658228595 -0.2866305 -0.19753066 -0.4532851 > ewApply(tmp5,abs) BufferedMatrix object Matrix size: 10 20 Buffer size: 1 1 Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests Prefix: BM Mode: Col mode Read Only: FALSE Memory usage : 1.9 Kilobytes. Disk usage : 1.6 Kilobytes. > tmp5[1:4,1:4] [,1] [,2] [,3] [,4] [1,] 1.000545e+02 2.2055563 1.02042638 0.4326305 [2,] 1.394229e-03 0.6393145 0.65209975 0.4051067 [3,] 1.090443e+00 1.2408841 0.08846564 1.8860308 [4,] 6.582286e-01 0.2866305 0.19753066 0.4532851 > ewApply(tmp5,sqrt) BufferedMatrix object Matrix size: 10 20 Buffer size: 1 1 Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests Prefix: BM Mode: Col mode Read Only: FALSE Memory usage : 1.9 Kilobytes. Disk usage : 1.6 Kilobytes. > tmp5[1:4,1:4] [,1] [,2] [,3] [,4] [1,] 10.00272424 1.4851116 1.0101616 0.6577465 [2,] 0.03733937 0.7995714 0.8075269 0.6364800 [3,] 1.04424274 1.1139498 0.2974317 1.3733284 [4,] 0.81131288 0.5353789 0.4444442 0.6732645 > > my.function <- function(x,power){ + (x+5)^power + } > > ewApply(tmp5,my.function,power=2) BufferedMatrix object Matrix size: 10 20 Buffer size: 1 1 Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests Prefix: BM Mode: Col mode Read Only: FALSE Memory usage : 1.9 Kilobytes. Disk usage : 1.6 Kilobytes. > tmp5[1:4,1:4] [,1] [,2] [,3] [,4] [1,] 225.08173 42.05667 36.12204 32.01010 [2,] 25.37479 33.63503 33.72737 31.76991 [3,] 36.53287 37.38038 28.06278 40.61931 [4,] 33.77136 30.64042 29.64197 32.18593 > > > > ## testing functions that elementwise transform the matrix > sqrt(tmp5) <pointer: 0x6000012a8000> > exp(tmp5) <pointer: 0x6000012a8000> > log(tmp5,2) <pointer: 0x6000012a8000> > pow(tmp5,2) > > > > > > ## testing functions that apply to entire matrix > Max(tmp5) [1] 468.4781 > Min(tmp5) [1] 52.8143 > mean(tmp5) [1] 72.28286 > Sum(tmp5) [1] 14456.57 > Var(tmp5) [1] 868.2591 > > > ## testing functions applied to rows or columns > > rowMeans(tmp5) [1] 90.59199 71.44488 70.54063 69.57852 70.76386 69.36540 70.33739 73.60038 [9] 67.58401 69.02158 > rowSums(tmp5) [1] 1811.840 1428.898 1410.813 1391.570 1415.277 1387.308 1406.748 1472.008 [9] 1351.680 1380.432 > rowVars(tmp5) [1] 8009.37699 82.64009 77.51873 91.04153 98.75671 67.26805 [7] 50.98907 96.05362 59.21725 44.87249 > rowSd(tmp5) [1] 89.495123 9.090659 8.804472 9.541568 9.937641 8.201710 7.140663 [8] 9.800695 7.695274 6.698693 > rowMax(tmp5) [1] 468.47814 88.08544 84.54378 92.65718 89.11221 91.71363 81.67798 [8] 89.49452 81.27402 83.14395 > rowMin(tmp5) [1] 54.27614 52.81430 56.48477 56.18752 55.47744 55.07022 58.54884 56.05263 [9] 54.50615 56.43958 > > colMeans(tmp5) [1] 109.47032 74.76525 67.06379 72.62154 65.14744 70.67368 68.01533 [8] 74.16641 67.75651 68.64727 66.06092 76.46060 69.21105 71.00278 [15] 69.06332 64.76797 71.05217 71.02658 73.80335 74.88102 > colSums(tmp5) [1] 1094.7032 747.6525 670.6379 726.2154 651.4744 706.7368 680.1533 [8] 741.6641 677.5651 686.4727 660.6092 764.6060 692.1105 710.0278 [15] 690.6332 647.6797 710.5217 710.2658 738.0335 748.8102 > colVars(tmp5) [1] 16002.52580 43.18515 68.90415 80.37512 44.23841 111.53477 [7] 65.04158 66.19404 64.64558 132.46030 56.94208 27.05580 [13] 47.67848 63.29194 64.63705 43.20652 53.56701 44.00648 [19] 112.91471 148.40486 > colSd(tmp5) [1] 126.501090 6.571541 8.300852 8.965217 6.651196 10.561003 [7] 8.064836 8.135972 8.040248 11.509140 7.545998 5.201519 [13] 6.904960 7.955623 8.039717 6.573167 7.318949 6.633738 [19] 10.626134 12.182153 > colMax(tmp5) [1] 468.47814 87.53545 84.30026 84.90696 76.55528 87.33914 88.08544 [8] 85.67180 81.90352 89.49452 83.14395 82.98834 82.12095 87.54198 [15] 81.84846 77.82901 81.77200 79.71841 92.65718 91.71363 > colMin(tmp5) [1] 52.81430 63.77402 58.34043 63.27103 55.04487 54.27614 60.89762 59.73930 [9] 60.13992 55.07022 56.18752 68.88711 56.75628 59.32434 58.54884 54.50615 [17] 61.73871 62.78660 55.27262 56.05263 > > > ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default) > > > which.row <- sample(1:10,1,replace=TRUE) > which.col <- sample(1:20,1,replace=TRUE) > > tmp5[which.row,which.col] <- NA > > Max(tmp5) [1] NA > Min(tmp5) [1] NA > mean(tmp5) [1] NA > Sum(tmp5) [1] NA > Var(tmp5) [1] NA > > rowMeans(tmp5) [1] 90.59199 71.44488 70.54063 NA 70.76386 69.36540 70.33739 73.60038 [9] 67.58401 69.02158 > rowSums(tmp5) [1] 1811.840 1428.898 1410.813 NA 1415.277 1387.308 1406.748 1472.008 [9] 1351.680 1380.432 > rowVars(tmp5) [1] 8009.37699 82.64009 77.51873 92.77706 98.75671 67.26805 [7] 50.98907 96.05362 59.21725 44.87249 > rowSd(tmp5) [1] 89.495123 9.090659 8.804472 9.632085 9.937641 8.201710 7.140663 [8] 9.800695 7.695274 6.698693 > rowMax(tmp5) [1] 468.47814 88.08544 84.54378 NA 89.11221 91.71363 81.67798 [8] 89.49452 81.27402 83.14395 > rowMin(tmp5) [1] 54.27614 52.81430 56.48477 NA 55.47744 55.07022 58.54884 56.05263 [9] 54.50615 56.43958 > > colMeans(tmp5) [1] 109.47032 74.76525 67.06379 72.62154 65.14744 70.67368 68.01533 [8] 74.16641 67.75651 68.64727 66.06092 76.46060 69.21105 71.00278 [15] 69.06332 64.76797 71.05217 NA 73.80335 74.88102 > colSums(tmp5) [1] 1094.7032 747.6525 670.6379 726.2154 651.4744 706.7368 680.1533 [8] 741.6641 677.5651 686.4727 660.6092 764.6060 692.1105 710.0278 [15] 690.6332 647.6797 710.5217 NA 738.0335 748.8102 > colVars(tmp5) [1] 16002.52580 43.18515 68.90415 80.37512 44.23841 111.53477 [7] 65.04158 66.19404 64.64558 132.46030 56.94208 27.05580 [13] 47.67848 63.29194 64.63705 43.20652 53.56701 NA [19] 112.91471 148.40486 > colSd(tmp5) [1] 126.501090 6.571541 8.300852 8.965217 6.651196 10.561003 [7] 8.064836 8.135972 8.040248 11.509140 7.545998 5.201519 [13] 6.904960 7.955623 8.039717 6.573167 7.318949 NA [19] 10.626134 12.182153 > colMax(tmp5) [1] 468.47814 87.53545 84.30026 84.90696 76.55528 87.33914 88.08544 [8] 85.67180 81.90352 89.49452 83.14395 82.98834 82.12095 87.54198 [15] 81.84846 77.82901 81.77200 NA 92.65718 91.71363 > colMin(tmp5) [1] 52.81430 63.77402 58.34043 63.27103 55.04487 54.27614 60.89762 59.73930 [9] 60.13992 55.07022 56.18752 68.88711 56.75628 59.32434 58.54884 54.50615 [17] 61.73871 NA 55.27262 56.05263 > > Max(tmp5,na.rm=TRUE) [1] 468.4781 > Min(tmp5,na.rm=TRUE) [1] 52.8143 > mean(tmp5,na.rm=TRUE) [1] 72.25858 > Sum(tmp5,na.rm=TRUE) [1] 14379.46 > Var(tmp5,na.rm=TRUE) [1] 872.5257 > > rowMeans(tmp5,na.rm=TRUE) [1] 90.59199 71.44488 70.54063 69.18182 70.76386 69.36540 70.33739 73.60038 [9] 67.58401 69.02158 > rowSums(tmp5,na.rm=TRUE) [1] 1811.840 1428.898 1410.813 1314.455 1415.277 1387.308 1406.748 1472.008 [9] 1351.680 1380.432 > rowVars(tmp5,na.rm=TRUE) [1] 8009.37699 82.64009 77.51873 92.77706 98.75671 67.26805 [7] 50.98907 96.05362 59.21725 44.87249 > rowSd(tmp5,na.rm=TRUE) [1] 89.495123 9.090659 8.804472 9.632085 9.937641 8.201710 7.140663 [8] 9.800695 7.695274 6.698693 > rowMax(tmp5,na.rm=TRUE) [1] 468.47814 88.08544 84.54378 92.65718 89.11221 91.71363 81.67798 [8] 89.49452 81.27402 83.14395 > rowMin(tmp5,na.rm=TRUE) [1] 54.27614 52.81430 56.48477 56.18752 55.47744 55.07022 58.54884 56.05263 [9] 54.50615 56.43958 > > colMeans(tmp5,na.rm=TRUE) [1] 109.47032 74.76525 67.06379 72.62154 65.14744 70.67368 68.01533 [8] 74.16641 67.75651 68.64727 66.06092 76.46060 69.21105 71.00278 [15] 69.06332 64.76797 71.05217 70.34999 73.80335 74.88102 > colSums(tmp5,na.rm=TRUE) [1] 1094.7032 747.6525 670.6379 726.2154 651.4744 706.7368 680.1533 [8] 741.6641 677.5651 686.4727 660.6092 764.6060 692.1105 710.0278 [15] 690.6332 647.6797 710.5217 633.1499 738.0335 748.8102 > colVars(tmp5,na.rm=TRUE) [1] 16002.52580 43.18515 68.90415 80.37512 44.23841 111.53477 [7] 65.04158 66.19404 64.64558 132.46030 56.94208 27.05580 [13] 47.67848 63.29194 64.63705 43.20652 53.56701 44.35734 [19] 112.91471 148.40486 > colSd(tmp5,na.rm=TRUE) [1] 126.501090 6.571541 8.300852 8.965217 6.651196 10.561003 [7] 8.064836 8.135972 8.040248 11.509140 7.545998 5.201519 [13] 6.904960 7.955623 8.039717 6.573167 7.318949 6.660130 [19] 10.626134 12.182153 > colMax(tmp5,na.rm=TRUE) [1] 468.47814 87.53545 84.30026 84.90696 76.55528 87.33914 88.08544 [8] 85.67180 81.90352 89.49452 83.14395 82.98834 82.12095 87.54198 [15] 81.84846 77.82901 81.77200 79.71841 92.65718 91.71363 > colMin(tmp5,na.rm=TRUE) [1] 52.81430 63.77402 58.34043 63.27103 55.04487 54.27614 60.89762 59.73930 [9] 60.13992 55.07022 56.18752 68.88711 56.75628 59.32434 58.54884 54.50615 [17] 61.73871 62.78660 55.27262 56.05263 > > # now set an entire row to NA > > tmp5[which.row,] <- NA > rowMeans(tmp5,na.rm=TRUE) [1] 90.59199 71.44488 70.54063 NaN 70.76386 69.36540 70.33739 73.60038 [9] 67.58401 69.02158 > rowSums(tmp5,na.rm=TRUE) [1] 1811.840 1428.898 1410.813 0.000 1415.277 1387.308 1406.748 1472.008 [9] 1351.680 1380.432 > rowVars(tmp5,na.rm=TRUE) [1] 8009.37699 82.64009 77.51873 NA 98.75671 67.26805 [7] 50.98907 96.05362 59.21725 44.87249 > rowSd(tmp5,na.rm=TRUE) [1] 89.495123 9.090659 8.804472 NA 9.937641 8.201710 7.140663 [8] 9.800695 7.695274 6.698693 > rowMax(tmp5,na.rm=TRUE) [1] 468.47814 88.08544 84.54378 NA 89.11221 91.71363 81.67798 [8] 89.49452 81.27402 83.14395 > rowMin(tmp5,na.rm=TRUE) [1] 54.27614 52.81430 56.48477 NA 55.47744 55.07022 58.54884 56.05263 [9] 54.50615 56.43958 > > > # now set an entire col to NA > > > tmp5[,which.col] <- NA > colMeans(tmp5,na.rm=TRUE) [1] 113.82362 75.98649 67.66022 73.24718 65.38888 68.82196 68.02881 [8] 74.23709 68.60280 69.41495 67.15797 77.28582 69.65591 70.75852 [15] 70.04544 64.81122 69.86108 NaN 71.70848 74.82051 > colSums(tmp5,na.rm=TRUE) [1] 1024.4126 683.8784 608.9420 659.2246 588.4999 619.3976 612.2593 [8] 668.1338 617.4252 624.7345 604.4217 695.5724 626.9032 636.8267 [15] 630.4090 583.3010 628.7497 0.0000 645.3764 673.3846 > colVars(tmp5,na.rm=TRUE) [1] 17789.64063 31.80453 73.51517 86.01849 49.11242 86.90193 [7] 73.16973 74.41210 64.66901 142.38794 50.52038 22.77673 [13] 51.41188 70.53223 61.86529 48.58630 44.30251 NA [19] 77.65866 166.91429 > colSd(tmp5,na.rm=TRUE) [1] 133.377812 5.639551 8.574099 9.274615 7.008026 9.322121 [7] 8.553931 8.626245 8.041704 11.932642 7.107769 4.772497 [13] 7.170208 8.398347 7.865449 6.970387 6.656013 NA [19] 8.812415 12.919531 > colMax(tmp5,na.rm=TRUE) [1] 468.47814 87.53545 84.30026 84.90696 76.55528 81.05375 88.08544 [8] 85.67180 81.90352 89.49452 83.14395 82.98834 82.12095 87.54198 [15] 81.84846 77.82901 81.07550 -Inf 83.68980 91.71363 > colMin(tmp5,na.rm=TRUE) [1] 52.81430 70.00691 58.34043 63.27103 55.04487 54.27614 60.89762 59.73930 [9] 61.03690 55.07022 60.74250 68.88711 56.75628 59.32434 58.54884 54.50615 [17] 61.73871 Inf 55.27262 56.05263 > > > > > copymatrix <- matrix(rnorm(200,150,15),10,20) > > tmp5[1:10,1:20] <- copymatrix > which.row <- 3 > which.col <- 1 > cat(which.row," ",which.col,"\n") 3 1 > tmp5[which.row,which.col] <- NA > copymatrix[which.row,which.col] <- NA > > rowVars(tmp5,na.rm=TRUE) [1] 390.7986 375.5453 186.3528 184.6971 158.4866 127.4261 269.5802 148.6598 [9] 166.1448 317.0698 > apply(copymatrix,1,var,na.rm=TRUE) [1] 390.7986 375.5453 186.3528 184.6971 158.4866 127.4261 269.5802 148.6598 [9] 166.1448 317.0698 > > > > copymatrix <- matrix(rnorm(200,150,15),10,20) > > tmp5[1:10,1:20] <- copymatrix > which.row <- 1 > which.col <- 3 > cat(which.row," ",which.col,"\n") 1 3 > tmp5[which.row,which.col] <- NA > copymatrix[which.row,which.col] <- NA > > colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE) [1] -5.684342e-14 -1.136868e-13 -5.684342e-14 0.000000e+00 -1.136868e-13 [6] 2.842171e-13 -1.136868e-13 -2.842171e-14 -8.526513e-14 -5.684342e-14 [11] -8.526513e-14 0.000000e+00 -8.526513e-14 0.000000e+00 0.000000e+00 [16] -5.684342e-14 0.000000e+00 -1.136868e-13 -2.842171e-14 5.684342e-14 > > > > > > > > > > > ## making sure these things agree > ## > ## first when there is no NA > > > > agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){ + + if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){ + stop("No agreement in Max") + } + + + if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){ + stop("No agreement in Min") + } + + + if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){ + + cat(Sum(buff.matrix,na.rm=TRUE),"\n") + cat(sum(r.matrix,na.rm=TRUE),"\n") + cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n") + + stop("No agreement in Sum") + } + + if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){ + stop("No agreement in mean") + } + + + if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){ + stop("No agreement in Var") + } + + + + if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in rowMeans") + } + + + if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){ + stop("No agreement in colMeans") + } + + + if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){ + stop("No agreement in rowSums") + } + + + if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){ + stop("No agreement in colSums") + } + + ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when + ### computing variance + my.Var <- function(x,na.rm=FALSE){ + if (all(is.na(x))){ + return(NA) + } else { + var(x,na.rm=na.rm) + } + + } + + if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in rowVars") + } + + + if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in rowVars") + } + + + if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in colMax") + } + + + if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in colMax") + } + + + + if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in colMin") + } + + + if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in colMin") + } + + if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in colMedian") + } + + if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){ + stop("No agreement in colRanges") + } + + + + } > > > > > > > > > > for (rep in 1:20){ + copymatrix <- matrix(rnorm(200,150,15),10,20) + + tmp5[1:10,1:20] <- copymatrix + + + agree.checks(tmp5,copymatrix) + + ## now lets assign some NA values and check agreement + + which.row <- sample(1:10,1,replace=TRUE) + which.col <- sample(1:20,1,replace=TRUE) + + cat(which.row," ",which.col,"\n") + + tmp5[which.row,which.col] <- NA + copymatrix[which.row,which.col] <- NA + + agree.checks(tmp5,copymatrix) + + ## make an entire row NA + tmp5[which.row,] <- NA + copymatrix[which.row,] <- NA + + + agree.checks(tmp5,copymatrix) + + ### also make an entire col NA + tmp5[,which.col] <- NA + copymatrix[,which.col] <- NA + + agree.checks(tmp5,copymatrix) + + ### now make 1 element non NA with NA in the rest of row and column + + tmp5[which.row,which.col] <- rnorm(1,150,15) + copymatrix[which.row,which.col] <- tmp5[which.row,which.col] + + agree.checks(tmp5,copymatrix) + } 10 17 10 1 7 4 6 5 5 17 4 20 2 2 1 5 5 10 9 20 8 10 7 4 9 14 5 11 10 9 1 16 1 11 6 13 5 9 4 3 There were 50 or more warnings (use warnings() to see the first 50) > > > ### now test 1 by n and n by 1 matrix > > > err.tol <- 1e-12 > > rm(tmp5) > > dataset1 <- rnorm(100) > dataset2 <- rnorm(100) > > tmp <- createBufferedMatrix(1,100) > tmp[1,] <- dataset1 > > tmp2 <- createBufferedMatrix(100,1) > tmp2[,1] <- dataset2 > > > > > > Max(tmp) [1] 3.179357 > Min(tmp) [1] -2.28282 > mean(tmp) [1] 0.1385766 > Sum(tmp) [1] 13.85766 > Var(tmp) [1] 1.104985 > > rowMeans(tmp) [1] 0.1385766 > rowSums(tmp) [1] 13.85766 > rowVars(tmp) [1] 1.104985 > rowSd(tmp) [1] 1.051183 > rowMax(tmp) [1] 3.179357 > rowMin(tmp) [1] -2.28282 > > colMeans(tmp) [1] 0.291327650 0.415696406 0.770555946 -1.012300987 0.517747013 [6] -0.024367350 -0.191397030 -0.984518338 -0.775120936 -0.375123502 [11] -0.429706795 -1.267580006 1.909579231 0.266233419 -0.737653855 [16] 0.998183977 1.073990731 0.487334485 0.687848591 -0.240367457 [21] -1.335937260 0.943776817 0.665780795 -0.002758145 -1.462610126 [26] -2.133369170 -0.554625566 0.598433320 -0.078865241 0.332644926 [31] 1.245133651 -0.252507585 1.762548841 -0.914382941 0.876735352 [36] -0.054545347 1.389157463 0.116110400 -0.086892879 -0.348204354 [41] 1.746354172 -0.271294960 -0.135224916 -0.449332332 -0.300558500 [46] 1.869744665 0.422542870 0.343910614 2.518821622 -0.348473920 [51] 2.068302283 0.175088202 0.889384903 -0.510246993 -2.282820270 [56] 0.696725380 1.362237677 0.519336187 -2.056455597 0.374541201 [61] 0.640532103 -0.636588914 3.179356630 -0.474145180 -0.006883002 [66] -1.398531582 -0.651014600 0.303122595 0.109097326 -1.164090850 [71] 1.194714377 0.442297604 -0.247389835 -1.686112386 -0.672208751 [76] -0.114011451 1.462872389 -0.692486363 -0.632558956 0.307464659 [81] -1.154077578 -1.915223189 0.924588940 0.171686329 0.042795958 [86] 0.920381738 1.095137866 0.931580997 0.650889313 -0.903135047 [91] 1.623796293 0.175403865 0.750723129 0.742803019 -0.755243724 [96] 0.343600614 0.221449913 3.009607068 0.207246387 -1.208351160 > colSums(tmp) [1] 0.291327650 0.415696406 0.770555946 -1.012300987 0.517747013 [6] -0.024367350 -0.191397030 -0.984518338 -0.775120936 -0.375123502 [11] -0.429706795 -1.267580006 1.909579231 0.266233419 -0.737653855 [16] 0.998183977 1.073990731 0.487334485 0.687848591 -0.240367457 [21] -1.335937260 0.943776817 0.665780795 -0.002758145 -1.462610126 [26] -2.133369170 -0.554625566 0.598433320 -0.078865241 0.332644926 [31] 1.245133651 -0.252507585 1.762548841 -0.914382941 0.876735352 [36] -0.054545347 1.389157463 0.116110400 -0.086892879 -0.348204354 [41] 1.746354172 -0.271294960 -0.135224916 -0.449332332 -0.300558500 [46] 1.869744665 0.422542870 0.343910614 2.518821622 -0.348473920 [51] 2.068302283 0.175088202 0.889384903 -0.510246993 -2.282820270 [56] 0.696725380 1.362237677 0.519336187 -2.056455597 0.374541201 [61] 0.640532103 -0.636588914 3.179356630 -0.474145180 -0.006883002 [66] -1.398531582 -0.651014600 0.303122595 0.109097326 -1.164090850 [71] 1.194714377 0.442297604 -0.247389835 -1.686112386 -0.672208751 [76] -0.114011451 1.462872389 -0.692486363 -0.632558956 0.307464659 [81] -1.154077578 -1.915223189 0.924588940 0.171686329 0.042795958 [86] 0.920381738 1.095137866 0.931580997 0.650889313 -0.903135047 [91] 1.623796293 0.175403865 0.750723129 0.742803019 -0.755243724 [96] 0.343600614 0.221449913 3.009607068 0.207246387 -1.208351160 > colVars(tmp) [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > colSd(tmp) [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > colMax(tmp) [1] 0.291327650 0.415696406 0.770555946 -1.012300987 0.517747013 [6] -0.024367350 -0.191397030 -0.984518338 -0.775120936 -0.375123502 [11] -0.429706795 -1.267580006 1.909579231 0.266233419 -0.737653855 [16] 0.998183977 1.073990731 0.487334485 0.687848591 -0.240367457 [21] -1.335937260 0.943776817 0.665780795 -0.002758145 -1.462610126 [26] -2.133369170 -0.554625566 0.598433320 -0.078865241 0.332644926 [31] 1.245133651 -0.252507585 1.762548841 -0.914382941 0.876735352 [36] -0.054545347 1.389157463 0.116110400 -0.086892879 -0.348204354 [41] 1.746354172 -0.271294960 -0.135224916 -0.449332332 -0.300558500 [46] 1.869744665 0.422542870 0.343910614 2.518821622 -0.348473920 [51] 2.068302283 0.175088202 0.889384903 -0.510246993 -2.282820270 [56] 0.696725380 1.362237677 0.519336187 -2.056455597 0.374541201 [61] 0.640532103 -0.636588914 3.179356630 -0.474145180 -0.006883002 [66] -1.398531582 -0.651014600 0.303122595 0.109097326 -1.164090850 [71] 1.194714377 0.442297604 -0.247389835 -1.686112386 -0.672208751 [76] -0.114011451 1.462872389 -0.692486363 -0.632558956 0.307464659 [81] -1.154077578 -1.915223189 0.924588940 0.171686329 0.042795958 [86] 0.920381738 1.095137866 0.931580997 0.650889313 -0.903135047 [91] 1.623796293 0.175403865 0.750723129 0.742803019 -0.755243724 [96] 0.343600614 0.221449913 3.009607068 0.207246387 -1.208351160 > colMin(tmp) [1] 0.291327650 0.415696406 0.770555946 -1.012300987 0.517747013 [6] -0.024367350 -0.191397030 -0.984518338 -0.775120936 -0.375123502 [11] -0.429706795 -1.267580006 1.909579231 0.266233419 -0.737653855 [16] 0.998183977 1.073990731 0.487334485 0.687848591 -0.240367457 [21] -1.335937260 0.943776817 0.665780795 -0.002758145 -1.462610126 [26] -2.133369170 -0.554625566 0.598433320 -0.078865241 0.332644926 [31] 1.245133651 -0.252507585 1.762548841 -0.914382941 0.876735352 [36] -0.054545347 1.389157463 0.116110400 -0.086892879 -0.348204354 [41] 1.746354172 -0.271294960 -0.135224916 -0.449332332 -0.300558500 [46] 1.869744665 0.422542870 0.343910614 2.518821622 -0.348473920 [51] 2.068302283 0.175088202 0.889384903 -0.510246993 -2.282820270 [56] 0.696725380 1.362237677 0.519336187 -2.056455597 0.374541201 [61] 0.640532103 -0.636588914 3.179356630 -0.474145180 -0.006883002 [66] -1.398531582 -0.651014600 0.303122595 0.109097326 -1.164090850 [71] 1.194714377 0.442297604 -0.247389835 -1.686112386 -0.672208751 [76] -0.114011451 1.462872389 -0.692486363 -0.632558956 0.307464659 [81] -1.154077578 -1.915223189 0.924588940 0.171686329 0.042795958 [86] 0.920381738 1.095137866 0.931580997 0.650889313 -0.903135047 [91] 1.623796293 0.175403865 0.750723129 0.742803019 -0.755243724 [96] 0.343600614 0.221449913 3.009607068 0.207246387 -1.208351160 > colMedians(tmp) [1] 0.291327650 0.415696406 0.770555946 -1.012300987 0.517747013 [6] -0.024367350 -0.191397030 -0.984518338 -0.775120936 -0.375123502 [11] -0.429706795 -1.267580006 1.909579231 0.266233419 -0.737653855 [16] 0.998183977 1.073990731 0.487334485 0.687848591 -0.240367457 [21] -1.335937260 0.943776817 0.665780795 -0.002758145 -1.462610126 [26] -2.133369170 -0.554625566 0.598433320 -0.078865241 0.332644926 [31] 1.245133651 -0.252507585 1.762548841 -0.914382941 0.876735352 [36] -0.054545347 1.389157463 0.116110400 -0.086892879 -0.348204354 [41] 1.746354172 -0.271294960 -0.135224916 -0.449332332 -0.300558500 [46] 1.869744665 0.422542870 0.343910614 2.518821622 -0.348473920 [51] 2.068302283 0.175088202 0.889384903 -0.510246993 -2.282820270 [56] 0.696725380 1.362237677 0.519336187 -2.056455597 0.374541201 [61] 0.640532103 -0.636588914 3.179356630 -0.474145180 -0.006883002 [66] -1.398531582 -0.651014600 0.303122595 0.109097326 -1.164090850 [71] 1.194714377 0.442297604 -0.247389835 -1.686112386 -0.672208751 [76] -0.114011451 1.462872389 -0.692486363 -0.632558956 0.307464659 [81] -1.154077578 -1.915223189 0.924588940 0.171686329 0.042795958 [86] 0.920381738 1.095137866 0.931580997 0.650889313 -0.903135047 [91] 1.623796293 0.175403865 0.750723129 0.742803019 -0.755243724 [96] 0.343600614 0.221449913 3.009607068 0.207246387 -1.208351160 > colRanges(tmp) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 0.2913277 0.4156964 0.7705559 -1.012301 0.517747 -0.02436735 -0.191397 [2,] 0.2913277 0.4156964 0.7705559 -1.012301 0.517747 -0.02436735 -0.191397 [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,] -0.9845183 -0.7751209 -0.3751235 -0.4297068 -1.26758 1.909579 0.2662334 [2,] -0.9845183 -0.7751209 -0.3751235 -0.4297068 -1.26758 1.909579 0.2662334 [,15] [,16] [,17] [,18] [,19] [,20] [,21] [1,] -0.7376539 0.998184 1.073991 0.4873345 0.6878486 -0.2403675 -1.335937 [2,] -0.7376539 0.998184 1.073991 0.4873345 0.6878486 -0.2403675 -1.335937 [,22] [,23] [,24] [,25] [,26] [,27] [,28] [1,] 0.9437768 0.6657808 -0.002758145 -1.46261 -2.133369 -0.5546256 0.5984333 [2,] 0.9437768 0.6657808 -0.002758145 -1.46261 -2.133369 -0.5546256 0.5984333 [,29] [,30] [,31] [,32] [,33] [,34] [,35] [1,] -0.07886524 0.3326449 1.245134 -0.2525076 1.762549 -0.9143829 0.8767354 [2,] -0.07886524 0.3326449 1.245134 -0.2525076 1.762549 -0.9143829 0.8767354 [,36] [,37] [,38] [,39] [,40] [,41] [,42] [1,] -0.05454535 1.389157 0.1161104 -0.08689288 -0.3482044 1.746354 -0.271295 [2,] -0.05454535 1.389157 0.1161104 -0.08689288 -0.3482044 1.746354 -0.271295 [,43] [,44] [,45] [,46] [,47] [,48] [,49] [1,] -0.1352249 -0.4493323 -0.3005585 1.869745 0.4225429 0.3439106 2.518822 [2,] -0.1352249 -0.4493323 -0.3005585 1.869745 0.4225429 0.3439106 2.518822 [,50] [,51] [,52] [,53] [,54] [,55] [,56] [1,] -0.3484739 2.068302 0.1750882 0.8893849 -0.510247 -2.28282 0.6967254 [2,] -0.3484739 2.068302 0.1750882 0.8893849 -0.510247 -2.28282 0.6967254 [,57] [,58] [,59] [,60] [,61] [,62] [,63] [1,] 1.362238 0.5193362 -2.056456 0.3745412 0.6405321 -0.6365889 3.179357 [2,] 1.362238 0.5193362 -2.056456 0.3745412 0.6405321 -0.6365889 3.179357 [,64] [,65] [,66] [,67] [,68] [,69] [,70] [1,] -0.4741452 -0.006883002 -1.398532 -0.6510146 0.3031226 0.1090973 -1.164091 [2,] -0.4741452 -0.006883002 -1.398532 -0.6510146 0.3031226 0.1090973 -1.164091 [,71] [,72] [,73] [,74] [,75] [,76] [,77] [1,] 1.194714 0.4422976 -0.2473898 -1.686112 -0.6722088 -0.1140115 1.462872 [2,] 1.194714 0.4422976 -0.2473898 -1.686112 -0.6722088 -0.1140115 1.462872 [,78] [,79] [,80] [,81] [,82] [,83] [,84] [1,] -0.6924864 -0.632559 0.3074647 -1.154078 -1.915223 0.9245889 0.1716863 [2,] -0.6924864 -0.632559 0.3074647 -1.154078 -1.915223 0.9245889 0.1716863 [,85] [,86] [,87] [,88] [,89] [,90] [,91] [1,] 0.04279596 0.9203817 1.095138 0.931581 0.6508893 -0.903135 1.623796 [2,] 0.04279596 0.9203817 1.095138 0.931581 0.6508893 -0.903135 1.623796 [,92] [,93] [,94] [,95] [,96] [,97] [,98] [1,] 0.1754039 0.7507231 0.742803 -0.7552437 0.3436006 0.2214499 3.009607 [2,] 0.1754039 0.7507231 0.742803 -0.7552437 0.3436006 0.2214499 3.009607 [,99] [,100] [1,] 0.2072464 -1.208351 [2,] 0.2072464 -1.208351 > > > Max(tmp2) [1] 2.67319 > Min(tmp2) [1] -2.102804 > mean(tmp2) [1] 0.05120803 > Sum(tmp2) [1] 5.120803 > Var(tmp2) [1] 1.044543 > > rowMeans(tmp2) [1] 0.661544190 1.663757684 1.881619553 -0.437414589 0.216803502 [6] 1.212399623 1.462617075 -0.219386846 -0.608324649 -0.734519838 [11] 1.534066387 -0.688178934 0.760276496 -1.958587746 0.399681666 [16] -0.425206832 1.005604468 -0.016900204 1.473734112 0.231407523 [21] 0.704561568 2.360736100 0.586244433 0.771874431 -1.516631566 [26] -0.076827875 1.684654750 1.637424778 -0.209934960 0.548068216 [31] 0.226148680 0.144289833 -0.246323538 1.366983492 1.491361033 [36] -0.828953455 -1.071860881 -0.905766107 -1.391752978 1.522094254 [41] 0.242403756 -0.328600802 0.737258666 0.743228744 -0.096143996 [46] 0.492054407 -1.106157687 0.036136357 -0.336634931 0.901205381 [51] -0.228474331 -1.061475715 -1.373165564 -1.058296518 -1.887671179 [56] 0.740478064 -0.647466824 0.441863432 0.051072444 1.113292911 [61] -0.560578464 -0.821982662 -1.925451899 -0.743415253 -0.004431287 [66] -0.011805785 -0.656299641 1.162901156 -1.816539023 1.182795549 [71] -0.700543805 0.348066514 -0.884583994 0.380417631 -1.596145608 [76] 0.749900146 2.673189647 -1.185495000 0.054179173 -0.207625186 [81] 1.175751633 -0.040806534 0.090428099 0.540619112 0.693225261 [86] -0.756039091 -1.227543654 0.167909399 -0.575835860 0.226478936 [91] -1.749894762 1.126315581 -1.103799771 -0.559174590 0.114353547 [96] 0.264307036 0.563644133 -2.102803899 0.436929016 0.813897242 > rowSums(tmp2) [1] 0.661544190 1.663757684 1.881619553 -0.437414589 0.216803502 [6] 1.212399623 1.462617075 -0.219386846 -0.608324649 -0.734519838 [11] 1.534066387 -0.688178934 0.760276496 -1.958587746 0.399681666 [16] -0.425206832 1.005604468 -0.016900204 1.473734112 0.231407523 [21] 0.704561568 2.360736100 0.586244433 0.771874431 -1.516631566 [26] -0.076827875 1.684654750 1.637424778 -0.209934960 0.548068216 [31] 0.226148680 0.144289833 -0.246323538 1.366983492 1.491361033 [36] -0.828953455 -1.071860881 -0.905766107 -1.391752978 1.522094254 [41] 0.242403756 -0.328600802 0.737258666 0.743228744 -0.096143996 [46] 0.492054407 -1.106157687 0.036136357 -0.336634931 0.901205381 [51] -0.228474331 -1.061475715 -1.373165564 -1.058296518 -1.887671179 [56] 0.740478064 -0.647466824 0.441863432 0.051072444 1.113292911 [61] -0.560578464 -0.821982662 -1.925451899 -0.743415253 -0.004431287 [66] -0.011805785 -0.656299641 1.162901156 -1.816539023 1.182795549 [71] -0.700543805 0.348066514 -0.884583994 0.380417631 -1.596145608 [76] 0.749900146 2.673189647 -1.185495000 0.054179173 -0.207625186 [81] 1.175751633 -0.040806534 0.090428099 0.540619112 0.693225261 [86] -0.756039091 -1.227543654 0.167909399 -0.575835860 0.226478936 [91] -1.749894762 1.126315581 -1.103799771 -0.559174590 0.114353547 [96] 0.264307036 0.563644133 -2.102803899 0.436929016 0.813897242 > rowVars(tmp2) [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > rowSd(tmp2) [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > rowMax(tmp2) [1] 0.661544190 1.663757684 1.881619553 -0.437414589 0.216803502 [6] 1.212399623 1.462617075 -0.219386846 -0.608324649 -0.734519838 [11] 1.534066387 -0.688178934 0.760276496 -1.958587746 0.399681666 [16] -0.425206832 1.005604468 -0.016900204 1.473734112 0.231407523 [21] 0.704561568 2.360736100 0.586244433 0.771874431 -1.516631566 [26] -0.076827875 1.684654750 1.637424778 -0.209934960 0.548068216 [31] 0.226148680 0.144289833 -0.246323538 1.366983492 1.491361033 [36] -0.828953455 -1.071860881 -0.905766107 -1.391752978 1.522094254 [41] 0.242403756 -0.328600802 0.737258666 0.743228744 -0.096143996 [46] 0.492054407 -1.106157687 0.036136357 -0.336634931 0.901205381 [51] -0.228474331 -1.061475715 -1.373165564 -1.058296518 -1.887671179 [56] 0.740478064 -0.647466824 0.441863432 0.051072444 1.113292911 [61] -0.560578464 -0.821982662 -1.925451899 -0.743415253 -0.004431287 [66] -0.011805785 -0.656299641 1.162901156 -1.816539023 1.182795549 [71] -0.700543805 0.348066514 -0.884583994 0.380417631 -1.596145608 [76] 0.749900146 2.673189647 -1.185495000 0.054179173 -0.207625186 [81] 1.175751633 -0.040806534 0.090428099 0.540619112 0.693225261 [86] -0.756039091 -1.227543654 0.167909399 -0.575835860 0.226478936 [91] -1.749894762 1.126315581 -1.103799771 -0.559174590 0.114353547 [96] 0.264307036 0.563644133 -2.102803899 0.436929016 0.813897242 > rowMin(tmp2) [1] 0.661544190 1.663757684 1.881619553 -0.437414589 0.216803502 [6] 1.212399623 1.462617075 -0.219386846 -0.608324649 -0.734519838 [11] 1.534066387 -0.688178934 0.760276496 -1.958587746 0.399681666 [16] -0.425206832 1.005604468 -0.016900204 1.473734112 0.231407523 [21] 0.704561568 2.360736100 0.586244433 0.771874431 -1.516631566 [26] -0.076827875 1.684654750 1.637424778 -0.209934960 0.548068216 [31] 0.226148680 0.144289833 -0.246323538 1.366983492 1.491361033 [36] -0.828953455 -1.071860881 -0.905766107 -1.391752978 1.522094254 [41] 0.242403756 -0.328600802 0.737258666 0.743228744 -0.096143996 [46] 0.492054407 -1.106157687 0.036136357 -0.336634931 0.901205381 [51] -0.228474331 -1.061475715 -1.373165564 -1.058296518 -1.887671179 [56] 0.740478064 -0.647466824 0.441863432 0.051072444 1.113292911 [61] -0.560578464 -0.821982662 -1.925451899 -0.743415253 -0.004431287 [66] -0.011805785 -0.656299641 1.162901156 -1.816539023 1.182795549 [71] -0.700543805 0.348066514 -0.884583994 0.380417631 -1.596145608 [76] 0.749900146 2.673189647 -1.185495000 0.054179173 -0.207625186 [81] 1.175751633 -0.040806534 0.090428099 0.540619112 0.693225261 [86] -0.756039091 -1.227543654 0.167909399 -0.575835860 0.226478936 [91] -1.749894762 1.126315581 -1.103799771 -0.559174590 0.114353547 [96] 0.264307036 0.563644133 -2.102803899 0.436929016 0.813897242 > > colMeans(tmp2) [1] 0.05120803 > colSums(tmp2) [1] 5.120803 > colVars(tmp2) [1] 1.044543 > colSd(tmp2) [1] 1.022029 > colMax(tmp2) [1] 2.67319 > colMin(tmp2) [1] -2.102804 > colMedians(tmp2) [1] 0.07230364 > colRanges(tmp2) [,1] [1,] -2.102804 [2,] 2.673190 > > dataset1 <- matrix(dataset1,1,100) > > agree.checks(tmp,dataset1) > > dataset2 <- matrix(dataset2,100,1) > agree.checks(tmp2,dataset2) > > > tmp <- createBufferedMatrix(10,10) > > tmp[1:10,1:10] <- rnorm(100) > colApply(tmp,sum) [1] -1.4160095 4.4077901 -1.3575729 -0.2320401 -6.8046045 4.5052264 [7] 3.9511305 -2.0861539 1.6165042 1.5080551 > colApply(tmp,quantile)[,1] [,1] [1,] -1.4398583 [2,] -0.6570138 [3,] -0.4062888 [4,] 0.3885159 [5,] 1.3426230 > > rowApply(tmp,sum) [1] -3.4582695 4.7632672 -2.4759107 -0.1299302 6.3065269 -0.4402246 [7] 3.3273834 -2.1786783 -1.2133121 -0.4085267 > rowApply(tmp,rank)[1:10,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 6 10 4 6 1 1 8 6 8 4 [2,] 7 1 10 10 8 4 3 7 3 9 [3,] 4 6 7 2 3 5 2 3 10 8 [4,] 8 8 9 4 6 6 5 8 1 1 [5,] 2 2 1 3 7 3 7 1 2 6 [6,] 10 7 6 7 4 8 9 4 7 3 [7,] 9 4 3 9 10 10 1 5 4 7 [8,] 3 5 2 5 9 2 6 9 6 2 [9,] 5 9 5 1 5 9 10 2 9 5 [10,] 1 3 8 8 2 7 4 10 5 10 > > tmp <- createBufferedMatrix(5,20) > > tmp[1:5,1:20] <- rnorm(100) > colApply(tmp,sum) [1] -0.2487050 0.4583924 -0.8957410 -0.5678858 0.4888015 -0.6449123 [7] -0.4717920 2.8299373 -2.2541821 0.7302280 -1.1192170 1.0767514 [13] 4.3823162 -0.9270026 0.6463943 -0.9195390 0.5332690 2.8795741 [19] 2.1177773 0.8190624 > colApply(tmp,quantile)[,1] [,1] [1,] -0.5009863 [2,] -0.4881496 [3,] -0.4217623 [4,] 0.5652001 [5,] 0.5969932 > > rowApply(tmp,sum) [1] 9.216712 1.687936 5.487408 -5.267426 -2.211104 > rowApply(tmp,rank)[1:5,] [,1] [,2] [,3] [,4] [,5] [1,] 12 6 13 8 7 [2,] 13 2 15 17 13 [3,] 5 9 14 4 9 [4,] 1 8 2 10 19 [5,] 9 13 17 9 6 > > > as.matrix(tmp) [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0.5969932 0.6205317 -0.08829132 -0.4746744 0.3350766 -0.19711577 [2,] -0.4881496 -1.4338633 0.26611944 0.1755825 0.4124442 -1.14165958 [3,] 0.5652001 0.6363139 0.60520208 -1.4261659 0.7619146 0.38446899 [4,] -0.4217623 0.4174188 -1.37747139 -0.3516088 -0.4208267 0.05078214 [5,] -0.5009863 0.2179913 -0.30129981 1.5089809 -0.5998073 0.25861193 [,7] [,8] [,9] [,10] [,11] [,12] [1,] 1.1091811 0.6576577 -0.4306816 1.7644032 1.1939608 0.7513348 [2,] -1.3678822 0.7675459 -0.5105275 1.5219486 0.2699232 -2.6932458 [3,] -0.1443877 -0.1767945 1.5592480 0.5385616 0.2831882 1.9788292 [4,] 0.1548687 0.3847235 -1.5360405 -0.8143702 -1.1482726 0.6772462 [5,] -0.2235719 1.1968047 -1.3361804 -2.2803151 -1.7180166 0.3625870 [,13] [,14] [,15] [,16] [,17] [,18] [1,] 0.9757493 -0.24600176 0.53805373 0.2924600 0.2325333 0.4777561 [2,] 0.5319294 0.85482074 1.41302292 0.2994772 0.3383113 1.4784594 [3,] 0.7504358 0.04063659 -0.07279546 0.2421074 -0.1470870 -1.5177141 [4,] 0.3710903 -1.47849676 -1.42996551 -1.1506642 0.9317853 1.4006361 [5,] 1.7531113 -0.09796143 0.19807861 -0.6029193 -0.8222740 1.0404366 [,19] [,20] [1,] 1.0261327 0.08165274 [2,] 1.2128247 -0.21914562 [3,] -0.7493395 1.37558570 [4,] 0.3988359 0.07466656 [5,] 0.2293234 -0.49369701 > > > is.BufferedMatrix(tmp) [1] TRUE > > as.BufferedMatrix(as.matrix(tmp)) BufferedMatrix object Matrix size: 5 20 Buffer size: 1 1 Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests Prefix: BM Mode: Col mode Read Only: FALSE Memory usage : 1.9 Kilobytes. Disk usage : 800 bytes. > > > > subBufferedMatrix(tmp,1:5,1:5) BufferedMatrix object Matrix size: 5 5 Buffer size: 1 1 Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests Prefix: BM Mode: Col mode Read Only: FALSE Memory usage : 650 bytes. Disk usage : 200 bytes. > subBufferedMatrix(tmp,,5:8) BufferedMatrix object Matrix size: 5 4 Buffer size: 1 1 Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests Prefix: BM Mode: Col mode Read Only: FALSE Memory usage : 561 bytes. Disk usage : 160 bytes. > subBufferedMatrix(tmp,1:3,) BufferedMatrix object Matrix size: 3 20 Buffer size: 1 1 Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests Prefix: BM Mode: Col mode Read Only: FALSE Memory usage : 1.9 Kilobytes. Disk usage : 480 bytes. > > > rm(tmp) > > > ### > ### Testing colnames and rownames > ### > > tmp <- createBufferedMatrix(5,20) > tmp[1:5,1:20] <- rnorm(100) > > > colnames(tmp) NULL > rownames(tmp) NULL > > > colnames(tmp) <- colnames(tmp,do.NULL=FALSE) > rownames(tmp) <- rownames(tmp,do.NULL=FALSE) > > colnames(tmp) [1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9" [10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18" [19] "col19" "col20" > rownames(tmp) [1] "row1" "row2" "row3" "row4" "row5" > > > tmp["row1",] col1 col2 col3 col4 col5 col6 col7 row1 0.5839688 -2.318557 0.6310199 0.3060224 -0.9033936 1.08473 1.374935 col8 col9 col10 col11 col12 col13 col14 col15 row1 -1.112802 2.539817 1.425712 0.4292864 1.295388 0.672567 2.654474 -1.372817 col16 col17 col18 col19 col20 row1 -0.6308947 -0.6594455 0.7657239 -0.1603167 0.3263057 > tmp[,"col10"] col10 row1 1.4257123 row2 0.5934118 row3 -0.7535909 row4 0.4023018 row5 -0.4098240 > tmp[c("row1","row5"),] col1 col2 col3 col4 col5 col6 col7 row1 0.5839688 -2.318557 0.6310199 0.3060224 -0.9033936 1.084730 1.374935 row5 -1.5479852 -1.273437 -0.8893508 0.3810477 0.6908891 -2.303146 0.408666 col8 col9 col10 col11 col12 col13 col14 row1 -1.1128018 2.5398171 1.425712 0.4292864 1.2953877 0.6725670 2.6544736 row5 0.7886952 0.4312648 -0.409824 -1.8395600 0.6775686 -0.4059611 0.3616368 col15 col16 col17 col18 col19 col20 row1 -1.3728172 -0.6308947 -0.6594455 0.7657239 -0.1603167 0.3263057 row5 -0.4988272 0.7388616 0.9219818 1.1403320 0.1294781 1.0766985 > tmp[,c("col6","col20")] col6 col20 row1 1.0847300 0.3263057 row2 -0.8061073 -0.6542777 row3 0.8193074 -0.3051745 row4 -0.7833007 2.0907696 row5 -2.3031461 1.0766985 > tmp[c("row1","row5"),c("col6","col20")] col6 col20 row1 1.084730 0.3263057 row5 -2.303146 1.0766985 > > > > > tmp["row1",] <- rnorm(20,mean=10) > tmp[,"col10"] <- rnorm(5,mean=30) > tmp[c("row1","row5"),] <- rnorm(40,mean=50) > tmp[,c("col6","col20")] <- rnorm(10,mean=75) > tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105) > > tmp["row1",] col1 col2 col3 col4 col5 col6 col7 col8 row1 49.18779 51.74227 49.08119 49.38296 49.89186 103.5052 50.06615 51.43171 col9 col10 col11 col12 col13 col14 col15 col16 row1 50.06039 50.57352 49.82331 50.27731 51.12626 50.67558 51.00347 50.46562 col17 col18 col19 col20 row1 51.40725 50.18973 47.21095 105.0462 > tmp[,"col10"] col10 row1 50.57352 row2 30.79114 row3 29.46617 row4 29.56933 row5 50.31679 > tmp[c("row1","row5"),] col1 col2 col3 col4 col5 col6 col7 col8 row1 49.18779 51.74227 49.08119 49.38296 49.89186 103.5052 50.06615 51.43171 row5 50.81767 49.90269 49.50508 49.62552 48.52651 104.5622 51.33889 50.09029 col9 col10 col11 col12 col13 col14 col15 col16 row1 50.06039 50.57352 49.82331 50.27731 51.12626 50.67558 51.00347 50.46562 row5 48.91761 50.31679 49.40927 50.66236 51.15245 50.55636 50.82615 48.28776 col17 col18 col19 col20 row1 51.40725 50.18973 47.21095 105.0462 row5 49.61876 49.11666 49.76668 105.5960 > tmp[,c("col6","col20")] col6 col20 row1 103.50516 105.04621 row2 75.52163 74.76260 row3 75.02738 73.16135 row4 73.98224 74.47670 row5 104.56218 105.59598 > tmp[c("row1","row5"),c("col6","col20")] col6 col20 row1 103.5052 105.0462 row5 104.5622 105.5960 > > > subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2] col6 col20 row1 103.5052 105.0462 row5 104.5622 105.5960 > > > > > > tmp <- createBufferedMatrix(5,20) > tmp[1:5,1:20] <- rnorm(100) > colnames(tmp) <- colnames(tmp,do.NULL=FALSE) > > tmp[,"col13"] col13 [1,] -0.88153920 [2,] -1.71057801 [3,] -0.06299495 [4,] 0.46818927 [5,] -0.21993053 > tmp[,c("col17","col7")] col17 col7 [1,] 0.06045834 -0.2084273 [2,] 0.07699159 1.5225667 [3,] -2.07667188 -0.2439941 [4,] 0.71699370 -0.2971075 [5,] -1.51629768 1.4571659 > > subBufferedMatrix(tmp,,c("col6","col20"))[,1:2] col6 col20 [1,] 0.9283099 -0.03310446 [2,] 0.8952653 0.27047095 [3,] -1.6926320 -0.89673262 [4,] 0.6514717 0.29713588 [5,] -1.1010081 0.35834721 > subBufferedMatrix(tmp,1,c("col6"))[,1] col1 [1,] 0.9283099 > subBufferedMatrix(tmp,1:2,c("col6"))[,1] col6 [1,] 0.9283099 [2,] 0.8952653 > > > > tmp <- createBufferedMatrix(5,20) > tmp[1:5,1:20] <- rnorm(100) > rownames(tmp) <- rownames(tmp,do.NULL=FALSE) > > > > > subBufferedMatrix(tmp,c("row3","row1"),)[,1:20] [,1] [,2] [,3] [,4] [,5] [,6] [,7] row3 -0.6417552 2.114790 0.7776375 1.785588 -2.3144129 -0.7269392 -1.7514356 row1 -0.5113882 -1.677698 -1.2983038 -1.179693 0.1746518 -0.5873540 0.7642195 [,8] [,9] [,10] [,11] [,12] [,13] row3 -0.5872177 -0.7100668 1.06818754 -0.6464725 1.8895988 0.8006465 row1 0.2698018 -0.7895297 -0.07788302 -0.7131610 -0.5920267 0.2796672 [,14] [,15] [,16] [,17] [,18] [,19] [,20] row3 -0.6505705 -0.01479884 1.367468 -0.8717948 0.2958838 -1.5598291 1.2209008 row1 1.6916500 -0.26679777 1.300429 1.1968268 -1.1099571 0.5845537 0.2678283 > subBufferedMatrix(tmp,c("row2"),1:10)[,1:10] [,1] [,2] [,3] [,4] [,5] [,6] [,7] row2 -0.2911335 0.4912074 -1.697319 -0.006028621 0.8435978 0.5414807 0.2865308 [,8] [,9] [,10] row2 1.454632 1.969451 -0.7022868 > subBufferedMatrix(tmp,c("row5"),1:20)[,1:20] [,1] [,2] [,3] [,4] [,5] [,6] [,7] row5 0.4493257 1.330193 0.5134659 -0.8151192 1.149753 0.5335657 -1.169437 [,8] [,9] [,10] [,11] [,12] [,13] [,14] row5 -0.7880299 0.4765243 0.1622792 0.2812958 0.3692194 0.4611659 0.4294402 [,15] [,16] [,17] [,18] [,19] [,20] row5 0.8814249 0.5080998 -1.454108 0.2367317 0.0118645 0.5713197 > > > colnames(tmp) <- colnames(tmp,do.NULL=FALSE) > rownames(tmp) <- rownames(tmp,do.NULL=FALSE) > > colnames(tmp) [1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9" [10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18" [19] "col19" "col20" > rownames(tmp) [1] "row1" "row2" "row3" "row4" "row5" > > > colnames(tmp) <- NULL > rownames(tmp) <- NULL > > colnames(tmp) NULL > rownames(tmp) NULL > > > colnames(tmp) <- colnames(tmp,do.NULL=FALSE) > rownames(tmp) <- rownames(tmp,do.NULL=FALSE) > > dimnames(tmp) [[1]] [1] "row1" "row2" "row3" "row4" "row5" [[2]] [1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9" [10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18" [19] "col19" "col20" > > dimnames(tmp) <- NULL > > colnames(tmp) <- colnames(tmp,do.NULL=FALSE) > dimnames(tmp) [[1]] NULL [[2]] [1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9" [10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18" [19] "col19" "col20" > > > dimnames(tmp) <- NULL > rownames(tmp) <- rownames(tmp,do.NULL=FALSE) > dimnames(tmp) [[1]] [1] "row1" "row2" "row3" "row4" "row5" [[2]] NULL > > dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE))) > dimnames(tmp) [[1]] NULL [[2]] [1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9" [10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18" [19] "col19" "col20" > > > > ### > ### Testing logical indexing > ### > ### > > tmp <- createBufferedMatrix(230,15) > tmp[1:230,1:15] <- rnorm(230*15) > x <-tmp[1:230,1:15] > > for (rep in 1:10){ + which.cols <- sample(c(TRUE,FALSE),15,replace=T) + which.rows <- sample(c(TRUE,FALSE),230,replace=T) + + if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){ + stop("No agreement when logical indexing\n") + } + + if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){ + stop("No agreement when logical indexing in subBufferedMatrix cols\n") + } + if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){ + stop("No agreement when logical indexing in subBufferedMatrix rows\n") + } + + + if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){ + stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n") + } + } > > > ## > ## Test the ReadOnlyMode > ## > > ReadOnlyMode(tmp) <pointer: 0x6000012dc0c0> > is.ReadOnlyMode(tmp) [1] TRUE > > filenames(tmp) [1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea4e7c9829" [2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea55e9d400" [3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea6a5d7810" [4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea1e7598fe" [5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea3a8f5b51" [6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea19b440e0" [7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea90f3f4f" [8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea4805602e" [9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea58ed90f2" [10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea54c72d7a" [11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea607ad011" [12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea1ef23d93" [13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea31a88dc4" [14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea30f35854" [15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1dea382c0be7" > > > ### testing coercion functions > ### > > tmp <- as(tmp,"matrix") > tmp <- as(tmp,"BufferedMatrix") > > > > ### testing whether can move storage from one location to another > > MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE) <pointer: 0x6000012b8000> > MoveStorageDirectory(tmp,getwd(),full.path=TRUE) <pointer: 0x6000012b8000> Warning message: In dir.create(new.directory) : '/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists > > > RowMode(tmp) <pointer: 0x6000012b8000> > rowMedians(tmp) [1] -0.179105126 0.140689204 0.073861947 -0.165279018 0.322702856 [6] 0.105088891 0.184503161 -0.266601847 -0.556055069 -0.319181485 [11] 0.053408909 0.109829063 0.034010706 -0.046187189 -0.203901344 [16] 0.487592983 -0.446903081 -0.515625463 0.039473840 -0.407578837 [21] 0.318905366 -0.917995726 -0.137167898 0.177134243 -0.408017362 [26] 0.158901226 0.434856541 0.345410912 -0.544619923 -0.517956230 [31] 0.271769153 -0.281848458 -0.206444850 -0.563611766 -0.371521760 [36] 0.326635200 0.192078326 0.029571289 -0.309979571 -0.258894741 [41] 0.248686116 0.130508556 0.454388454 -0.030507420 -0.317236110 [46] 0.555983523 0.190199877 -0.306884738 -0.852657806 -0.225853642 [51] 0.227482959 0.046171141 -0.354769659 -0.498629808 0.023837308 [56] 0.161902726 0.127075833 0.221790644 -0.145110121 0.605214575 [61] 0.004532226 -0.231524312 0.028834219 -0.420050854 -0.316103412 [66] 0.341109596 0.438393965 -0.258440781 0.052324700 0.399565819 [71] -0.781073956 -0.429317862 0.413925298 0.134014507 -0.141321909 [76] 0.714665398 -0.692832526 0.340007928 -0.031058274 -0.437957126 [81] 0.176223894 -0.295529277 0.463280531 -0.119443149 -0.352477893 [86] 0.234093125 0.165430734 0.522618479 0.353584681 -0.236479046 [91] 0.564772260 0.347174584 -0.115972569 -0.883734688 -0.251099158 [96] -0.293415825 0.716368564 -0.085622971 0.157502239 0.402589960 [101] 0.060292700 -0.425087618 -0.304865495 -0.065872617 0.610267352 [106] 0.009510674 -0.040300953 -0.353800492 0.062958651 0.109715506 [111] -0.292046126 -0.049623159 -0.719102889 -0.201596805 -0.435362203 [116] -0.759470443 0.485536977 0.066848295 0.344496986 0.240209259 [121] 0.180894183 -0.179478811 -0.236671645 0.087941195 -0.322558746 [126] -0.026574528 0.230980838 0.180479816 0.026780913 0.034593615 [131] 0.196541331 -0.163878252 -0.032840208 0.154782477 0.621044467 [136] -0.237970802 -0.299351408 0.269742930 0.237226462 -0.070740155 [141] -0.029441220 0.370808802 0.062432654 0.021202529 0.037560844 [146] 0.119208147 -0.314044179 0.093824400 0.146778134 -0.213591456 [151] 0.107494375 -0.062841782 -0.085845134 -0.041824423 -0.271907956 [156] 0.075132911 0.014859278 -0.881744534 0.167280795 0.229790017 [161] 0.095620509 0.270527746 0.036807230 -0.190468368 0.144119406 [166] -0.159935927 -0.412874308 -0.169947891 0.444452087 -0.274494617 [171] 0.054713532 0.024242349 -0.125868438 -0.139378260 0.189222419 [176] -0.096186319 0.249121996 -0.131814660 0.405942980 -0.412851243 [181] -0.097511125 -0.777371334 -0.522094264 -0.230058264 -0.079669973 [186] -0.451812320 0.129094902 0.337749169 -0.290523785 0.210377246 [191] 0.070569182 0.079837617 -0.124691884 0.459246003 -0.475914706 [196] -0.194620918 -0.374294761 0.665395441 0.172427256 0.481372016 [201] 0.299908111 -0.119451256 -0.065487409 -0.205968560 0.451620454 [206] -0.083422561 0.023126613 -0.206355378 -0.048310345 0.116044954 [211] -0.152056404 -0.109726802 0.034388760 -0.470926092 0.184292946 [216] -0.293410992 0.115228987 -0.004438235 -0.435184290 0.587779653 [221] 0.393922922 0.600417185 0.300601413 -0.227921805 0.547099828 [226] -0.231386785 -0.041409267 -0.096708968 -0.225931414 -0.078837165 > > proc.time() user system elapsed 2.631 15.336 18.687
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths()); Attaching package: 'BufferedMatrix' The following objects are masked from 'package:base': colMeans, colSums, rowMeans, rowSums > > prefix <- "dbmtest" > directory <- getwd() > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_Test_C",P) RBufferedMatrix Checking dimensions Rows: 5 Cols: 5 Buffer Rows: 1 Buffer Cols: 1 Assigning Values 0.000000 1.000000 2.000000 3.000000 4.000000 1.000000 2.000000 3.000000 4.000000 5.000000 2.000000 3.000000 4.000000 5.000000 6.000000 3.000000 4.000000 5.000000 6.000000 7.000000 4.000000 5.000000 6.000000 7.000000 8.000000 <pointer: 0x600001714000> > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 5 Buffer Rows: 1 Buffer Cols: 1 Printing Values 0.000000 1.000000 2.000000 3.000000 4.000000 1.000000 2.000000 3.000000 4.000000 5.000000 2.000000 3.000000 4.000000 5.000000 6.000000 3.000000 4.000000 5.000000 6.000000 7.000000 4.000000 5.000000 6.000000 7.000000 8.000000 <pointer: 0x600001714000> > .Call("R_bm_Test_C",P) RBufferedMatrix Checking dimensions Rows: 5 Cols: 10 Buffer Rows: 1 Buffer Cols: 1 Assigning Values 0.000000 1.000000 2.000000 3.000000 4.000000 1.000000 2.000000 3.000000 4.000000 5.000000 2.000000 3.000000 4.000000 5.000000 6.000000 3.000000 4.000000 5.000000 6.000000 7.000000 4.000000 5.000000 6.000000 7.000000 8.000000 <pointer: 0x600001714000> > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 10 Buffer Rows: 1 Buffer Cols: 1 Printing Values 0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000 3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000 4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000 <pointer: 0x600001714000> > rm(P) > > #P <- .Call("R_bm_Destroy",P) > #.Call("R_bm_Destroy",P) > #.Call("R_bm_Test_C",P) > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_setRows",P,5) [1] TRUE > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 0 Buffer Rows: 1 Buffer Cols: 1 Printing Values <pointer: 0x600001770060> > .Call("R_bm_AddColumn",P) <pointer: 0x600001770060> > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 1 Buffer Rows: 1 Buffer Cols: 1 Printing Values 0.000000 0.000000 0.000000 0.000000 0.000000 <pointer: 0x600001770060> > .Call("R_bm_AddColumn",P) <pointer: 0x600001770060> > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 2 Buffer Rows: 1 Buffer Cols: 1 Printing Values 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 <pointer: 0x600001770060> > rm(P) > > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_setRows",P,5) [1] TRUE > .Call("R_bm_AddColumn",P) <pointer: 0x600001718000> > .Call("R_bm_AddColumn",P) <pointer: 0x600001718000> > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 2 Buffer Rows: 1 Buffer Cols: 1 Printing Values 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 <pointer: 0x600001718000> > > .Call("R_bm_ResizeBuffer",P,5,5) <pointer: 0x600001718000> > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 2 Buffer Rows: 5 Buffer Cols: 5 Printing Values 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 <pointer: 0x600001718000> > > .Call("R_bm_RowMode",P) <pointer: 0x600001718000> > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 2 Buffer Rows: 5 Buffer Cols: 5 Printing Values 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 <pointer: 0x600001718000> > > .Call("R_bm_ColMode",P) <pointer: 0x600001718000> > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 2 Buffer Rows: 5 Buffer Cols: 5 Printing Values 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 <pointer: 0x600001718000> > rm(P) > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_setRows",P,10) [1] TRUE > .Call("R_bm_AddColumn",P) <pointer: 0x600001704000> > .Call("R_bm_SetPrefix",P,"BufferedMatrixFile") <pointer: 0x600001704000> > .Call("R_bm_AddColumn",P) <pointer: 0x600001704000> > .Call("R_bm_AddColumn",P) <pointer: 0x600001704000> > dir(pattern="BufferedMatrixFile") [1] "BufferedMatrixFile25bd16b1587f" "BufferedMatrixFile25bd5529057c" > rm(P) > dir(pattern="BufferedMatrixFile") [1] "BufferedMatrixFile25bd16b1587f" "BufferedMatrixFile25bd5529057c" > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_setRows",P,10) [1] TRUE > .Call("R_bm_AddColumn",P) <pointer: 0x600001704240> > .Call("R_bm_AddColumn",P) <pointer: 0x600001704240> > .Call("R_bm_ReadOnlyModeToggle",P) <pointer: 0x600001704240> > .Call("R_bm_isReadOnlyMode",P) [1] TRUE > .Call("R_bm_ReadOnlyModeToggle",P) <pointer: 0x600001704240> > .Call("R_bm_isReadOnlyMode",P) [1] FALSE > .Call("R_bm_isRowMode",P) [1] FALSE > .Call("R_bm_RowMode",P) <pointer: 0x600001704240> > .Call("R_bm_isRowMode",P) [1] TRUE > .Call("R_bm_ColMode",P) <pointer: 0x600001704240> > .Call("R_bm_isRowMode",P) [1] FALSE > rm(P) > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_setRows",P,10) [1] TRUE > .Call("R_bm_AddColumn",P) <pointer: 0x600001704420> > .Call("R_bm_AddColumn",P) <pointer: 0x600001704420> > > .Call("R_bm_getSize",P) [1] 10 2 > .Call("R_bm_getBufferSize",P) [1] 1 1 > .Call("R_bm_ResizeBuffer",P,5,5) <pointer: 0x600001704420> > > .Call("R_bm_getBufferSize",P) [1] 5 5 > .Call("R_bm_ResizeBuffer",P,-1,5) <pointer: 0x600001704420> > rm(P) > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_Test_C",P) RBufferedMatrix Checking dimensions Rows: 5 Cols: 5 Buffer Rows: 1 Buffer Cols: 1 Assigning Values 0.000000 1.000000 2.000000 3.000000 4.000000 1.000000 2.000000 3.000000 4.000000 5.000000 2.000000 3.000000 4.000000 5.000000 6.000000 3.000000 4.000000 5.000000 6.000000 7.000000 4.000000 5.000000 6.000000 7.000000 8.000000 <pointer: 0x600001704600> > .Call("R_bm_getValue",P,3,3) [1] 6 > > .Call("R_bm_getValue",P,100000,10000) [1] NA > .Call("R_bm_setValue",P,3,3,12345.0) [1] TRUE > .Call("R_bm_Test_C2",P) Checking dimensions Rows: 5 Cols: 5 Buffer Rows: 1 Buffer Cols: 1 Printing Values 0.000000 1.000000 2.000000 3.000000 4.000000 1.000000 2.000000 3.000000 4.000000 5.000000 2.000000 3.000000 4.000000 5.000000 6.000000 3.000000 4.000000 5.000000 12345.000000 7.000000 4.000000 5.000000 6.000000 7.000000 8.000000 <pointer: 0x600001704600> > rm(P) > > proc.time() user system elapsed 0.301 0.139 0.430
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths()); Attaching package: 'BufferedMatrix' The following objects are masked from 'package:base': colMeans, colSums, rowMeans, rowSums > > Temp <- createBufferedMatrix(100) > dim(Temp) [1] 100 0 > buffer.dim(Temp) [1] 1 1 > > > proc.time() user system elapsed 0.341 0.101 0.463