Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-22 12:06 -0400 (Fri, 22 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4541 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 252/2319 | 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: 2025-08-21 18:26:56 -0400 (Thu, 21 Aug 2025) |
EndedAt: 2025-08-21 18:27:13 -0400 (Thu, 21 Aug 2025) |
EllapsedTime: 16.2 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 (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * 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 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.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-arm64/Resources/library’ * installing *source* package ‘BufferedMatrix’ ... ** this is package ‘BufferedMatrix’ version ‘1.73.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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 (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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 0.119 0.036 0.152
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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 480828 25.7 1056621 56.5 NA 634345 33.9 Vcells 891019 6.8 8388608 64.0 196608 2109860 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] "Thu Aug 21 18:27:05 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] "Thu Aug 21 18:27:05 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: 0x600002ce8000> > > > > 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] "Thu Aug 21 18:27:06 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] "Thu Aug 21 18:27:07 2025" > > ColMode(tmp2) <pointer: 0x600002ce8000> > > > > ### 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,] 99.5821344 0.35395647 0.1305382 0.7253107 [2,] -0.4216381 0.80109307 2.5521365 -0.4404414 [3,] -0.7776395 -0.06729214 -1.4953353 -1.4865712 [4,] -0.2135513 -0.12370911 0.8417434 -0.6278315 > 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,] 99.5821344 0.35395647 0.1305382 0.7253107 [2,] 0.4216381 0.80109307 2.5521365 0.4404414 [3,] 0.7776395 0.06729214 1.4953353 1.4865712 [4,] 0.2135513 0.12370911 0.8417434 0.6278315 > 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,] 9.9790848 0.5949424 0.3613007 0.8516517 [2,] 0.6493366 0.8950380 1.5975408 0.6636576 [3,] 0.8818387 0.2594073 1.2228390 1.2192503 [4,] 0.4621161 0.3517231 0.9174657 0.7923582 > > 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,] 224.37298 31.30338 28.74355 34.24183 [2,] 31.91500 34.75147 43.52754 32.07702 [3,] 34.59603 27.66137 38.72373 38.67907 [4,] 29.83471 28.64094 35.01640 33.55141 > > > > ## testing functions that elementwise transform the matrix > sqrt(tmp5) <pointer: 0x600002cfc300> > exp(tmp5) <pointer: 0x600002cfc300> > log(tmp5,2) <pointer: 0x600002cfc300> > pow(tmp5,2) > > > > > > ## testing functions that apply to entire matrix > Max(tmp5) [1] 467.003 > Min(tmp5) [1] 54.32841 > mean(tmp5) [1] 72.30324 > Sum(tmp5) [1] 14460.65 > Var(tmp5) [1] 858.0132 > > > ## testing functions applied to rows or columns > > rowMeans(tmp5) [1] 88.71339 69.50624 69.92938 67.63221 72.43514 70.74718 68.20302 71.80963 [9] 72.41236 71.64386 > rowSums(tmp5) [1] 1774.268 1390.125 1398.588 1352.644 1448.703 1414.944 1364.060 1436.193 [9] 1448.247 1432.877 > rowVars(tmp5) [1] 7969.59415 56.83063 96.78305 52.53864 100.41874 70.49949 [7] 64.58613 67.17111 116.00817 50.53838 > rowSd(tmp5) [1] 89.272583 7.538610 9.837838 7.248354 10.020915 8.396397 8.036550 [8] 8.195798 10.770709 7.109035 > rowMax(tmp5) [1] 467.00297 90.59688 90.86169 82.11805 91.66360 88.44808 84.21163 [8] 89.61913 90.95653 82.48526 > rowMin(tmp5) [1] 57.85217 60.10992 54.50615 54.64201 54.47242 57.86681 57.16068 59.35394 [9] 54.32841 60.22232 > > colMeans(tmp5) [1] 104.72932 67.89867 76.79592 72.16639 70.40079 68.22939 72.05781 [8] 69.43152 70.22019 69.61190 70.82327 73.06843 67.32642 71.92486 [15] 66.82799 67.91943 71.97914 74.83276 68.41889 71.40175 > colSums(tmp5) [1] 1047.2932 678.9867 767.9592 721.6639 704.0079 682.2939 720.5781 [8] 694.3152 702.2019 696.1190 708.2327 730.6843 673.2642 719.2486 [15] 668.2799 679.1943 719.7914 748.3276 684.1889 714.0175 > colVars(tmp5) [1] 16257.30143 73.14632 135.16807 34.63085 40.90978 104.94285 [7] 84.77728 40.86483 80.12812 45.64330 74.40222 74.32357 [13] 141.74244 42.80450 30.11218 56.04017 64.50142 62.23071 [19] 109.43593 51.35488 > colSd(tmp5) [1] 127.504123 8.552562 11.626180 5.884798 6.396075 10.244162 [7] 9.207458 6.392560 8.951431 6.755982 8.625672 8.621112 [13] 11.905563 6.542515 5.487457 7.485998 8.031278 7.888644 [19] 10.461163 7.166232 > colMax(tmp5) [1] 467.00297 87.43833 90.59688 80.50542 79.12932 89.61913 86.12021 [8] 79.70780 90.86169 82.22077 88.47921 90.95653 91.66360 82.61182 [15] 78.31775 81.68184 81.07161 84.21163 82.41080 84.11144 > colMin(tmp5) [1] 54.32841 57.57351 59.82592 65.05159 61.41229 57.85217 54.47242 57.55173 [9] 59.12232 61.76682 59.72033 62.69676 54.50615 60.86959 57.97181 59.10172 [17] 60.14474 61.12814 54.64201 59.72968 > > > ### 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] 88.71339 69.50624 69.92938 67.63221 72.43514 70.74718 NA 71.80963 [9] 72.41236 71.64386 > rowSums(tmp5) [1] 1774.268 1390.125 1398.588 1352.644 1448.703 1414.944 NA 1436.193 [9] 1448.247 1432.877 > rowVars(tmp5) [1] 7969.59415 56.83063 96.78305 52.53864 100.41874 70.49949 [7] 65.75175 67.17111 116.00817 50.53838 > rowSd(tmp5) [1] 89.272583 7.538610 9.837838 7.248354 10.020915 8.396397 8.108745 [8] 8.195798 10.770709 7.109035 > rowMax(tmp5) [1] 467.00297 90.59688 90.86169 82.11805 91.66360 88.44808 NA [8] 89.61913 90.95653 82.48526 > rowMin(tmp5) [1] 57.85217 60.10992 54.50615 54.64201 54.47242 57.86681 NA 59.35394 [9] 54.32841 60.22232 > > colMeans(tmp5) [1] 104.72932 67.89867 76.79592 72.16639 70.40079 68.22939 72.05781 [8] 69.43152 70.22019 NA 70.82327 73.06843 67.32642 71.92486 [15] 66.82799 67.91943 71.97914 74.83276 68.41889 71.40175 > colSums(tmp5) [1] 1047.2932 678.9867 767.9592 721.6639 704.0079 682.2939 720.5781 [8] 694.3152 702.2019 NA 708.2327 730.6843 673.2642 719.2486 [15] 668.2799 679.1943 719.7914 748.3276 684.1889 714.0175 > colVars(tmp5) [1] 16257.30143 73.14632 135.16807 34.63085 40.90978 104.94285 [7] 84.77728 40.86483 80.12812 NA 74.40222 74.32357 [13] 141.74244 42.80450 30.11218 56.04017 64.50142 62.23071 [19] 109.43593 51.35488 > colSd(tmp5) [1] 127.504123 8.552562 11.626180 5.884798 6.396075 10.244162 [7] 9.207458 6.392560 8.951431 NA 8.625672 8.621112 [13] 11.905563 6.542515 5.487457 7.485998 8.031278 7.888644 [19] 10.461163 7.166232 > colMax(tmp5) [1] 467.00297 87.43833 90.59688 80.50542 79.12932 89.61913 86.12021 [8] 79.70780 90.86169 NA 88.47921 90.95653 91.66360 82.61182 [15] 78.31775 81.68184 81.07161 84.21163 82.41080 84.11144 > colMin(tmp5) [1] 54.32841 57.57351 59.82592 65.05159 61.41229 57.85217 54.47242 57.55173 [9] 59.12232 NA 59.72033 62.69676 54.50615 60.86959 57.97181 59.10172 [17] 60.14474 61.12814 54.64201 59.72968 > > Max(tmp5,na.rm=TRUE) [1] 467.003 > Min(tmp5,na.rm=TRUE) [1] 54.32841 > mean(tmp5,na.rm=TRUE) [1] 72.35619 > Sum(tmp5,na.rm=TRUE) [1] 14398.88 > Var(tmp5,na.rm=TRUE) [1] 861.7831 > > rowMeans(tmp5,na.rm=TRUE) [1] 88.71339 69.50624 69.92938 67.63221 72.43514 70.74718 68.54177 71.80963 [9] 72.41236 71.64386 > rowSums(tmp5,na.rm=TRUE) [1] 1774.268 1390.125 1398.588 1352.644 1448.703 1414.944 1302.294 1436.193 [9] 1448.247 1432.877 > rowVars(tmp5,na.rm=TRUE) [1] 7969.59415 56.83063 96.78305 52.53864 100.41874 70.49949 [7] 65.75175 67.17111 116.00817 50.53838 > rowSd(tmp5,na.rm=TRUE) [1] 89.272583 7.538610 9.837838 7.248354 10.020915 8.396397 8.108745 [8] 8.195798 10.770709 7.109035 > rowMax(tmp5,na.rm=TRUE) [1] 467.00297 90.59688 90.86169 82.11805 91.66360 88.44808 84.21163 [8] 89.61913 90.95653 82.48526 > rowMin(tmp5,na.rm=TRUE) [1] 57.85217 60.10992 54.50615 54.64201 54.47242 57.86681 57.16068 59.35394 [9] 54.32841 60.22232 > > colMeans(tmp5,na.rm=TRUE) [1] 104.72932 67.89867 76.79592 72.16639 70.40079 68.22939 72.05781 [8] 69.43152 70.22019 70.48358 70.82327 73.06843 67.32642 71.92486 [15] 66.82799 67.91943 71.97914 74.83276 68.41889 71.40175 > colSums(tmp5,na.rm=TRUE) [1] 1047.2932 678.9867 767.9592 721.6639 704.0079 682.2939 720.5781 [8] 694.3152 702.2019 634.3522 708.2327 730.6843 673.2642 719.2486 [15] 668.2799 679.1943 719.7914 748.3276 684.1889 714.0175 > colVars(tmp5,na.rm=TRUE) [1] 16257.30143 73.14632 135.16807 34.63085 40.90978 104.94285 [7] 84.77728 40.86483 80.12812 42.80075 74.40222 74.32357 [13] 141.74244 42.80450 30.11218 56.04017 64.50142 62.23071 [19] 109.43593 51.35488 > colSd(tmp5,na.rm=TRUE) [1] 127.504123 8.552562 11.626180 5.884798 6.396075 10.244162 [7] 9.207458 6.392560 8.951431 6.542228 8.625672 8.621112 [13] 11.905563 6.542515 5.487457 7.485998 8.031278 7.888644 [19] 10.461163 7.166232 > colMax(tmp5,na.rm=TRUE) [1] 467.00297 87.43833 90.59688 80.50542 79.12932 89.61913 86.12021 [8] 79.70780 90.86169 82.22077 88.47921 90.95653 91.66360 82.61182 [15] 78.31775 81.68184 81.07161 84.21163 82.41080 84.11144 > colMin(tmp5,na.rm=TRUE) [1] 54.32841 57.57351 59.82592 65.05159 61.41229 57.85217 54.47242 57.55173 [9] 59.12232 64.22805 59.72033 62.69676 54.50615 60.86959 57.97181 59.10172 [17] 60.14474 61.12814 54.64201 59.72968 > > # now set an entire row to NA > > tmp5[which.row,] <- NA > rowMeans(tmp5,na.rm=TRUE) [1] 88.71339 69.50624 69.92938 67.63221 72.43514 70.74718 NaN 71.80963 [9] 72.41236 71.64386 > rowSums(tmp5,na.rm=TRUE) [1] 1774.268 1390.125 1398.588 1352.644 1448.703 1414.944 0.000 1436.193 [9] 1448.247 1432.877 > rowVars(tmp5,na.rm=TRUE) [1] 7969.59415 56.83063 96.78305 52.53864 100.41874 70.49949 [7] NA 67.17111 116.00817 50.53838 > rowSd(tmp5,na.rm=TRUE) [1] 89.272583 7.538610 9.837838 7.248354 10.020915 8.396397 NA [8] 8.195798 10.770709 7.109035 > rowMax(tmp5,na.rm=TRUE) [1] 467.00297 90.59688 90.86169 82.11805 91.66360 88.44808 NA [8] 89.61913 90.95653 82.48526 > rowMin(tmp5,na.rm=TRUE) [1] 57.85217 60.10992 54.50615 54.64201 54.47242 57.86681 NA 59.35394 [9] 54.32841 60.22232 > > > # now set an entire col to NA > > > tmp5[,which.col] <- NA > colMeans(tmp5,na.rm=TRUE) [1] 109.78497 68.66521 78.56049 72.53985 70.09281 68.56927 72.10530 [8] 70.33000 70.13027 NaN 71.70809 71.91709 68.45595 71.83392 [15] 66.82480 68.48892 72.80090 73.79067 67.07427 71.02010 > colSums(tmp5,na.rm=TRUE) [1] 988.0647 617.9869 707.0444 652.8586 630.8353 617.1234 648.9477 632.9700 [9] 631.1724 0.0000 645.3728 647.2538 616.1035 646.5053 601.4232 616.4003 [17] 655.2081 664.1160 603.6684 639.1809 > colVars(tmp5,na.rm=TRUE) [1] 18001.91890 75.67928 117.03513 37.39067 44.95643 116.76111 [7] 95.34907 36.89113 90.05317 NA 74.89468 68.70120 [13] 145.10714 48.06203 33.87609 59.39659 64.96719 57.79244 [19] 102.77552 56.13556 > colSd(tmp5,na.rm=TRUE) [1] 134.171230 8.699384 10.818278 6.114791 6.704956 10.805606 [7] 9.764685 6.073807 9.489635 NA 8.654171 8.288619 [13] 12.046043 6.932678 5.820317 7.706919 8.060222 7.602134 [19] 10.137826 7.492366 > colMax(tmp5,na.rm=TRUE) [1] 467.00297 87.43833 90.59688 80.50542 79.12932 89.61913 86.12021 [8] 79.70780 90.86169 -Inf 88.47921 90.95653 91.66360 82.61182 [15] 78.31775 81.68184 81.07161 83.29926 82.41080 84.11144 > colMin(tmp5,na.rm=TRUE) [1] 54.32841 57.57351 59.82592 65.05159 61.41229 57.85217 54.47242 57.55173 [9] 59.12232 Inf 59.72033 62.69676 54.50615 60.86959 57.97181 59.10172 [17] 60.14474 61.12814 54.64201 59.72968 > > > > > 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] 267.74655 152.86204 242.83759 218.62334 401.15855 88.15682 186.44418 [8] 268.34667 169.86912 173.72098 > apply(copymatrix,1,var,na.rm=TRUE) [1] 267.74655 152.86204 242.83759 218.62334 401.15855 88.15682 186.44418 [8] 268.34667 169.86912 173.72098 > > > > 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] 2.842171e-14 1.136868e-13 -2.842171e-14 -2.842171e-14 5.684342e-14 [6] -1.705303e-13 -2.842171e-14 -2.273737e-13 2.842171e-14 -1.705303e-13 [11] 0.000000e+00 -1.136868e-13 -2.842171e-14 0.000000e+00 -1.989520e-13 [16] -2.842171e-14 -5.684342e-14 1.136868e-13 -1.136868e-13 0.000000e+00 > > > > > > > > > > > ## 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) + } 6 10 4 15 5 10 4 7 3 1 2 19 10 15 6 1 7 1 2 14 4 2 4 9 6 12 7 14 8 8 9 10 7 5 4 9 1 2 3 9 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] 1.99248 > Min(tmp) [1] -2.490274 > mean(tmp) [1] -0.02694016 > Sum(tmp) [1] -2.694016 > Var(tmp) [1] 0.797784 > > rowMeans(tmp) [1] -0.02694016 > rowSums(tmp) [1] -2.694016 > rowVars(tmp) [1] 0.797784 > rowSd(tmp) [1] 0.8931876 > rowMax(tmp) [1] 1.99248 > rowMin(tmp) [1] -2.490274 > > colMeans(tmp) [1] 0.438612461 -0.011014176 -0.036662539 -0.250662134 1.283470284 [6] -0.743108110 -0.475930969 -0.154234061 -0.909799698 0.120066385 [11] -0.471146328 -1.306078701 -0.359347827 1.588919607 0.609650490 [16] -0.041970825 -0.519045792 -0.299927236 -1.915487019 0.891487310 [21] 0.118554174 -0.457402191 0.464127502 0.159476958 0.431911800 [26] -0.130894068 0.025232167 0.258570058 1.054101727 -0.715630977 [31] -1.035540802 0.162845902 0.204477320 0.303049111 0.743628618 [36] 0.036040889 1.892024592 0.103452055 0.621386237 0.658532551 [41] -0.562782587 0.853123845 -0.584105063 0.851076019 0.886054923 [46] 0.856238291 -0.556064763 0.218923810 -1.951566308 -1.229078853 [51] 0.960642276 -0.322375001 -1.592664826 0.009525485 0.582701505 [56] -1.238067716 -0.167090977 -0.730336927 1.143156054 -0.831198621 [61] -2.032051212 -0.027025699 -0.974901679 -1.241296537 0.265886046 [66] 1.164727862 0.375153864 0.394000424 0.555074032 0.623129515 [71] 0.799493396 -0.975910383 -0.158936824 -1.580613832 -1.064626456 [76] -0.647907157 -0.591109811 1.421808851 -2.490274047 0.220531485 [81] -0.593268474 0.413318206 0.850886977 -1.525409546 0.401399971 [86] 0.237144819 1.040530463 0.687322066 0.365346456 0.741943965 [91] -0.179164354 0.926995618 -0.678708973 -0.072101707 0.441612992 [96] -1.782104792 0.128226446 -0.350927817 1.293464490 1.992479775 > colSums(tmp) [1] 0.438612461 -0.011014176 -0.036662539 -0.250662134 1.283470284 [6] -0.743108110 -0.475930969 -0.154234061 -0.909799698 0.120066385 [11] -0.471146328 -1.306078701 -0.359347827 1.588919607 0.609650490 [16] -0.041970825 -0.519045792 -0.299927236 -1.915487019 0.891487310 [21] 0.118554174 -0.457402191 0.464127502 0.159476958 0.431911800 [26] -0.130894068 0.025232167 0.258570058 1.054101727 -0.715630977 [31] -1.035540802 0.162845902 0.204477320 0.303049111 0.743628618 [36] 0.036040889 1.892024592 0.103452055 0.621386237 0.658532551 [41] -0.562782587 0.853123845 -0.584105063 0.851076019 0.886054923 [46] 0.856238291 -0.556064763 0.218923810 -1.951566308 -1.229078853 [51] 0.960642276 -0.322375001 -1.592664826 0.009525485 0.582701505 [56] -1.238067716 -0.167090977 -0.730336927 1.143156054 -0.831198621 [61] -2.032051212 -0.027025699 -0.974901679 -1.241296537 0.265886046 [66] 1.164727862 0.375153864 0.394000424 0.555074032 0.623129515 [71] 0.799493396 -0.975910383 -0.158936824 -1.580613832 -1.064626456 [76] -0.647907157 -0.591109811 1.421808851 -2.490274047 0.220531485 [81] -0.593268474 0.413318206 0.850886977 -1.525409546 0.401399971 [86] 0.237144819 1.040530463 0.687322066 0.365346456 0.741943965 [91] -0.179164354 0.926995618 -0.678708973 -0.072101707 0.441612992 [96] -1.782104792 0.128226446 -0.350927817 1.293464490 1.992479775 > 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] 0.438612461 -0.011014176 -0.036662539 -0.250662134 1.283470284 [6] -0.743108110 -0.475930969 -0.154234061 -0.909799698 0.120066385 [11] -0.471146328 -1.306078701 -0.359347827 1.588919607 0.609650490 [16] -0.041970825 -0.519045792 -0.299927236 -1.915487019 0.891487310 [21] 0.118554174 -0.457402191 0.464127502 0.159476958 0.431911800 [26] -0.130894068 0.025232167 0.258570058 1.054101727 -0.715630977 [31] -1.035540802 0.162845902 0.204477320 0.303049111 0.743628618 [36] 0.036040889 1.892024592 0.103452055 0.621386237 0.658532551 [41] -0.562782587 0.853123845 -0.584105063 0.851076019 0.886054923 [46] 0.856238291 -0.556064763 0.218923810 -1.951566308 -1.229078853 [51] 0.960642276 -0.322375001 -1.592664826 0.009525485 0.582701505 [56] -1.238067716 -0.167090977 -0.730336927 1.143156054 -0.831198621 [61] -2.032051212 -0.027025699 -0.974901679 -1.241296537 0.265886046 [66] 1.164727862 0.375153864 0.394000424 0.555074032 0.623129515 [71] 0.799493396 -0.975910383 -0.158936824 -1.580613832 -1.064626456 [76] -0.647907157 -0.591109811 1.421808851 -2.490274047 0.220531485 [81] -0.593268474 0.413318206 0.850886977 -1.525409546 0.401399971 [86] 0.237144819 1.040530463 0.687322066 0.365346456 0.741943965 [91] -0.179164354 0.926995618 -0.678708973 -0.072101707 0.441612992 [96] -1.782104792 0.128226446 -0.350927817 1.293464490 1.992479775 > colMin(tmp) [1] 0.438612461 -0.011014176 -0.036662539 -0.250662134 1.283470284 [6] -0.743108110 -0.475930969 -0.154234061 -0.909799698 0.120066385 [11] -0.471146328 -1.306078701 -0.359347827 1.588919607 0.609650490 [16] -0.041970825 -0.519045792 -0.299927236 -1.915487019 0.891487310 [21] 0.118554174 -0.457402191 0.464127502 0.159476958 0.431911800 [26] -0.130894068 0.025232167 0.258570058 1.054101727 -0.715630977 [31] -1.035540802 0.162845902 0.204477320 0.303049111 0.743628618 [36] 0.036040889 1.892024592 0.103452055 0.621386237 0.658532551 [41] -0.562782587 0.853123845 -0.584105063 0.851076019 0.886054923 [46] 0.856238291 -0.556064763 0.218923810 -1.951566308 -1.229078853 [51] 0.960642276 -0.322375001 -1.592664826 0.009525485 0.582701505 [56] -1.238067716 -0.167090977 -0.730336927 1.143156054 -0.831198621 [61] -2.032051212 -0.027025699 -0.974901679 -1.241296537 0.265886046 [66] 1.164727862 0.375153864 0.394000424 0.555074032 0.623129515 [71] 0.799493396 -0.975910383 -0.158936824 -1.580613832 -1.064626456 [76] -0.647907157 -0.591109811 1.421808851 -2.490274047 0.220531485 [81] -0.593268474 0.413318206 0.850886977 -1.525409546 0.401399971 [86] 0.237144819 1.040530463 0.687322066 0.365346456 0.741943965 [91] -0.179164354 0.926995618 -0.678708973 -0.072101707 0.441612992 [96] -1.782104792 0.128226446 -0.350927817 1.293464490 1.992479775 > colMedians(tmp) [1] 0.438612461 -0.011014176 -0.036662539 -0.250662134 1.283470284 [6] -0.743108110 -0.475930969 -0.154234061 -0.909799698 0.120066385 [11] -0.471146328 -1.306078701 -0.359347827 1.588919607 0.609650490 [16] -0.041970825 -0.519045792 -0.299927236 -1.915487019 0.891487310 [21] 0.118554174 -0.457402191 0.464127502 0.159476958 0.431911800 [26] -0.130894068 0.025232167 0.258570058 1.054101727 -0.715630977 [31] -1.035540802 0.162845902 0.204477320 0.303049111 0.743628618 [36] 0.036040889 1.892024592 0.103452055 0.621386237 0.658532551 [41] -0.562782587 0.853123845 -0.584105063 0.851076019 0.886054923 [46] 0.856238291 -0.556064763 0.218923810 -1.951566308 -1.229078853 [51] 0.960642276 -0.322375001 -1.592664826 0.009525485 0.582701505 [56] -1.238067716 -0.167090977 -0.730336927 1.143156054 -0.831198621 [61] -2.032051212 -0.027025699 -0.974901679 -1.241296537 0.265886046 [66] 1.164727862 0.375153864 0.394000424 0.555074032 0.623129515 [71] 0.799493396 -0.975910383 -0.158936824 -1.580613832 -1.064626456 [76] -0.647907157 -0.591109811 1.421808851 -2.490274047 0.220531485 [81] -0.593268474 0.413318206 0.850886977 -1.525409546 0.401399971 [86] 0.237144819 1.040530463 0.687322066 0.365346456 0.741943965 [91] -0.179164354 0.926995618 -0.678708973 -0.072101707 0.441612992 [96] -1.782104792 0.128226446 -0.350927817 1.293464490 1.992479775 > colRanges(tmp) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 0.4386125 -0.01101418 -0.03666254 -0.2506621 1.28347 -0.7431081 -0.475931 [2,] 0.4386125 -0.01101418 -0.03666254 -0.2506621 1.28347 -0.7431081 -0.475931 [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,] -0.1542341 -0.9097997 0.1200664 -0.4711463 -1.306079 -0.3593478 1.58892 [2,] -0.1542341 -0.9097997 0.1200664 -0.4711463 -1.306079 -0.3593478 1.58892 [,15] [,16] [,17] [,18] [,19] [,20] [,21] [1,] 0.6096505 -0.04197083 -0.5190458 -0.2999272 -1.915487 0.8914873 0.1185542 [2,] 0.6096505 -0.04197083 -0.5190458 -0.2999272 -1.915487 0.8914873 0.1185542 [,22] [,23] [,24] [,25] [,26] [,27] [,28] [1,] -0.4574022 0.4641275 0.159477 0.4319118 -0.1308941 0.02523217 0.2585701 [2,] -0.4574022 0.4641275 0.159477 0.4319118 -0.1308941 0.02523217 0.2585701 [,29] [,30] [,31] [,32] [,33] [,34] [,35] [1,] 1.054102 -0.715631 -1.035541 0.1628459 0.2044773 0.3030491 0.7436286 [2,] 1.054102 -0.715631 -1.035541 0.1628459 0.2044773 0.3030491 0.7436286 [,36] [,37] [,38] [,39] [,40] [,41] [,42] [1,] 0.03604089 1.892025 0.1034521 0.6213862 0.6585326 -0.5627826 0.8531238 [2,] 0.03604089 1.892025 0.1034521 0.6213862 0.6585326 -0.5627826 0.8531238 [,43] [,44] [,45] [,46] [,47] [,48] [,49] [1,] -0.5841051 0.851076 0.8860549 0.8562383 -0.5560648 0.2189238 -1.951566 [2,] -0.5841051 0.851076 0.8860549 0.8562383 -0.5560648 0.2189238 -1.951566 [,50] [,51] [,52] [,53] [,54] [,55] [,56] [1,] -1.229079 0.9606423 -0.322375 -1.592665 0.009525485 0.5827015 -1.238068 [2,] -1.229079 0.9606423 -0.322375 -1.592665 0.009525485 0.5827015 -1.238068 [,57] [,58] [,59] [,60] [,61] [,62] [,63] [1,] -0.167091 -0.7303369 1.143156 -0.8311986 -2.032051 -0.0270257 -0.9749017 [2,] -0.167091 -0.7303369 1.143156 -0.8311986 -2.032051 -0.0270257 -0.9749017 [,64] [,65] [,66] [,67] [,68] [,69] [,70] [1,] -1.241297 0.265886 1.164728 0.3751539 0.3940004 0.555074 0.6231295 [2,] -1.241297 0.265886 1.164728 0.3751539 0.3940004 0.555074 0.6231295 [,71] [,72] [,73] [,74] [,75] [,76] [,77] [1,] 0.7994934 -0.9759104 -0.1589368 -1.580614 -1.064626 -0.6479072 -0.5911098 [2,] 0.7994934 -0.9759104 -0.1589368 -1.580614 -1.064626 -0.6479072 -0.5911098 [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85] [1,] 1.421809 -2.490274 0.2205315 -0.5932685 0.4133182 0.850887 -1.52541 0.4014 [2,] 1.421809 -2.490274 0.2205315 -0.5932685 0.4133182 0.850887 -1.52541 0.4014 [,86] [,87] [,88] [,89] [,90] [,91] [,92] [1,] 0.2371448 1.04053 0.6873221 0.3653465 0.741944 -0.1791644 0.9269956 [2,] 0.2371448 1.04053 0.6873221 0.3653465 0.741944 -0.1791644 0.9269956 [,93] [,94] [,95] [,96] [,97] [,98] [,99] [1,] -0.678709 -0.07210171 0.441613 -1.782105 0.1282264 -0.3509278 1.293464 [2,] -0.678709 -0.07210171 0.441613 -1.782105 0.1282264 -0.3509278 1.293464 [,100] [1,] 1.99248 [2,] 1.99248 > > > Max(tmp2) [1] 2.765029 > Min(tmp2) [1] -2.711265 > mean(tmp2) [1] 0.0584716 > Sum(tmp2) [1] 5.84716 > Var(tmp2) [1] 1.222714 > > rowMeans(tmp2) [1] -2.101588722 -0.054828659 0.966520622 0.826295007 -2.711264673 [6] -0.473350652 -1.168360991 -1.781322181 0.155589351 -0.008652725 [11] -0.364387263 -2.224855733 1.900743173 -0.612219342 0.841149238 [16] -0.675359224 0.189621620 0.132119428 0.884403659 0.457866058 [21] -1.211686283 0.661640036 0.598889900 1.189589058 0.376338975 [26] -0.008946045 0.033544025 0.028054888 0.390738619 -1.237752440 [31] 0.957881127 0.817342067 -0.792633659 0.923572246 0.120896014 [36] -1.428052062 -0.392936433 0.106312839 -0.306283055 -0.084304232 [41] -0.555579384 -2.129398674 -1.543904267 0.695334773 2.590907188 [46] -0.303769571 1.096600958 0.548612256 0.471781216 1.362780921 [51] 0.274304163 0.088471136 1.200077276 0.105357950 0.050935776 [56] -0.548755785 2.049388654 0.276826885 1.533807489 1.767124081 [61] -0.888159510 1.709791711 -0.945514901 0.860294366 -0.538020209 [66] -1.383448692 -0.650026069 1.340080854 2.765028698 0.072649153 [71] 0.286331879 2.268590934 0.514041407 -0.176986438 0.558995857 [76] 0.013171831 0.142479545 -0.120798436 -0.411040379 -2.676120791 [81] -0.733557727 -1.272401184 0.443780173 -0.784918390 -0.292138591 [86] 0.846325673 1.558686837 0.609679633 0.591618040 -1.217448238 [91] 0.375265253 0.462017011 2.094260102 -0.615405419 -0.587052033 [96] 0.338500610 0.444469742 -2.308074975 -1.072231986 0.273217895 > rowSums(tmp2) [1] -2.101588722 -0.054828659 0.966520622 0.826295007 -2.711264673 [6] -0.473350652 -1.168360991 -1.781322181 0.155589351 -0.008652725 [11] -0.364387263 -2.224855733 1.900743173 -0.612219342 0.841149238 [16] -0.675359224 0.189621620 0.132119428 0.884403659 0.457866058 [21] -1.211686283 0.661640036 0.598889900 1.189589058 0.376338975 [26] -0.008946045 0.033544025 0.028054888 0.390738619 -1.237752440 [31] 0.957881127 0.817342067 -0.792633659 0.923572246 0.120896014 [36] -1.428052062 -0.392936433 0.106312839 -0.306283055 -0.084304232 [41] -0.555579384 -2.129398674 -1.543904267 0.695334773 2.590907188 [46] -0.303769571 1.096600958 0.548612256 0.471781216 1.362780921 [51] 0.274304163 0.088471136 1.200077276 0.105357950 0.050935776 [56] -0.548755785 2.049388654 0.276826885 1.533807489 1.767124081 [61] -0.888159510 1.709791711 -0.945514901 0.860294366 -0.538020209 [66] -1.383448692 -0.650026069 1.340080854 2.765028698 0.072649153 [71] 0.286331879 2.268590934 0.514041407 -0.176986438 0.558995857 [76] 0.013171831 0.142479545 -0.120798436 -0.411040379 -2.676120791 [81] -0.733557727 -1.272401184 0.443780173 -0.784918390 -0.292138591 [86] 0.846325673 1.558686837 0.609679633 0.591618040 -1.217448238 [91] 0.375265253 0.462017011 2.094260102 -0.615405419 -0.587052033 [96] 0.338500610 0.444469742 -2.308074975 -1.072231986 0.273217895 > 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] -2.101588722 -0.054828659 0.966520622 0.826295007 -2.711264673 [6] -0.473350652 -1.168360991 -1.781322181 0.155589351 -0.008652725 [11] -0.364387263 -2.224855733 1.900743173 -0.612219342 0.841149238 [16] -0.675359224 0.189621620 0.132119428 0.884403659 0.457866058 [21] -1.211686283 0.661640036 0.598889900 1.189589058 0.376338975 [26] -0.008946045 0.033544025 0.028054888 0.390738619 -1.237752440 [31] 0.957881127 0.817342067 -0.792633659 0.923572246 0.120896014 [36] -1.428052062 -0.392936433 0.106312839 -0.306283055 -0.084304232 [41] -0.555579384 -2.129398674 -1.543904267 0.695334773 2.590907188 [46] -0.303769571 1.096600958 0.548612256 0.471781216 1.362780921 [51] 0.274304163 0.088471136 1.200077276 0.105357950 0.050935776 [56] -0.548755785 2.049388654 0.276826885 1.533807489 1.767124081 [61] -0.888159510 1.709791711 -0.945514901 0.860294366 -0.538020209 [66] -1.383448692 -0.650026069 1.340080854 2.765028698 0.072649153 [71] 0.286331879 2.268590934 0.514041407 -0.176986438 0.558995857 [76] 0.013171831 0.142479545 -0.120798436 -0.411040379 -2.676120791 [81] -0.733557727 -1.272401184 0.443780173 -0.784918390 -0.292138591 [86] 0.846325673 1.558686837 0.609679633 0.591618040 -1.217448238 [91] 0.375265253 0.462017011 2.094260102 -0.615405419 -0.587052033 [96] 0.338500610 0.444469742 -2.308074975 -1.072231986 0.273217895 > rowMin(tmp2) [1] -2.101588722 -0.054828659 0.966520622 0.826295007 -2.711264673 [6] -0.473350652 -1.168360991 -1.781322181 0.155589351 -0.008652725 [11] -0.364387263 -2.224855733 1.900743173 -0.612219342 0.841149238 [16] -0.675359224 0.189621620 0.132119428 0.884403659 0.457866058 [21] -1.211686283 0.661640036 0.598889900 1.189589058 0.376338975 [26] -0.008946045 0.033544025 0.028054888 0.390738619 -1.237752440 [31] 0.957881127 0.817342067 -0.792633659 0.923572246 0.120896014 [36] -1.428052062 -0.392936433 0.106312839 -0.306283055 -0.084304232 [41] -0.555579384 -2.129398674 -1.543904267 0.695334773 2.590907188 [46] -0.303769571 1.096600958 0.548612256 0.471781216 1.362780921 [51] 0.274304163 0.088471136 1.200077276 0.105357950 0.050935776 [56] -0.548755785 2.049388654 0.276826885 1.533807489 1.767124081 [61] -0.888159510 1.709791711 -0.945514901 0.860294366 -0.538020209 [66] -1.383448692 -0.650026069 1.340080854 2.765028698 0.072649153 [71] 0.286331879 2.268590934 0.514041407 -0.176986438 0.558995857 [76] 0.013171831 0.142479545 -0.120798436 -0.411040379 -2.676120791 [81] -0.733557727 -1.272401184 0.443780173 -0.784918390 -0.292138591 [86] 0.846325673 1.558686837 0.609679633 0.591618040 -1.217448238 [91] 0.375265253 0.462017011 2.094260102 -0.615405419 -0.587052033 [96] 0.338500610 0.444469742 -2.308074975 -1.072231986 0.273217895 > > colMeans(tmp2) [1] 0.0584716 > colSums(tmp2) [1] 5.84716 > colVars(tmp2) [1] 1.222714 > colSd(tmp2) [1] 1.105764 > colMax(tmp2) [1] 2.765029 > colMin(tmp2) [1] -2.711265 > colMedians(tmp2) [1] 0.1136044 > colRanges(tmp2) [,1] [1,] -2.711265 [2,] 2.765029 > > 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] 1.0538055 -2.5627278 4.5536595 -1.0696600 0.5842662 -1.5786387 [7] -6.8546460 -3.6942740 0.2988695 1.3936033 > colApply(tmp,quantile)[,1] [,1] [1,] -0.78387148 [2,] -0.52857284 [3,] 0.01042956 [4,] 0.39348788 [5,] 1.48336496 > > rowApply(tmp,sum) [1] -1.9603732 3.5230036 -0.8644282 0.4122239 -6.7970557 -6.3680244 [7] -1.7226024 -0.1211394 4.9300434 1.0926098 > rowApply(tmp,rank)[1:10,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 7 3 6 7 6 6 4 5 8 9 [2,] 6 2 4 5 10 5 2 1 10 2 [3,] 8 6 10 8 5 3 10 8 7 7 [4,] 3 10 8 1 7 1 9 7 5 3 [5,] 10 1 2 3 9 10 7 6 6 4 [6,] 4 4 1 4 8 8 6 9 3 8 [7,] 1 7 7 10 4 2 1 4 1 6 [8,] 2 5 5 9 1 9 5 2 2 5 [9,] 5 9 9 6 2 7 8 3 4 1 [10,] 9 8 3 2 3 4 3 10 9 10 > > tmp <- createBufferedMatrix(5,20) > > tmp[1:5,1:20] <- rnorm(100) > colApply(tmp,sum) [1] 1.9783187 -0.1653680 0.8073154 -3.3093549 -0.9897680 -0.6976712 [7] -1.5377022 -1.8851672 2.4574155 0.5956300 2.0737052 0.3011893 [13] 0.7658694 1.4197873 0.8914790 1.5184000 2.8681853 -1.0307827 [19] -0.4796038 3.8288659 > colApply(tmp,quantile)[,1] [,1] [1,] -1.3023062 [2,] 0.4322262 [3,] 0.6500303 [4,] 0.8629569 [5,] 1.3354115 > > rowApply(tmp,sum) [1] 4.88466431 2.81804194 6.29860326 -4.62505001 0.03448356 > rowApply(tmp,rank)[1:5,] [,1] [,2] [,3] [,4] [,5] [1,] 12 16 18 4 15 [2,] 19 1 12 17 4 [3,] 5 13 4 15 18 [4,] 14 2 6 1 5 [5,] 9 7 8 8 7 > > > as.matrix(tmp) [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0.4322262 1.5084417 -0.5043188 0.6772682 0.1783632 -0.2288377 [2,] 0.8629569 -1.3466410 0.4814990 -1.1918881 -0.1276498 -0.4932033 [3,] 1.3354115 0.2638050 -0.5488793 -0.1004071 0.1212181 0.5651341 [4,] -1.3023062 0.4698064 0.4166367 -1.8762279 -0.5826800 -0.7922461 [5,] 0.6500303 -1.0607800 0.9623778 -0.8180999 -0.5790195 0.2514819 [,7] [,8] [,9] [,10] [,11] [,12] [1,] -1.4035562 -0.4449909 1.2214449 -0.5343741 -0.68409162 0.80200131 [2,] 0.9689516 -0.1355000 0.1199620 -0.4587774 1.39709011 -0.99382053 [3,] 0.2224229 1.7169921 1.1785098 -0.6911445 0.04848964 0.20852547 [4,] 0.4779445 -1.7258379 -0.2243383 0.4204700 0.66122562 -0.09377721 [5,] -1.8034650 -1.2958305 0.1618371 1.8594561 0.65099149 0.37826027 [,13] [,14] [,15] [,16] [,17] [,18] [1,] -0.1759297 0.34419025 0.46330052 0.715678457 1.17038670 -0.78026517 [2,] 0.7639321 -0.08846567 0.83986905 0.042417325 0.91592567 -0.01198027 [3,] -0.9983398 -0.75698626 1.13959690 0.609980261 1.58801747 -0.16822673 [4,] 0.1299041 2.52313060 -0.07647614 0.008337635 -0.79483178 -0.60955391 [5,] 1.0463027 -0.60208166 -1.47481134 0.141986281 -0.01131276 0.53924341 [,19] [,20] [1,] 0.3338485 1.79387863 [2,] 0.2317017 1.04166253 [3,] 0.1486797 0.41580399 [4,] -1.5766492 -0.07758066 [5,] 0.3828155 0.65510137 > > > 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 : 563 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 0.7008303 -0.5515757 1.749169 0.7925639 -0.1676955 0.4986415 0.4724833 col8 col9 col10 col11 col12 col13 col14 row1 -1.068704 1.076197 1.049201 -0.07410155 1.066241 0.3247658 0.6843887 col15 col16 col17 col18 col19 col20 row1 1.526504 0.6815813 -1.023362 1.932828 0.6696529 1.271597 > tmp[,"col10"] col10 row1 1.0492007 row2 -1.4068611 row3 -0.5494088 row4 1.5224434 row5 0.1152975 > tmp[c("row1","row5"),] col1 col2 col3 col4 col5 col6 col7 row1 0.7008303 -0.5515757 1.749169 0.7925639 -0.1676955 0.4986415 0.47248331 row5 0.1650255 -0.1467553 1.780451 0.4013584 -0.7976003 0.4640973 0.01147993 col8 col9 col10 col11 col12 col13 col14 row1 -1.0687042 1.0761967 1.0492007 -0.07410155 1.066241 0.3247658 0.6843887 row5 0.5600865 0.8016805 0.1152975 -0.21373098 -1.018696 -1.6730264 -1.3926524 col15 col16 col17 col18 col19 col20 row1 1.526504 0.6815813 -1.0233618 1.9328279 0.6696529 1.2715973 row5 -1.957178 -0.1875480 0.6048339 0.4037206 -0.1060593 -0.1488295 > tmp[,c("col6","col20")] col6 col20 row1 0.4986415 1.2715973 row2 -0.3254734 0.9699923 row3 -0.7787077 1.4450303 row4 -0.6587929 -0.6678378 row5 0.4640973 -0.1488295 > tmp[c("row1","row5"),c("col6","col20")] col6 col20 row1 0.4986415 1.2715973 row5 0.4640973 -0.1488295 > > > > > 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 50.25421 50.23737 49.63429 49.23499 52.14728 103.3062 50.72401 49.59834 col9 col10 col11 col12 col13 col14 col15 col16 row1 49.37538 50.42715 51.26795 50.6637 48.82973 50.40041 49.24157 50.89385 col17 col18 col19 col20 row1 50.45449 49.43544 47.17657 106.6957 > tmp[,"col10"] col10 row1 50.42715 row2 30.01361 row3 30.30453 row4 29.50262 row5 51.39383 > tmp[c("row1","row5"),] col1 col2 col3 col4 col5 col6 col7 col8 row1 50.25421 50.23737 49.63429 49.23499 52.14728 103.3062 50.72401 49.59834 row5 48.84664 49.93671 48.32034 49.34542 48.01632 105.4601 49.64452 48.99981 col9 col10 col11 col12 col13 col14 col15 col16 row1 49.37538 50.42715 51.26795 50.66370 48.82973 50.40041 49.24157 50.89385 row5 49.89045 51.39383 47.84485 49.50176 50.47393 48.37527 49.44318 49.08881 col17 col18 col19 col20 row1 50.45449 49.43544 47.17657 106.6957 row5 50.23174 49.65900 48.93938 104.2511 > tmp[,c("col6","col20")] col6 col20 row1 103.30624 106.69572 row2 73.87813 72.62036 row3 76.15281 73.23142 row4 73.93496 77.07762 row5 105.46005 104.25110 > tmp[c("row1","row5"),c("col6","col20")] col6 col20 row1 103.3062 106.6957 row5 105.4601 104.2511 > > > subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2] col6 col20 row1 103.3062 106.6957 row5 105.4601 104.2511 > > > > > > tmp <- createBufferedMatrix(5,20) > tmp[1:5,1:20] <- rnorm(100) > colnames(tmp) <- colnames(tmp,do.NULL=FALSE) > > tmp[,"col13"] col13 [1,] 2.15754479 [2,] 0.42964275 [3,] 0.07934662 [4,] -0.56759925 [5,] 0.23022545 > tmp[,c("col17","col7")] col17 col7 [1,] 0.3237397 0.20874809 [2,] -0.2139555 -0.44723424 [3,] -1.4188799 -0.01460427 [4,] 0.5790337 -0.60524256 [5,] 1.6243831 -1.70028297 > > subBufferedMatrix(tmp,,c("col6","col20"))[,1:2] col6 col20 [1,] -0.85300934 -1.08375672 [2,] 0.05544815 0.06442323 [3,] -0.28292029 -0.16735177 [4,] 1.06279261 -1.01208971 [5,] 0.70317648 0.07141199 > subBufferedMatrix(tmp,1,c("col6"))[,1] col1 [1,] -0.8530093 > subBufferedMatrix(tmp,1:2,c("col6"))[,1] col6 [1,] -0.85300934 [2,] 0.05544815 > > > > 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] row3 0.04070722 -0.6820810 -0.7798950 -0.9365195 -0.9238822 0.1533425 row1 -0.49313808 0.3503868 -0.4221772 0.8427242 -0.5894958 -0.7907676 [,7] [,8] [,9] [,10] [,11] [,12] row3 1.2186762 -2.4318863 -1.03400137 -0.5643321 -1.2363415 -1.8312442 row1 -0.8829018 0.7216917 -0.04056506 -0.2053165 0.7719469 0.3055096 [,13] [,14] [,15] [,16] [,17] [,18] [,19] row3 -0.4809548 -1.806035 0.02521047 -0.230219 -0.8942802 0.7431558 0.6158897 row1 -1.1200248 0.114512 0.38840975 1.005411 -1.2046930 1.6796862 0.7159322 [,20] row3 -0.7718991 row1 -1.0237579 > subBufferedMatrix(tmp,c("row2"),1:10)[,1:10] [,1] [,2] [,3] [,4] [,5] [,6] [,7] row2 -0.8489029 0.2482509 0.561591 -0.7009278 -1.079838 -0.5588176 -0.2041284 [,8] [,9] [,10] row2 0.8465487 -0.2573595 0.5237579 > subBufferedMatrix(tmp,c("row5"),1:20)[,1:20] [,1] [,2] [,3] [,4] [,5] [,6] [,7] row5 0.02617216 1.197927 -1.276534 0.2956852 -1.978019 0.2563104 0.6500767 [,8] [,9] [,10] [,11] [,12] [,13] [,14] row5 -1.076815 -0.6012355 0.1359827 0.03744248 1.732438 0.5921429 -0.352303 [,15] [,16] [,17] [,18] [,19] [,20] row5 -1.984076 -0.8285452 0.143671 -0.7973313 0.8452343 -1.34846 > > > 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: 0x600002ce4420> > is.ReadOnlyMode(tmp) [1] TRUE > > filenames(tmp) [1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c24f6f430" [2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c51198e45" [3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c64cb7d9b" [4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c6ba37ecf" [5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c3ada7f3e" [6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c5ed7dda1" [7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c2e17a5ac" [8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c127dd6d8" [9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c3a40864" [10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c622df1a" [11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c5b65271b" [12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c4dea8c7d" [13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c61ad8a81" [14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c48604d40" [15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM165c2a6fc9df" > > > ### 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: 0x600002ce0180> > MoveStorageDirectory(tmp,getwd(),full.path=TRUE) <pointer: 0x600002ce0180> Warning message: In dir.create(new.directory) : '/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists > > > RowMode(tmp) <pointer: 0x600002ce0180> > rowMedians(tmp) [1] -0.0188079819 0.1730137711 -0.2678923193 0.0477986014 0.3846190443 [6] 0.2560653973 0.1810524534 -0.3678531540 -0.0906052903 -0.0227083403 [11] 0.1569012624 -0.0215893642 0.3704235006 -0.1630356510 -0.0369854787 [16] 0.3673885596 0.2570512979 0.5838485841 -0.1022053563 0.3974895635 [21] 0.1240590275 0.1750015997 -0.2441230476 0.4402739936 0.1790003740 [26] -0.1813405357 -0.2284424114 0.0239359285 -0.5663570795 -0.0979110487 [31] 0.1189690129 0.4073140454 -0.0120014590 0.2175682315 -0.0926918586 [36] 0.5104538294 0.0072740510 -0.1891306663 -0.6266416346 0.3151198151 [41] -0.6600045796 -0.3572057408 -0.0267113203 0.0787686772 -0.1534069254 [46] 0.5696197928 -0.0380143462 -0.4319852126 0.2005765116 0.1330762466 [51] 0.0389243536 0.5285690518 -0.0626973499 -0.0001495259 -0.0871384323 [56] -0.4500363127 0.0121159488 -0.3983960095 -0.3591537200 0.1901323028 [61] 0.3508113284 -0.1749403008 0.3048494146 0.5061397243 0.1538914239 [66] -0.0694309188 -0.6120331786 0.1785785427 -0.1877176911 0.3928095585 [71] 0.2294536209 0.1988933691 -0.1000485728 0.1932893751 0.2202120339 [76] -0.1220225294 -0.3592553592 0.5517579239 -0.3056740708 0.4207021591 [81] 0.3252766213 -0.0155944909 -0.1686176611 0.3198249871 -0.4873608600 [86] 0.0450237454 -0.3857044417 0.1187097707 -0.0107877682 -0.0695300023 [91] 0.1407360297 0.1607892422 -0.0415386035 0.2480765194 -0.2911431990 [96] 0.5264295962 0.0110848946 0.1798412298 -0.3631827718 -0.2323923228 [101] -0.6601186005 -0.0418564204 0.1808017208 -0.0452510758 -0.0561036444 [106] -0.0578800885 -0.1347162384 -0.3978742443 0.0782569279 0.1380228123 [111] -0.2844984130 0.4421014557 0.0683902881 -0.0140097081 -0.0236815652 [116] -0.0195069033 -0.5283874912 0.0038485864 -0.1804879233 0.3130173312 [121] 0.2676804741 -0.2017364484 0.3740123445 0.0469729838 0.2543045486 [126] 0.6273392516 -0.3182335180 0.1802878585 0.0926148132 0.1459880290 [131] 0.0546036796 -0.4773974769 0.0782521448 0.3141093290 0.0650839339 [136] -0.1649317915 0.5919990791 -0.3142199788 -0.0878873462 0.2323432902 [141] 0.4037384165 0.1553608681 0.0950218040 -0.3364742189 0.5436888111 [146] 0.5148333608 -0.2201583719 -0.4186506008 0.1529841205 0.2645186613 [151] 0.0475948849 0.0333733316 0.4539066355 -0.0398694998 0.4966224362 [156] 0.2582030573 -0.1838265221 -0.0555978864 0.5600811628 -0.2178285014 [161] 0.4383748417 -0.6886501276 0.1775435967 0.0378560030 0.0715991647 [166] -0.1022999833 0.4062177873 0.4386068839 0.0864907340 0.0411398453 [171] -0.5588624757 -0.0373495275 -0.2178310835 0.5449558864 -0.3765051778 [176] 0.2209844806 -0.1542071900 -0.3957489189 0.1218820362 -0.0296489638 [181] 0.4879968263 -0.0162380343 -0.6260883936 -0.1417475793 0.1204597266 [186] -0.3574806345 -0.1340000187 -0.0135517470 0.0376084046 0.3197214036 [191] 0.1382827135 -0.3685328697 0.3454508375 -0.1163214643 0.2937600800 [196] 0.2774209506 0.1627197876 -0.0031542678 0.1959023813 -0.1609946391 [201] 0.2081275172 -0.4827273803 -0.1240853173 -0.1488056231 0.2674196540 [206] 0.3644655063 -0.4890155836 -0.0781474739 0.1385820563 -0.1428338891 [211] 0.4501662010 -0.3025894473 -0.0343660205 -0.3005394545 -0.2262193892 [216] -0.4226823248 -0.2031263604 -0.1004101728 0.3753672173 0.2240782886 [221] -0.4488172341 0.0802976926 0.0371361736 0.1191295530 0.0642769420 [226] 0.0164794808 -0.3762847339 0.3173077817 -0.3929663335 -0.1448448021 > > proc.time() user system elapsed 0.623 3.068 3.949
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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: 0x600003ea8360> > .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: 0x600003ea8360> > .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: 0x600003ea8360> > .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: 0x600003ea8360> > 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: 0x600003e9c000> > .Call("R_bm_AddColumn",P) <pointer: 0x600003e9c000> > .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: 0x600003e9c000> > .Call("R_bm_AddColumn",P) <pointer: 0x600003e9c000> > .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: 0x600003e9c000> > 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: 0x600003e9c180> > .Call("R_bm_AddColumn",P) <pointer: 0x600003e9c180> > .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: 0x600003e9c180> > > .Call("R_bm_ResizeBuffer",P,5,5) <pointer: 0x600003e9c180> > .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: 0x600003e9c180> > > .Call("R_bm_RowMode",P) <pointer: 0x600003e9c180> > .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: 0x600003e9c180> > > .Call("R_bm_ColMode",P) <pointer: 0x600003e9c180> > .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: 0x600003e9c180> > 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: 0x600003e9c360> > .Call("R_bm_SetPrefix",P,"BufferedMatrixFile") <pointer: 0x600003e9c360> > .Call("R_bm_AddColumn",P) <pointer: 0x600003e9c360> > .Call("R_bm_AddColumn",P) <pointer: 0x600003e9c360> > dir(pattern="BufferedMatrixFile") [1] "BufferedMatrixFile172f15c7ba2c" "BufferedMatrixFile172f6b8fa9df" > rm(P) > dir(pattern="BufferedMatrixFile") [1] "BufferedMatrixFile172f15c7ba2c" "BufferedMatrixFile172f6b8fa9df" > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_setRows",P,10) [1] TRUE > .Call("R_bm_AddColumn",P) <pointer: 0x600003e98000> > .Call("R_bm_AddColumn",P) <pointer: 0x600003e98000> > .Call("R_bm_ReadOnlyModeToggle",P) <pointer: 0x600003e98000> > .Call("R_bm_isReadOnlyMode",P) [1] TRUE > .Call("R_bm_ReadOnlyModeToggle",P) <pointer: 0x600003e98000> > .Call("R_bm_isReadOnlyMode",P) [1] FALSE > .Call("R_bm_isRowMode",P) [1] FALSE > .Call("R_bm_RowMode",P) <pointer: 0x600003e98000> > .Call("R_bm_isRowMode",P) [1] TRUE > .Call("R_bm_ColMode",P) <pointer: 0x600003e98000> > .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: 0x600003e94000> > .Call("R_bm_AddColumn",P) <pointer: 0x600003e94000> > > .Call("R_bm_getSize",P) [1] 10 2 > .Call("R_bm_getBufferSize",P) [1] 1 1 > .Call("R_bm_ResizeBuffer",P,5,5) <pointer: 0x600003e94000> > > .Call("R_bm_getBufferSize",P) [1] 5 5 > .Call("R_bm_ResizeBuffer",P,-1,5) <pointer: 0x600003e94000> > 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: 0x600003e94180> > .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: 0x600003e94180> > rm(P) > > proc.time() user system elapsed 0.121 0.048 0.165
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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 0.107 0.020 0.125