Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-13 12:04 -0400 (Mon, 13 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: 2025-10-12 20:28:22 -0400 (Sun, 12 Oct 2025) |
EndedAt: 2025-10-12 20:30:14 -0400 (Sun, 12 Oct 2025) |
EllapsedTime: 111.4 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 0.360 0.175 0.851
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] "Sun Oct 12 20:28:50 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] "Sun Oct 12 20:28:52 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: 0x6000019f8000> > > > > 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] "Sun Oct 12 20:29:16 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] "Sun Oct 12 20:29:25 2025" > > ColMode(tmp2) <pointer: 0x6000019f8000> > > > > ### 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,] 100.0286675 0.5147302 -0.03107233 -2.1798147 [2,] -0.3995553 0.8834863 0.64490730 1.6604207 [3,] 1.1426208 1.0826454 -0.30496617 0.1625261 [4,] 0.3813134 -0.6325070 -0.71673363 -0.5928637 > 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 : 2 Kilobytes. Disk usage : 1.6 Kilobytes. > tmp5[1:4,1:4] [,1] [,2] [,3] [,4] [1,] 100.0286675 0.5147302 0.03107233 2.1798147 [2,] 0.3995553 0.8834863 0.64490730 1.6604207 [3,] 1.1426208 1.0826454 0.30496617 0.1625261 [4,] 0.3813134 0.6325070 0.71673363 0.5928637 > 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 : 2 Kilobytes. Disk usage : 1.6 Kilobytes. > tmp5[1:4,1:4] [,1] [,2] [,3] [,4] [1,] 10.0014333 0.7174470 0.1762735 1.4764195 [2,] 0.6321038 0.9399395 0.8030612 1.2885731 [3,] 1.0689344 1.0405025 0.5522374 0.4031452 [4,] 0.6175057 0.7953031 0.8466012 0.7699764 > > 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 : 2 Kilobytes. Disk usage : 1.6 Kilobytes. > tmp5[1:4,1:4] [,1] [,2] [,3] [,4] [1,] 225.04300 32.68920 26.79381 41.94401 [2,] 31.72059 35.28288 33.67552 39.54615 [3,] 36.83196 36.48767 30.82734 29.19398 [4,] 31.55637 33.58554 34.18275 33.29263 > > > > ## testing functions that elementwise transform the matrix > sqrt(tmp5) <pointer: 0x6000019e0000> > exp(tmp5) <pointer: 0x6000019e0000> > log(tmp5,2) <pointer: 0x6000019e0000> > pow(tmp5,2) > > > > > > ## testing functions that apply to entire matrix > Max(tmp5) [1] 468.3975 > Min(tmp5) [1] 52.699 > mean(tmp5) [1] 72.45231 > Sum(tmp5) [1] 14490.46 > Var(tmp5) [1] 871.1326 > > > ## testing functions applied to rows or columns > > rowMeans(tmp5) [1] 91.86080 72.53680 71.14375 71.41977 66.07180 71.37667 71.20213 69.68802 [9] 69.71830 69.50509 > rowSums(tmp5) [1] 1837.216 1450.736 1422.875 1428.395 1321.436 1427.533 1424.043 1393.760 [9] 1394.366 1390.102 > rowVars(tmp5) [1] 7955.12455 74.66628 108.81488 60.53816 73.58629 90.95123 [7] 92.28405 55.08504 77.42305 65.27560 > rowSd(tmp5) [1] 89.191505 8.640965 10.431437 7.780627 8.578245 9.536835 9.606459 [8] 7.421930 8.799037 8.079332 > rowMax(tmp5) [1] 468.39752 92.82984 84.60319 83.81959 85.40869 87.78999 84.34203 [8] 85.99230 85.47032 83.68679 > rowMin(tmp5) [1] 55.76780 58.26087 52.69900 59.05425 53.34551 55.17725 55.41327 59.73626 [9] 54.66615 57.19196 > > colMeans(tmp5) [1] 110.41483 73.03909 70.66802 72.01135 71.76644 64.70924 73.68326 [8] 75.53440 68.38537 68.74324 71.70102 70.45608 67.95266 68.65979 [15] 70.80706 69.94933 69.47177 73.70322 69.56828 67.82179 > colSums(tmp5) [1] 1104.1483 730.3909 706.6802 720.1135 717.6644 647.0924 736.8326 [8] 755.3440 683.8537 687.4324 717.0102 704.5608 679.5266 686.5979 [15] 708.0706 699.4933 694.7177 737.0322 695.6828 678.2179 > colVars(tmp5) [1] 15901.29018 93.35286 72.83692 110.85565 88.65098 108.55178 [7] 74.05514 50.23725 88.91002 93.10226 112.09405 107.66119 [13] 115.99157 17.47387 90.52689 70.26638 71.32242 46.91509 [19] 64.83795 66.14358 > colSd(tmp5) [1] 126.100318 9.661928 8.534455 10.528801 9.415465 10.418819 [7] 8.605530 7.087824 9.429211 9.648951 10.587448 10.375991 [13] 10.769938 4.180176 9.514562 8.382504 8.445260 6.849459 [19] 8.052202 8.132871 > colMax(tmp5) [1] 468.39752 85.99230 87.78999 87.30096 83.68679 85.47032 83.92947 [8] 85.77984 81.91359 83.40392 87.07409 84.34203 83.67313 77.21413 [15] 92.82984 81.30830 80.06549 82.10253 80.10512 80.00284 > colMin(tmp5) [1] 53.34551 57.85321 55.76780 56.60378 56.72295 52.78233 62.45924 65.05830 [9] 57.74821 57.84832 56.50281 54.71627 55.41327 62.72809 61.52130 56.49762 [17] 54.66615 64.12805 52.69900 59.73626 > > > ### 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] 91.86080 72.53680 71.14375 71.41977 66.07180 NA 71.20213 69.68802 [9] 69.71830 69.50509 > rowSums(tmp5) [1] 1837.216 1450.736 1422.875 1428.395 1321.436 NA 1424.043 1393.760 [9] 1394.366 1390.102 > rowVars(tmp5) [1] 7955.12455 74.66628 108.81488 60.53816 73.58629 94.51643 [7] 92.28405 55.08504 77.42305 65.27560 > rowSd(tmp5) [1] 89.191505 8.640965 10.431437 7.780627 8.578245 9.721956 9.606459 [8] 7.421930 8.799037 8.079332 > rowMax(tmp5) [1] 468.39752 92.82984 84.60319 83.81959 85.40869 NA 84.34203 [8] 85.99230 85.47032 83.68679 > rowMin(tmp5) [1] 55.76780 58.26087 52.69900 59.05425 53.34551 NA 55.41327 59.73626 [9] 54.66615 57.19196 > > colMeans(tmp5) [1] 110.41483 73.03909 70.66802 72.01135 71.76644 64.70924 73.68326 [8] 75.53440 68.38537 68.74324 71.70102 70.45608 67.95266 68.65979 [15] 70.80706 69.94933 NA 73.70322 69.56828 67.82179 > colSums(tmp5) [1] 1104.1483 730.3909 706.6802 720.1135 717.6644 647.0924 736.8326 [8] 755.3440 683.8537 687.4324 717.0102 704.5608 679.5266 686.5979 [15] 708.0706 699.4933 NA 737.0322 695.6828 678.2179 > colVars(tmp5) [1] 15901.29018 93.35286 72.83692 110.85565 88.65098 108.55178 [7] 74.05514 50.23725 88.91002 93.10226 112.09405 107.66119 [13] 115.99157 17.47387 90.52689 70.26638 NA 46.91509 [19] 64.83795 66.14358 > colSd(tmp5) [1] 126.100318 9.661928 8.534455 10.528801 9.415465 10.418819 [7] 8.605530 7.087824 9.429211 9.648951 10.587448 10.375991 [13] 10.769938 4.180176 9.514562 8.382504 NA 6.849459 [19] 8.052202 8.132871 > colMax(tmp5) [1] 468.39752 85.99230 87.78999 87.30096 83.68679 85.47032 83.92947 [8] 85.77984 81.91359 83.40392 87.07409 84.34203 83.67313 77.21413 [15] 92.82984 81.30830 NA 82.10253 80.10512 80.00284 > colMin(tmp5) [1] 53.34551 57.85321 55.76780 56.60378 56.72295 52.78233 62.45924 65.05830 [9] 57.74821 57.84832 56.50281 54.71627 55.41327 62.72809 61.52130 56.49762 [17] NA 64.12805 52.69900 59.73626 > > Max(tmp5,na.rm=TRUE) [1] 468.3975 > Min(tmp5,na.rm=TRUE) [1] 52.699 > mean(tmp5,na.rm=TRUE) [1] 72.43237 > Sum(tmp5,na.rm=TRUE) [1] 14414.04 > Var(tmp5,na.rm=TRUE) [1] 875.4524 > > rowMeans(tmp5,na.rm=TRUE) [1] 91.86080 72.53680 71.14375 71.41977 66.07180 71.11121 71.20213 69.68802 [9] 69.71830 69.50509 > rowSums(tmp5,na.rm=TRUE) [1] 1837.216 1450.736 1422.875 1428.395 1321.436 1351.113 1424.043 1393.760 [9] 1394.366 1390.102 > rowVars(tmp5,na.rm=TRUE) [1] 7955.12455 74.66628 108.81488 60.53816 73.58629 94.51643 [7] 92.28405 55.08504 77.42305 65.27560 > rowSd(tmp5,na.rm=TRUE) [1] 89.191505 8.640965 10.431437 7.780627 8.578245 9.721956 9.606459 [8] 7.421930 8.799037 8.079332 > rowMax(tmp5,na.rm=TRUE) [1] 468.39752 92.82984 84.60319 83.81959 85.40869 87.78999 84.34203 [8] 85.99230 85.47032 83.68679 > rowMin(tmp5,na.rm=TRUE) [1] 55.76780 58.26087 52.69900 59.05425 53.34551 55.17725 55.41327 59.73626 [9] 54.66615 57.19196 > > colMeans(tmp5,na.rm=TRUE) [1] 110.41483 73.03909 70.66802 72.01135 71.76644 64.70924 73.68326 [8] 75.53440 68.38537 68.74324 71.70102 70.45608 67.95266 68.65979 [15] 70.80706 69.94933 68.69971 73.70322 69.56828 67.82179 > colSums(tmp5,na.rm=TRUE) [1] 1104.1483 730.3909 706.6802 720.1135 717.6644 647.0924 736.8326 [8] 755.3440 683.8537 687.4324 717.0102 704.5608 679.5266 686.5979 [15] 708.0706 699.4933 618.2974 737.0322 695.6828 678.2179 > colVars(tmp5,na.rm=TRUE) [1] 15901.29018 93.35286 72.83692 110.85565 88.65098 108.55178 [7] 74.05514 50.23725 88.91002 93.10226 112.09405 107.66119 [13] 115.99157 17.47387 90.52689 70.26638 73.53179 46.91509 [19] 64.83795 66.14358 > colSd(tmp5,na.rm=TRUE) [1] 126.100318 9.661928 8.534455 10.528801 9.415465 10.418819 [7] 8.605530 7.087824 9.429211 9.648951 10.587448 10.375991 [13] 10.769938 4.180176 9.514562 8.382504 8.575068 6.849459 [19] 8.052202 8.132871 > colMax(tmp5,na.rm=TRUE) [1] 468.39752 85.99230 87.78999 87.30096 83.68679 85.47032 83.92947 [8] 85.77984 81.91359 83.40392 87.07409 84.34203 83.67313 77.21413 [15] 92.82984 81.30830 80.06549 82.10253 80.10512 80.00284 > colMin(tmp5,na.rm=TRUE) [1] 53.34551 57.85321 55.76780 56.60378 56.72295 52.78233 62.45924 65.05830 [9] 57.74821 57.84832 56.50281 54.71627 55.41327 62.72809 61.52130 56.49762 [17] 54.66615 64.12805 52.69900 59.73626 > > # now set an entire row to NA > > tmp5[which.row,] <- NA > rowMeans(tmp5,na.rm=TRUE) [1] 91.86080 72.53680 71.14375 71.41977 66.07180 NaN 71.20213 69.68802 [9] 69.71830 69.50509 > rowSums(tmp5,na.rm=TRUE) [1] 1837.216 1450.736 1422.875 1428.395 1321.436 0.000 1424.043 1393.760 [9] 1394.366 1390.102 > rowVars(tmp5,na.rm=TRUE) [1] 7955.12455 74.66628 108.81488 60.53816 73.58629 NA [7] 92.28405 55.08504 77.42305 65.27560 > rowSd(tmp5,na.rm=TRUE) [1] 89.191505 8.640965 10.431437 7.780627 8.578245 NA 9.606459 [8] 7.421930 8.799037 8.079332 > rowMax(tmp5,na.rm=TRUE) [1] 468.39752 92.82984 84.60319 83.81959 85.40869 NA 84.34203 [8] 85.99230 85.47032 83.68679 > rowMin(tmp5,na.rm=TRUE) [1] 55.76780 58.26087 52.69900 59.05425 53.34551 NA 55.41327 59.73626 [9] 54.66615 57.19196 > > > # now set an entire col to NA > > > tmp5[,which.col] <- NA > colMeans(tmp5,na.rm=TRUE) [1] 113.13800 71.89976 68.76558 72.71544 73.03025 65.76834 74.38865 [8] 76.69842 69.03777 68.35512 69.99290 69.95320 67.25165 68.65776 [15] 71.07128 71.44397 NaN 74.06958 69.56619 66.93301 > colSums(tmp5,na.rm=TRUE) [1] 1018.2420 647.0979 618.8902 654.4390 657.2722 591.9151 669.4978 [8] 690.2858 621.3399 615.1961 629.9361 629.5788 605.2649 617.9199 [15] 639.6415 642.9957 0.0000 666.6263 626.0957 602.3970 > colVars(tmp5,na.rm=TRUE) [1] 17805.52529 90.41873 41.22461 119.13549 81.76366 109.50148 [7] 77.71444 41.27400 95.23549 103.04534 93.28201 118.27388 [13] 124.96210 19.65805 101.05737 53.91792 NA 51.26947 [19] 72.94264 65.52463 > colSd(tmp5,na.rm=TRUE) [1] 133.437346 9.508877 6.420639 10.914920 9.042326 10.464296 [7] 8.815579 6.424485 9.758867 10.151125 9.658261 10.875380 [13] 11.178645 4.433740 10.052729 7.342882 NA 7.160270 [19] 8.540647 8.094729 > colMax(tmp5,na.rm=TRUE) [1] 468.39752 85.99230 77.20594 87.30096 83.68679 85.47032 83.92947 [8] 85.77984 81.91359 83.40392 84.60319 84.34203 83.67313 77.21413 [15] 92.82984 81.30830 -Inf 82.10253 80.10512 80.00284 > colMin(tmp5,na.rm=TRUE) [1] 53.34551 57.85321 55.76780 56.60378 56.72295 52.78233 62.45924 68.64706 [9] 57.74821 57.84832 56.50281 54.71627 55.41327 62.72809 61.52130 62.43829 [17] Inf 64.12805 52.69900 59.73626 > > > > > 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] 146.1431 107.9669 161.9040 219.0416 363.0176 272.1904 211.7721 366.5609 [9] 221.7057 152.1041 > apply(copymatrix,1,var,na.rm=TRUE) [1] 146.1431 107.9669 161.9040 219.0416 363.0176 272.1904 211.7721 366.5609 [9] 221.7057 152.1041 > > > > 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] -1.705303e-13 0.000000e+00 2.842171e-14 0.000000e+00 -1.705303e-13 [6] -1.136868e-13 -3.410605e-13 0.000000e+00 1.705303e-13 5.684342e-14 [11] -2.842171e-14 2.842171e-14 1.421085e-14 1.705303e-13 5.684342e-14 [16] 5.684342e-14 -8.526513e-14 1.136868e-13 2.842171e-14 1.136868e-13 > > > > > > > > > > > ## 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) + } 3 16 9 20 1 20 8 18 4 3 5 9 3 2 2 13 8 20 7 18 2 19 3 17 7 16 5 19 6 14 5 13 2 10 7 14 9 11 3 8 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] 1.910749 > Min(tmp) [1] -1.945917 > mean(tmp) [1] -0.03186931 > Sum(tmp) [1] -3.186931 > Var(tmp) [1] 0.8907916 > > rowMeans(tmp) [1] -0.03186931 > rowSums(tmp) [1] -3.186931 > rowVars(tmp) [1] 0.8907916 > rowSd(tmp) [1] 0.9438176 > rowMax(tmp) [1] 1.910749 > rowMin(tmp) [1] -1.945917 > > colMeans(tmp) [1] 0.078482226 -0.928120477 -1.540397338 0.632599303 0.118958200 [6] -0.872003271 -0.511158180 0.712654928 0.034247777 0.684975090 [11] 1.463264196 0.115904377 0.119461464 0.540296474 -0.279672497 [16] -0.378208254 -1.662199397 -0.779801072 -1.331237159 -0.411669168 [21] -1.568399182 -0.859330766 0.571492183 1.406978595 0.272476266 [26] 0.415474213 -0.495669243 0.444537350 1.170070840 0.999146445 [31] 0.911630461 -1.257038185 0.671331562 -0.239124952 -0.464077801 [36] -1.344712829 -0.803635966 -0.901445539 -1.520502737 -0.457098702 [41] 0.505014456 0.115429757 0.441471513 1.208629786 -1.196750602 [46] -0.311632502 -0.807734649 1.910748796 1.268459591 0.451900919 [51] 1.582515058 -0.500730151 1.904207800 -0.440214335 0.405414226 [56] 0.008853868 -0.189445982 1.730053195 -1.757677743 0.648103189 [61] 1.093165306 0.039412972 1.551318313 -1.143677317 0.561158463 [66] 0.280159851 -1.778984524 -1.003204300 0.289172591 1.237734914 [71] -1.505478030 0.443184920 1.084824936 0.027230626 -0.019148108 [76] -1.945916562 0.302093017 0.328091995 0.567015206 1.148935482 [81] -0.719111436 -1.322588628 -1.210568878 0.649806958 0.766002180 [86] 0.038143888 1.374614758 -1.432908259 -0.403353261 -0.895212543 [91] 0.586496660 0.037862452 -0.997465377 -1.042396357 0.040506733 [96] 0.701672948 0.211496918 -0.988343582 -0.355189464 0.481418076 > colSums(tmp) [1] 0.078482226 -0.928120477 -1.540397338 0.632599303 0.118958200 [6] -0.872003271 -0.511158180 0.712654928 0.034247777 0.684975090 [11] 1.463264196 0.115904377 0.119461464 0.540296474 -0.279672497 [16] -0.378208254 -1.662199397 -0.779801072 -1.331237159 -0.411669168 [21] -1.568399182 -0.859330766 0.571492183 1.406978595 0.272476266 [26] 0.415474213 -0.495669243 0.444537350 1.170070840 0.999146445 [31] 0.911630461 -1.257038185 0.671331562 -0.239124952 -0.464077801 [36] -1.344712829 -0.803635966 -0.901445539 -1.520502737 -0.457098702 [41] 0.505014456 0.115429757 0.441471513 1.208629786 -1.196750602 [46] -0.311632502 -0.807734649 1.910748796 1.268459591 0.451900919 [51] 1.582515058 -0.500730151 1.904207800 -0.440214335 0.405414226 [56] 0.008853868 -0.189445982 1.730053195 -1.757677743 0.648103189 [61] 1.093165306 0.039412972 1.551318313 -1.143677317 0.561158463 [66] 0.280159851 -1.778984524 -1.003204300 0.289172591 1.237734914 [71] -1.505478030 0.443184920 1.084824936 0.027230626 -0.019148108 [76] -1.945916562 0.302093017 0.328091995 0.567015206 1.148935482 [81] -0.719111436 -1.322588628 -1.210568878 0.649806958 0.766002180 [86] 0.038143888 1.374614758 -1.432908259 -0.403353261 -0.895212543 [91] 0.586496660 0.037862452 -0.997465377 -1.042396357 0.040506733 [96] 0.701672948 0.211496918 -0.988343582 -0.355189464 0.481418076 > 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] 0.078482226 -0.928120477 -1.540397338 0.632599303 0.118958200 [6] -0.872003271 -0.511158180 0.712654928 0.034247777 0.684975090 [11] 1.463264196 0.115904377 0.119461464 0.540296474 -0.279672497 [16] -0.378208254 -1.662199397 -0.779801072 -1.331237159 -0.411669168 [21] -1.568399182 -0.859330766 0.571492183 1.406978595 0.272476266 [26] 0.415474213 -0.495669243 0.444537350 1.170070840 0.999146445 [31] 0.911630461 -1.257038185 0.671331562 -0.239124952 -0.464077801 [36] -1.344712829 -0.803635966 -0.901445539 -1.520502737 -0.457098702 [41] 0.505014456 0.115429757 0.441471513 1.208629786 -1.196750602 [46] -0.311632502 -0.807734649 1.910748796 1.268459591 0.451900919 [51] 1.582515058 -0.500730151 1.904207800 -0.440214335 0.405414226 [56] 0.008853868 -0.189445982 1.730053195 -1.757677743 0.648103189 [61] 1.093165306 0.039412972 1.551318313 -1.143677317 0.561158463 [66] 0.280159851 -1.778984524 -1.003204300 0.289172591 1.237734914 [71] -1.505478030 0.443184920 1.084824936 0.027230626 -0.019148108 [76] -1.945916562 0.302093017 0.328091995 0.567015206 1.148935482 [81] -0.719111436 -1.322588628 -1.210568878 0.649806958 0.766002180 [86] 0.038143888 1.374614758 -1.432908259 -0.403353261 -0.895212543 [91] 0.586496660 0.037862452 -0.997465377 -1.042396357 0.040506733 [96] 0.701672948 0.211496918 -0.988343582 -0.355189464 0.481418076 > colMin(tmp) [1] 0.078482226 -0.928120477 -1.540397338 0.632599303 0.118958200 [6] -0.872003271 -0.511158180 0.712654928 0.034247777 0.684975090 [11] 1.463264196 0.115904377 0.119461464 0.540296474 -0.279672497 [16] -0.378208254 -1.662199397 -0.779801072 -1.331237159 -0.411669168 [21] -1.568399182 -0.859330766 0.571492183 1.406978595 0.272476266 [26] 0.415474213 -0.495669243 0.444537350 1.170070840 0.999146445 [31] 0.911630461 -1.257038185 0.671331562 -0.239124952 -0.464077801 [36] -1.344712829 -0.803635966 -0.901445539 -1.520502737 -0.457098702 [41] 0.505014456 0.115429757 0.441471513 1.208629786 -1.196750602 [46] -0.311632502 -0.807734649 1.910748796 1.268459591 0.451900919 [51] 1.582515058 -0.500730151 1.904207800 -0.440214335 0.405414226 [56] 0.008853868 -0.189445982 1.730053195 -1.757677743 0.648103189 [61] 1.093165306 0.039412972 1.551318313 -1.143677317 0.561158463 [66] 0.280159851 -1.778984524 -1.003204300 0.289172591 1.237734914 [71] -1.505478030 0.443184920 1.084824936 0.027230626 -0.019148108 [76] -1.945916562 0.302093017 0.328091995 0.567015206 1.148935482 [81] -0.719111436 -1.322588628 -1.210568878 0.649806958 0.766002180 [86] 0.038143888 1.374614758 -1.432908259 -0.403353261 -0.895212543 [91] 0.586496660 0.037862452 -0.997465377 -1.042396357 0.040506733 [96] 0.701672948 0.211496918 -0.988343582 -0.355189464 0.481418076 > colMedians(tmp) [1] 0.078482226 -0.928120477 -1.540397338 0.632599303 0.118958200 [6] -0.872003271 -0.511158180 0.712654928 0.034247777 0.684975090 [11] 1.463264196 0.115904377 0.119461464 0.540296474 -0.279672497 [16] -0.378208254 -1.662199397 -0.779801072 -1.331237159 -0.411669168 [21] -1.568399182 -0.859330766 0.571492183 1.406978595 0.272476266 [26] 0.415474213 -0.495669243 0.444537350 1.170070840 0.999146445 [31] 0.911630461 -1.257038185 0.671331562 -0.239124952 -0.464077801 [36] -1.344712829 -0.803635966 -0.901445539 -1.520502737 -0.457098702 [41] 0.505014456 0.115429757 0.441471513 1.208629786 -1.196750602 [46] -0.311632502 -0.807734649 1.910748796 1.268459591 0.451900919 [51] 1.582515058 -0.500730151 1.904207800 -0.440214335 0.405414226 [56] 0.008853868 -0.189445982 1.730053195 -1.757677743 0.648103189 [61] 1.093165306 0.039412972 1.551318313 -1.143677317 0.561158463 [66] 0.280159851 -1.778984524 -1.003204300 0.289172591 1.237734914 [71] -1.505478030 0.443184920 1.084824936 0.027230626 -0.019148108 [76] -1.945916562 0.302093017 0.328091995 0.567015206 1.148935482 [81] -0.719111436 -1.322588628 -1.210568878 0.649806958 0.766002180 [86] 0.038143888 1.374614758 -1.432908259 -0.403353261 -0.895212543 [91] 0.586496660 0.037862452 -0.997465377 -1.042396357 0.040506733 [96] 0.701672948 0.211496918 -0.988343582 -0.355189464 0.481418076 > colRanges(tmp) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 0.07848223 -0.9281205 -1.540397 0.6325993 0.1189582 -0.8720033 -0.5111582 [2,] 0.07848223 -0.9281205 -1.540397 0.6325993 0.1189582 -0.8720033 -0.5111582 [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,] 0.7126549 0.03424778 0.6849751 1.463264 0.1159044 0.1194615 0.5402965 [2,] 0.7126549 0.03424778 0.6849751 1.463264 0.1159044 0.1194615 0.5402965 [,15] [,16] [,17] [,18] [,19] [,20] [,21] [1,] -0.2796725 -0.3782083 -1.662199 -0.7798011 -1.331237 -0.4116692 -1.568399 [2,] -0.2796725 -0.3782083 -1.662199 -0.7798011 -1.331237 -0.4116692 -1.568399 [,22] [,23] [,24] [,25] [,26] [,27] [,28] [1,] -0.8593308 0.5714922 1.406979 0.2724763 0.4154742 -0.4956692 0.4445373 [2,] -0.8593308 0.5714922 1.406979 0.2724763 0.4154742 -0.4956692 0.4445373 [,29] [,30] [,31] [,32] [,33] [,34] [,35] [1,] 1.170071 0.9991464 0.9116305 -1.257038 0.6713316 -0.239125 -0.4640778 [2,] 1.170071 0.9991464 0.9116305 -1.257038 0.6713316 -0.239125 -0.4640778 [,36] [,37] [,38] [,39] [,40] [,41] [,42] [1,] -1.344713 -0.803636 -0.9014455 -1.520503 -0.4570987 0.5050145 0.1154298 [2,] -1.344713 -0.803636 -0.9014455 -1.520503 -0.4570987 0.5050145 0.1154298 [,43] [,44] [,45] [,46] [,47] [,48] [,49] [1,] 0.4414715 1.20863 -1.196751 -0.3116325 -0.8077346 1.910749 1.26846 [2,] 0.4414715 1.20863 -1.196751 -0.3116325 -0.8077346 1.910749 1.26846 [,50] [,51] [,52] [,53] [,54] [,55] [,56] [1,] 0.4519009 1.582515 -0.5007302 1.904208 -0.4402143 0.4054142 0.008853868 [2,] 0.4519009 1.582515 -0.5007302 1.904208 -0.4402143 0.4054142 0.008853868 [,57] [,58] [,59] [,60] [,61] [,62] [,63] [1,] -0.189446 1.730053 -1.757678 0.6481032 1.093165 0.03941297 1.551318 [2,] -0.189446 1.730053 -1.757678 0.6481032 1.093165 0.03941297 1.551318 [,64] [,65] [,66] [,67] [,68] [,69] [,70] [1,] -1.143677 0.5611585 0.2801599 -1.778985 -1.003204 0.2891726 1.237735 [2,] -1.143677 0.5611585 0.2801599 -1.778985 -1.003204 0.2891726 1.237735 [,71] [,72] [,73] [,74] [,75] [,76] [,77] [1,] -1.505478 0.4431849 1.084825 0.02723063 -0.01914811 -1.945917 0.302093 [2,] -1.505478 0.4431849 1.084825 0.02723063 -0.01914811 -1.945917 0.302093 [,78] [,79] [,80] [,81] [,82] [,83] [,84] [1,] 0.328092 0.5670152 1.148935 -0.7191114 -1.322589 -1.210569 0.649807 [2,] 0.328092 0.5670152 1.148935 -0.7191114 -1.322589 -1.210569 0.649807 [,85] [,86] [,87] [,88] [,89] [,90] [,91] [1,] 0.7660022 0.03814389 1.374615 -1.432908 -0.4033533 -0.8952125 0.5864967 [2,] 0.7660022 0.03814389 1.374615 -1.432908 -0.4033533 -0.8952125 0.5864967 [,92] [,93] [,94] [,95] [,96] [,97] [,98] [1,] 0.03786245 -0.9974654 -1.042396 0.04050673 0.7016729 0.2114969 -0.9883436 [2,] 0.03786245 -0.9974654 -1.042396 0.04050673 0.7016729 0.2114969 -0.9883436 [,99] [,100] [1,] -0.3551895 0.4814181 [2,] -0.3551895 0.4814181 > > > Max(tmp2) [1] 1.67617 > Min(tmp2) [1] -3.204137 > mean(tmp2) [1] -0.0224827 > Sum(tmp2) [1] -2.24827 > Var(tmp2) [1] 0.9090627 > > rowMeans(tmp2) [1] 0.43478771 1.47974411 -0.39860967 -0.34173000 -0.52393744 1.09028336 [7] 1.13265838 -1.14819143 -0.66723304 -0.12499104 0.04061691 -0.59934721 [13] 0.88666629 0.05551185 -1.63196150 0.65369050 0.24048190 0.62678692 [19] -0.68880372 -0.07071675 -0.11541751 1.24976708 -2.13511388 -0.35821315 [25] 0.04460318 -1.55159391 -0.28608720 -0.02064841 0.90215905 0.46619122 [31] -0.25921933 -0.70491403 -0.40454710 0.45359702 -0.91480794 0.12190792 [37] -0.90713104 -0.35746734 0.21164082 0.11410864 1.32365950 -0.81596471 [43] -0.11993752 0.91351343 0.81420998 1.53535481 0.53957086 -0.33672530 [49] 0.39931605 -0.65178674 0.09119851 -0.67757802 1.48496081 1.22853605 [55] 0.59041858 -0.11513704 -0.53960161 -1.23685341 -0.89986007 1.67617035 [61] -1.03553026 -1.14609590 -0.61537718 0.22625033 0.57147921 -0.41273412 [67] -0.36577172 -0.40633889 0.34979181 -1.96027981 -3.20413734 -0.57956578 [73] 0.86056540 -1.02804583 1.32555776 0.56114956 -0.25874191 -1.57150075 [79] 1.20641393 0.19077670 1.35020079 0.60349595 0.05635594 1.40209396 [85] -0.57487504 -0.93666595 0.74164131 0.63435975 0.56872217 -0.97855747 [91] -1.34306174 -1.88585405 1.19471278 0.10018110 1.37706419 0.48371229 [97] 0.04465220 0.78520113 -1.40744470 1.62994514 > rowSums(tmp2) [1] 0.43478771 1.47974411 -0.39860967 -0.34173000 -0.52393744 1.09028336 [7] 1.13265838 -1.14819143 -0.66723304 -0.12499104 0.04061691 -0.59934721 [13] 0.88666629 0.05551185 -1.63196150 0.65369050 0.24048190 0.62678692 [19] -0.68880372 -0.07071675 -0.11541751 1.24976708 -2.13511388 -0.35821315 [25] 0.04460318 -1.55159391 -0.28608720 -0.02064841 0.90215905 0.46619122 [31] -0.25921933 -0.70491403 -0.40454710 0.45359702 -0.91480794 0.12190792 [37] -0.90713104 -0.35746734 0.21164082 0.11410864 1.32365950 -0.81596471 [43] -0.11993752 0.91351343 0.81420998 1.53535481 0.53957086 -0.33672530 [49] 0.39931605 -0.65178674 0.09119851 -0.67757802 1.48496081 1.22853605 [55] 0.59041858 -0.11513704 -0.53960161 -1.23685341 -0.89986007 1.67617035 [61] -1.03553026 -1.14609590 -0.61537718 0.22625033 0.57147921 -0.41273412 [67] -0.36577172 -0.40633889 0.34979181 -1.96027981 -3.20413734 -0.57956578 [73] 0.86056540 -1.02804583 1.32555776 0.56114956 -0.25874191 -1.57150075 [79] 1.20641393 0.19077670 1.35020079 0.60349595 0.05635594 1.40209396 [85] -0.57487504 -0.93666595 0.74164131 0.63435975 0.56872217 -0.97855747 [91] -1.34306174 -1.88585405 1.19471278 0.10018110 1.37706419 0.48371229 [97] 0.04465220 0.78520113 -1.40744470 1.62994514 > 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] 0.43478771 1.47974411 -0.39860967 -0.34173000 -0.52393744 1.09028336 [7] 1.13265838 -1.14819143 -0.66723304 -0.12499104 0.04061691 -0.59934721 [13] 0.88666629 0.05551185 -1.63196150 0.65369050 0.24048190 0.62678692 [19] -0.68880372 -0.07071675 -0.11541751 1.24976708 -2.13511388 -0.35821315 [25] 0.04460318 -1.55159391 -0.28608720 -0.02064841 0.90215905 0.46619122 [31] -0.25921933 -0.70491403 -0.40454710 0.45359702 -0.91480794 0.12190792 [37] -0.90713104 -0.35746734 0.21164082 0.11410864 1.32365950 -0.81596471 [43] -0.11993752 0.91351343 0.81420998 1.53535481 0.53957086 -0.33672530 [49] 0.39931605 -0.65178674 0.09119851 -0.67757802 1.48496081 1.22853605 [55] 0.59041858 -0.11513704 -0.53960161 -1.23685341 -0.89986007 1.67617035 [61] -1.03553026 -1.14609590 -0.61537718 0.22625033 0.57147921 -0.41273412 [67] -0.36577172 -0.40633889 0.34979181 -1.96027981 -3.20413734 -0.57956578 [73] 0.86056540 -1.02804583 1.32555776 0.56114956 -0.25874191 -1.57150075 [79] 1.20641393 0.19077670 1.35020079 0.60349595 0.05635594 1.40209396 [85] -0.57487504 -0.93666595 0.74164131 0.63435975 0.56872217 -0.97855747 [91] -1.34306174 -1.88585405 1.19471278 0.10018110 1.37706419 0.48371229 [97] 0.04465220 0.78520113 -1.40744470 1.62994514 > rowMin(tmp2) [1] 0.43478771 1.47974411 -0.39860967 -0.34173000 -0.52393744 1.09028336 [7] 1.13265838 -1.14819143 -0.66723304 -0.12499104 0.04061691 -0.59934721 [13] 0.88666629 0.05551185 -1.63196150 0.65369050 0.24048190 0.62678692 [19] -0.68880372 -0.07071675 -0.11541751 1.24976708 -2.13511388 -0.35821315 [25] 0.04460318 -1.55159391 -0.28608720 -0.02064841 0.90215905 0.46619122 [31] -0.25921933 -0.70491403 -0.40454710 0.45359702 -0.91480794 0.12190792 [37] -0.90713104 -0.35746734 0.21164082 0.11410864 1.32365950 -0.81596471 [43] -0.11993752 0.91351343 0.81420998 1.53535481 0.53957086 -0.33672530 [49] 0.39931605 -0.65178674 0.09119851 -0.67757802 1.48496081 1.22853605 [55] 0.59041858 -0.11513704 -0.53960161 -1.23685341 -0.89986007 1.67617035 [61] -1.03553026 -1.14609590 -0.61537718 0.22625033 0.57147921 -0.41273412 [67] -0.36577172 -0.40633889 0.34979181 -1.96027981 -3.20413734 -0.57956578 [73] 0.86056540 -1.02804583 1.32555776 0.56114956 -0.25874191 -1.57150075 [79] 1.20641393 0.19077670 1.35020079 0.60349595 0.05635594 1.40209396 [85] -0.57487504 -0.93666595 0.74164131 0.63435975 0.56872217 -0.97855747 [91] -1.34306174 -1.88585405 1.19471278 0.10018110 1.37706419 0.48371229 [97] 0.04465220 0.78520113 -1.40744470 1.62994514 > > colMeans(tmp2) [1] -0.0224827 > colSums(tmp2) [1] -2.24827 > colVars(tmp2) [1] 0.9090627 > colSd(tmp2) [1] 0.9534478 > colMax(tmp2) [1] 1.67617 > colMin(tmp2) [1] -3.204137 > colMedians(tmp2) [1] 0.04261004 > colRanges(tmp2) [,1] [1,] -3.204137 [2,] 1.676170 > > 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] -1.7438947 1.8118100 4.3978516 -0.5091717 -4.0295876 -0.8474091 [7] -0.6336609 -0.4051156 2.4658972 -1.2044572 > colApply(tmp,quantile)[,1] [,1] [1,] -1.9364402 [2,] -0.6726488 [3,] -0.1817944 [4,] 0.3754228 [5,] 1.3712041 > > rowApply(tmp,sum) [1] 2.96361192 2.20365172 -5.75669566 4.12084127 0.05759331 -3.09527140 [7] -0.28543548 -0.57037852 -1.02904727 0.69339221 > rowApply(tmp,rank)[1:10,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 2 4 3 10 3 6 7 9 1 4 [2,] 5 9 4 5 7 10 2 6 3 9 [3,] 6 10 10 4 8 5 3 8 4 10 [4,] 3 2 9 7 4 8 8 3 5 1 [5,] 1 3 1 9 9 3 9 4 7 2 [6,] 4 8 5 1 10 9 1 5 6 8 [7,] 10 5 2 3 6 4 5 2 10 3 [8,] 9 7 8 6 5 1 10 1 2 7 [9,] 8 6 6 8 2 7 4 7 8 5 [10,] 7 1 7 2 1 2 6 10 9 6 > > tmp <- createBufferedMatrix(5,20) > > tmp[1:5,1:20] <- rnorm(100) > colApply(tmp,sum) [1] 0.1008665 0.6440996 0.8634949 -3.1392527 -4.5058361 -0.6783987 [7] -1.7830640 -2.2491818 -1.4079351 -0.5377230 1.9825680 2.0285525 [13] -3.9465288 -1.1735175 2.3556394 3.0151219 0.2337230 0.6676985 [19] -0.2526639 0.4388722 > colApply(tmp,quantile)[,1] [,1] [1,] -1.2788961 [2,] -0.4491295 [3,] 0.3197870 [4,] 0.7263752 [5,] 0.7827299 > > rowApply(tmp,sum) [1] -6.7034342 -0.2089957 2.2852714 -0.9542010 -1.7621054 > rowApply(tmp,rank)[1:5,] [,1] [,2] [,3] [,4] [,5] [1,] 3 15 17 10 15 [2,] 14 3 14 12 17 [3,] 4 7 19 16 9 [4,] 13 10 8 2 2 [5,] 9 8 1 3 3 > > > as.matrix(tmp) [,1] [,2] [,3] [,4] [,5] [,6] [1,] -1.2788961 -0.022916157 -0.9539761 -0.08359956 -0.5425285 -0.6198232 [2,] 0.3197870 -0.895804672 -0.3061612 -0.11127000 -0.2645172 -0.4917262 [3,] 0.7827299 0.716095711 1.5191174 0.01020905 -1.5194261 -0.7355696 [4,] -0.4491295 -0.009236321 0.9179664 -1.10178816 -0.9748480 1.7811469 [5,] 0.7263752 0.855961059 -0.3134515 -1.85280406 -1.2045162 -0.6124265 [,7] [,8] [,9] [,10] [,11] [,12] [1,] -0.5513668 -2.3442118 -0.2690526 1.74368327 0.4434813 0.8592163 [2,] -0.2309024 0.8681486 -1.2345943 0.05166409 -0.3250229 0.1298793 [3,] 0.4494188 0.7596127 -0.5887128 -0.87388844 1.6067766 -1.5104016 [4,] -0.8239159 1.0416068 0.2369445 -1.50051937 -0.5513852 2.1720682 [5,] -0.6262977 -2.5743382 0.4474800 0.04133743 0.8087183 0.3777904 [,13] [,14] [,15] [,16] [,17] [,18] [1,] -1.9083884 0.1198435 -0.6796385 -0.4659616 0.82547757 0.2490434 [2,] -1.4597919 -0.6359614 0.8749565 0.9637663 0.05797304 1.2687839 [3,] 0.1988689 -0.3859520 1.0266522 0.3699674 0.35054924 0.4899282 [4,] -0.1085256 0.7170942 -0.8811644 1.1474341 -0.83177617 -0.8681374 [5,] -0.6686918 -0.9885417 2.0148337 0.9999156 -0.16850066 -0.4719195 [,19] [,20] [1,] -0.83644526 -0.3873749 [2,] 1.31397358 -0.1021759 [3,] -1.12923224 0.7485281 [4,] 0.04362853 -0.9116645 [5,] 0.35541153 1.0915594 > > > 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 : 655 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 : 567 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 0.02729558 1.405963 0.2592048 0.6576818 -0.2077211 1.223647 0.05166291 col8 col9 col10 col11 col12 col13 col14 row1 -2.158435 0.5048047 1.20532 -0.265535 -0.9494859 0.0829037 1.006601 col15 col16 col17 col18 col19 col20 row1 0.3184526 -1.781521 -1.266628 0.05675986 -0.3656424 1.123368 > tmp[,"col10"] col10 row1 1.2053201 row2 0.9388369 row3 -1.4220685 row4 0.4972253 row5 0.9983548 > tmp[c("row1","row5"),] col1 col2 col3 col4 col5 col6 col7 row1 0.02729558 1.405963 0.2592048 0.6576818 -0.2077211 1.223647 0.05166291 row5 0.52194276 1.408194 -0.5317153 0.8741244 0.5757025 0.294417 -1.08722739 col8 col9 col10 col11 col12 col13 col14 row1 -2.1584347 0.5048047 1.2053201 -0.265535 -0.9494859 0.0829037 1.0066009 row5 0.2937769 0.5322890 0.9983548 2.140555 -2.1486682 1.4805348 -0.2036449 col15 col16 col17 col18 col19 col20 row1 0.3184526 -1.7815210 -1.2666276 0.05675986 -0.3656424 1.12336797 row5 0.1196736 0.9340682 -0.6104031 -1.02853044 0.7157893 0.05526726 > tmp[,c("col6","col20")] col6 col20 row1 1.2236466 1.12336797 row2 1.5386455 0.97011211 row3 -0.7108664 1.07552247 row4 -0.2605030 0.79243867 row5 0.2944170 0.05526726 > tmp[c("row1","row5"),c("col6","col20")] col6 col20 row1 1.223647 1.12336797 row5 0.294417 0.05526726 > > > > > 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 49.89035 51.32689 49.72338 46.29479 50.26776 103.9283 49.53592 49.13774 col9 col10 col11 col12 col13 col14 col15 col16 row1 49.26001 49.77671 48.1726 50.84944 50.84039 50.89419 49.17928 49.89902 col17 col18 col19 col20 row1 50.33555 49.33046 51.62099 105.0125 > tmp[,"col10"] col10 row1 49.77671 row2 30.28406 row3 30.43287 row4 30.67080 row5 50.40035 > tmp[c("row1","row5"),] col1 col2 col3 col4 col5 col6 col7 col8 row1 49.89035 51.32689 49.72338 46.29479 50.26776 103.9283 49.53592 49.13774 row5 51.86569 50.26874 49.22040 49.39712 49.02024 105.3583 50.63343 49.57386 col9 col10 col11 col12 col13 col14 col15 col16 row1 49.26001 49.77671 48.17260 50.84944 50.84039 50.89419 49.17928 49.89902 row5 50.22587 50.40035 50.34694 50.48222 48.74445 49.77756 50.65991 50.20449 col17 col18 col19 col20 row1 50.33555 49.33046 51.62099 105.0125 row5 50.28523 49.35137 50.82065 105.8454 > tmp[,c("col6","col20")] col6 col20 row1 103.92829 105.01252 row2 75.80358 74.60289 row3 75.58579 73.05653 row4 72.23171 75.24232 row5 105.35834 105.84540 > tmp[c("row1","row5"),c("col6","col20")] col6 col20 row1 103.9283 105.0125 row5 105.3583 105.8454 > > > subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2] col6 col20 row1 103.9283 105.0125 row5 105.3583 105.8454 > > > > > > tmp <- createBufferedMatrix(5,20) > tmp[1:5,1:20] <- rnorm(100) > colnames(tmp) <- colnames(tmp,do.NULL=FALSE) > > tmp[,"col13"] col13 [1,] -0.4095230 [2,] -1.0676392 [3,] 0.2650336 [4,] 1.3160478 [5,] 0.7274828 > tmp[,c("col17","col7")] col17 col7 [1,] -0.7691606 -0.4130799 [2,] -1.4443185 -0.8527765 [3,] 0.1279721 -1.4602970 [4,] -1.0916362 -0.5589963 [5,] 1.5770961 0.7686465 > > subBufferedMatrix(tmp,,c("col6","col20"))[,1:2] col6 col20 [1,] 0.2223650 0.51914775 [2,] 1.0382091 -0.05251287 [3,] 1.1313522 0.43240911 [4,] -0.8385359 -1.13807084 [5,] -0.5841068 -1.40994570 > subBufferedMatrix(tmp,1,c("col6"))[,1] col1 [1,] 0.222365 > subBufferedMatrix(tmp,1:2,c("col6"))[,1] col6 [1,] 0.222365 [2,] 1.038209 > > > > 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 1.457406 0.8340323 -1.2462865 -0.5130275 0.4538627 -0.07326326 -0.1805232 row1 -1.192338 0.1145659 -0.3208531 -0.1430830 1.5773370 1.91754095 0.3071380 [,8] [,9] [,10] [,11] [,12] [,13] [,14] row3 1.4032061 0.8074411 1.38090922 0.2547329 2.082008 1.9479104 -0.7715174 row1 0.4470385 -0.6906552 -0.06547183 0.2072737 -1.727735 0.6718206 1.5989489 [,15] [,16] [,17] [,18] [,19] [,20] row3 -0.9988155 0.03429781 1.412017 0.04774232 0.3489014 0.07716814 row1 0.5788735 1.21186919 -1.843532 0.97394677 0.7284330 -0.29569460 > subBufferedMatrix(tmp,c("row2"),1:10)[,1:10] [,1] [,2] [,3] [,4] [,5] [,6] [,7] row2 0.2238655 0.09384494 -0.3409993 1.116803 -0.6553135 0.05419208 -0.5448447 [,8] [,9] [,10] row2 -0.3669718 0.2780728 0.6783077 > subBufferedMatrix(tmp,c("row5"),1:20)[,1:20] [,1] [,2] [,3] [,4] [,5] [,6] [,7] row5 -0.2424959 -0.5296245 0.8072873 0.9292234 1.232454 -2.013457 -1.976917 [,8] [,9] [,10] [,11] [,12] [,13] [,14] row5 -0.8010988 -0.7850246 -1.747174 -0.3393704 -0.645863 -0.5710496 0.5850045 [,15] [,16] [,17] [,18] [,19] [,20] row5 -0.4166805 -0.6573197 0.3031115 -1.008037 -0.7630937 1.926781 > > > 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: 0x6000019ac000> > is.ReadOnlyMode(tmp) [1] TRUE > > filenames(tmp) [1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c317b47119" [2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c3476d2c77" [3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c350825d43" [4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c31eb90300" [5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c347404c2" [6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c35ce45ed6" [7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c3150e633f" [8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c36395c7e5" [9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c37e76be76" [10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c325d275d7" [11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c31c3689a7" [12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c340874169" [13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c36fd77597" [14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c32a6945de" [15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM151c3656a0792" > > > ### 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: 0x6000019e0060> > MoveStorageDirectory(tmp,getwd(),full.path=TRUE) <pointer: 0x6000019e0060> Warning message: In dir.create(new.directory) : '/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists > > > RowMode(tmp) <pointer: 0x6000019e0060> > rowMedians(tmp) [1] -0.001064878 -0.339950363 -0.249309476 0.004469878 -0.487582837 [6] -0.300983194 -0.848982711 -0.343545270 0.365954136 0.111489059 [11] -0.304425960 0.565453749 0.171585788 -0.310736244 0.202431243 [16] -0.209218070 -0.205371183 0.439445173 0.480119891 0.565804530 [21] -0.492925231 0.151118026 0.247847615 -0.538040106 -0.008847785 [26] 0.074347886 0.054994749 0.034055403 0.175911993 0.087269218 [31] -0.145818897 0.229564301 0.468530741 0.345683764 -0.291823973 [36] 0.338179656 0.106028884 -0.150763627 -0.236462673 0.200667060 [41] -0.300004493 0.615407917 0.297143679 -0.039637876 0.256901516 [46] 0.099658778 0.277397209 0.036613654 -0.242223185 0.254531235 [51] -0.100275782 -0.026972757 0.389595845 0.025605930 -0.098730822 [56] 0.351632853 0.172852001 -0.114482225 -0.018322241 0.291808333 [61] -0.412487894 -0.070426005 0.327893920 0.036903268 0.077146991 [66] -0.234667424 0.144484275 -0.021405891 0.737782063 0.074831809 [71] 0.065460009 0.267002575 -0.053931517 -0.313595647 -0.244501985 [76] -0.315349127 0.115559633 -0.277082834 -0.172570979 -0.221458432 [81] 0.227747197 0.064460129 0.952650431 -0.319963192 -0.638609609 [86] -0.013545167 -0.149277575 -0.510761153 -0.066252013 0.224280704 [91] 0.200599239 -0.632286020 -0.449398622 0.036540032 -0.179969046 [96] 0.365037831 0.213404940 0.484611720 0.031173299 0.403422437 [101] -0.267834889 -0.250554007 -0.045573020 -0.274021901 0.150106213 [106] -0.450978014 -0.410672368 0.006751153 -0.027851681 -0.075241221 [111] 0.575814689 -0.311989118 -0.078492339 0.498703420 0.106620763 [116] 0.189280939 0.139972336 0.091971714 -0.257468272 -0.073116521 [121] -0.249552911 -0.500760031 -0.156898632 0.004080202 0.365013388 [126] 0.211880650 -0.288781323 0.292447214 0.029692348 -0.211594726 [131] -0.127127034 -0.083417338 0.116957036 0.939919257 -0.367285015 [136] 0.485268424 -0.362086256 0.352576199 0.658443400 0.041880896 [141] -0.134715882 0.440167610 0.314479361 0.101338465 -0.011353658 [146] 0.663535730 -0.195434402 -0.511351064 -0.121703030 -0.270902830 [151] 0.099719265 0.197567392 -0.262899531 0.309327281 -0.214148783 [156] -0.035750908 0.597272466 0.480098087 -0.246699012 -0.113552974 [161] -0.815779738 -0.287175952 0.222285528 0.172137384 0.542057680 [166] -0.467749090 -0.321390429 -0.041545065 0.494496071 0.161459869 [171] -0.400940566 0.117561597 -0.559945364 -0.002866672 0.334603330 [176] 0.180526381 0.219680860 -0.503523988 0.104028151 -0.335235876 [181] 0.359048658 -0.415761223 0.582464460 -0.061134353 0.271058786 [186] 0.325585773 0.371938936 -0.185204592 0.152981710 0.064618697 [191] 0.062519794 0.160634464 -0.363073654 0.939369619 0.198573420 [196] 0.302420628 -0.490762881 -0.206732343 -0.012450085 0.466305059 [201] -0.307743767 0.025964194 -0.220992921 0.225011268 -0.116586498 [206] -0.537538413 0.640380745 0.175564232 0.111879962 -0.106452265 [211] -0.253984469 -0.051660710 0.250047783 0.168234100 -0.333516893 [216] -0.241986136 0.118078382 -0.165785242 0.319570614 0.001400209 [221] 0.144843659 -0.027519398 0.309344297 -0.466957086 0.029214729 [226] -0.492402705 -0.194484229 -0.242516625 0.115014433 0.210186929 > > proc.time() user system elapsed 2.901 17.342 77.613
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: 0x600000dcc000> > .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: 0x600000dcc000> > .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: 0x600000dcc000> > .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: 0x600000dcc000> > 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: 0x600000dd40c0> > .Call("R_bm_AddColumn",P) <pointer: 0x600000dd40c0> > .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: 0x600000dd40c0> > .Call("R_bm_AddColumn",P) <pointer: 0x600000dd40c0> > .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: 0x600000dd40c0> > 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: 0x600000dd0000> > .Call("R_bm_AddColumn",P) <pointer: 0x600000dd0000> > .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: 0x600000dd0000> > > .Call("R_bm_ResizeBuffer",P,5,5) <pointer: 0x600000dd0000> > .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: 0x600000dd0000> > > .Call("R_bm_RowMode",P) <pointer: 0x600000dd0000> > .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: 0x600000dd0000> > > .Call("R_bm_ColMode",P) <pointer: 0x600000dd0000> > .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: 0x600000dd0000> > 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: 0x600000dbc000> > .Call("R_bm_SetPrefix",P,"BufferedMatrixFile") <pointer: 0x600000dbc000> > .Call("R_bm_AddColumn",P) <pointer: 0x600000dbc000> > .Call("R_bm_AddColumn",P) <pointer: 0x600000dbc000> > dir(pattern="BufferedMatrixFile") [1] "BufferedMatrixFile163952fe14346" "BufferedMatrixFile163956e07c138" > rm(P) > dir(pattern="BufferedMatrixFile") [1] "BufferedMatrixFile163952fe14346" "BufferedMatrixFile163956e07c138" > > > P <- .Call("R_bm_Create",prefix,directory,1,1) > .Call("R_bm_setRows",P,10) [1] TRUE > .Call("R_bm_AddColumn",P) <pointer: 0x600000dbc240> > .Call("R_bm_AddColumn",P) <pointer: 0x600000dbc240> > .Call("R_bm_ReadOnlyModeToggle",P) <pointer: 0x600000dbc240> > .Call("R_bm_isReadOnlyMode",P) [1] TRUE > .Call("R_bm_ReadOnlyModeToggle",P) <pointer: 0x600000dbc240> > .Call("R_bm_isReadOnlyMode",P) [1] FALSE > .Call("R_bm_isRowMode",P) [1] FALSE > .Call("R_bm_RowMode",P) <pointer: 0x600000dbc240> > .Call("R_bm_isRowMode",P) [1] TRUE > .Call("R_bm_ColMode",P) <pointer: 0x600000dbc240> > .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: 0x600000de80c0> > .Call("R_bm_AddColumn",P) <pointer: 0x600000de80c0> > > .Call("R_bm_getSize",P) [1] 10 2 > .Call("R_bm_getBufferSize",P) [1] 1 1 > .Call("R_bm_ResizeBuffer",P,5,5) <pointer: 0x600000de80c0> > > .Call("R_bm_getBufferSize",P) [1] 5 5 > .Call("R_bm_ResizeBuffer",P,-1,5) <pointer: 0x600000de80c0> > 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: 0x600000df4000> > .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: 0x600000df4000> > rm(P) > > proc.time() user system elapsed 0.296 0.136 0.425
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 0.342 0.100 0.428