Ben Bolstad
| Snapshot Date: 2025-12-16 13:40 -0500 (Tue, 16 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: ecdbf23 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-17 11:35 -0500 (Wed, 17 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4589 |
| 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 253/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | 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: 1.75.0 |
| 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_1.75.0.tar.gz |
| StartedAt: 2025-12-16 18:45:48 -0500 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 18:46:08 -0500 (Tue, 16 Dec 2025) |
| EllapsedTime: 20.3 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_1.75.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.75.0’
* 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-3.23-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: ‘MacOSX11.3.1.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 ... INFO
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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-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/4.6-arm64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.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/4.6-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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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
0.135 0.062 0.198
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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-3.23-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 481248 25.8 1058085 56.6 NA 633817 33.9
Vcells 891449 6.9 8388608 64.0 196608 2110969 16.2
>
>
>
>
> ##
> ## 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] "Tue Dec 16 18:45:59 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] "Tue Dec 16 18:45:59 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: 0x6000002dc000>
>
>
>
> 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] "Tue Dec 16 18:46:00 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] "Tue Dec 16 18:46:01 2025"
>
> ColMode(tmp2)
<pointer: 0x6000002dc000>
>
>
>
> ### 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,] 100.5751094 -0.4152576 0.7545663 0.3803852
[2,] 0.9019187 0.5301815 -0.5743683 -0.9043442
[3,] 0.4986565 -0.8692558 -0.2655492 1.0922155
[4,] 1.9829784 0.9091536 0.2636567 -0.1196489
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-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,] 100.5751094 0.4152576 0.7545663 0.3803852
[2,] 0.9019187 0.5301815 0.5743683 0.9043442
[3,] 0.4986565 0.8692558 0.2655492 1.0922155
[4,] 1.9829784 0.9091536 0.2636567 0.1196489
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0287142 0.6444049 0.8686578 0.6167538
[2,] 0.9496940 0.7281357 0.7578709 0.9509701
[3,] 0.7061562 0.9323389 0.5153146 1.0450911
[4,] 1.4081827 0.9534955 0.5134751 0.3459030
>
> 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-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.86225 31.85931 34.44114 31.54792
[2,] 35.39886 32.81154 33.15308 35.41405
[3,] 32.56022 35.19264 30.41870 36.54313
[4,] 41.06481 35.44411 30.39841 28.57868
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x6000002d8000>
> exp(tmp5)
<pointer: 0x6000002d8000>
> log(tmp5,2)
<pointer: 0x6000002d8000>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 470.1027
> Min(tmp5)
[1] 54.47073
> mean(tmp5)
[1] 72.36869
> Sum(tmp5)
[1] 14473.74
> Var(tmp5)
[1] 864.0659
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.77208 72.33771 69.32146 69.84152 69.08248 70.02420 70.07333 69.99181
[9] 69.52834 72.71399
> rowSums(tmp5)
[1] 1815.442 1446.754 1386.429 1396.830 1381.650 1400.484 1401.467 1399.836
[9] 1390.567 1454.280
> rowVars(tmp5)
[1] 8015.75940 38.65641 83.31350 67.33665 46.92809 62.12651
[7] 72.01803 119.33751 55.28848 78.91674
> rowSd(tmp5)
[1] 89.530773 6.217428 9.127623 8.205891 6.850408 7.882037 8.486344
[8] 10.924171 7.435623 8.883510
> rowMax(tmp5)
[1] 470.10269 82.15172 87.29822 85.47101 86.07281 82.86271 86.97874
[8] 95.03129 82.30404 91.57048
> rowMin(tmp5)
[1] 57.45126 59.23182 56.19639 59.08973 59.53333 54.47073 56.63028 54.80907
[9] 57.33317 58.84697
>
> colMeans(tmp5)
[1] 112.08936 70.82235 68.36748 69.65932 67.29718 68.56457 69.64929
[8] 74.17278 68.59959 71.38645 73.02963 72.21871 73.86555 70.62272
[15] 71.48865 71.18234 69.86742 71.00383 64.20275 69.28391
> colSums(tmp5)
[1] 1120.8936 708.2235 683.6748 696.5932 672.9718 685.6457 696.4929
[8] 741.7278 685.9959 713.8645 730.2963 722.1871 738.6555 706.2272
[15] 714.8865 711.8234 698.6742 710.0383 642.0275 692.8391
> colVars(tmp5)
[1] 15897.80924 50.36828 19.79015 39.83034 55.23069 62.37159
[7] 61.23144 83.91781 72.70554 72.45551 118.54209 76.05350
[13] 66.84047 63.65893 83.67227 104.55714 53.04353 83.75595
[19] 44.74546 37.39609
> colSd(tmp5)
[1] 126.086515 7.097061 4.448612 6.311128 7.431735 7.897568
[7] 7.825052 9.160666 8.526754 8.512080 10.887704 8.720866
[13] 8.175602 7.978655 9.147255 10.225318 7.283099 9.151828
[19] 6.689204 6.115234
> colMax(tmp5)
[1] 470.10269 79.24606 74.64722 78.93880 77.85751 79.28466 82.02821
[8] 87.29822 81.82593 85.76878 95.03129 84.69206 91.57048 80.81882
[15] 86.97874 91.43265 79.62766 86.37377 75.76115 82.30404
> colMin(tmp5)
[1] 58.84697 54.80907 62.64018 59.48277 54.47073 56.63028 57.45126 57.99813
[9] 57.33317 56.19639 59.08973 58.81818 63.43074 57.82249 59.23182 59.53912
[17] 58.15320 61.98201 55.19753 60.77750
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 90.77208 72.33771 69.32146 NA 69.08248 70.02420 70.07333 69.99181
[9] 69.52834 72.71399
> rowSums(tmp5)
[1] 1815.442 1446.754 1386.429 NA 1381.650 1400.484 1401.467 1399.836
[9] 1390.567 1454.280
> rowVars(tmp5)
[1] 8015.75940 38.65641 83.31350 56.79215 46.92809 62.12651
[7] 72.01803 119.33751 55.28848 78.91674
> rowSd(tmp5)
[1] 89.530773 6.217428 9.127623 7.536056 6.850408 7.882037 8.486344
[8] 10.924171 7.435623 8.883510
> rowMax(tmp5)
[1] 470.10269 82.15172 87.29822 NA 86.07281 82.86271 86.97874
[8] 95.03129 82.30404 91.57048
> rowMin(tmp5)
[1] 57.45126 59.23182 56.19639 NA 59.53333 54.47073 56.63028 54.80907
[9] 57.33317 58.84697
>
> colMeans(tmp5)
[1] NA 70.82235 68.36748 69.65932 67.29718 68.56457 69.64929 74.17278
[9] 68.59959 71.38645 73.02963 72.21871 73.86555 70.62272 71.48865 71.18234
[17] 69.86742 71.00383 64.20275 69.28391
> colSums(tmp5)
[1] NA 708.2235 683.6748 696.5932 672.9718 685.6457 696.4929 741.7278
[9] 685.9959 713.8645 730.2963 722.1871 738.6555 706.2272 714.8865 711.8234
[17] 698.6742 710.0383 642.0275 692.8391
> colVars(tmp5)
[1] NA 50.36828 19.79015 39.83034 55.23069 62.37159 61.23144
[8] 83.91781 72.70554 72.45551 118.54209 76.05350 66.84047 63.65893
[15] 83.67227 104.55714 53.04353 83.75595 44.74546 37.39609
> colSd(tmp5)
[1] NA 7.097061 4.448612 6.311128 7.431735 7.897568 7.825052
[8] 9.160666 8.526754 8.512080 10.887704 8.720866 8.175602 7.978655
[15] 9.147255 10.225318 7.283099 9.151828 6.689204 6.115234
> colMax(tmp5)
[1] NA 79.24606 74.64722 78.93880 77.85751 79.28466 82.02821 87.29822
[9] 81.82593 85.76878 95.03129 84.69206 91.57048 80.81882 86.97874 91.43265
[17] 79.62766 86.37377 75.76115 82.30404
> colMin(tmp5)
[1] NA 54.80907 62.64018 59.48277 54.47073 56.63028 57.45126 57.99813
[9] 57.33317 56.19639 59.08973 58.81818 63.43074 57.82249 59.23182 59.53912
[17] 58.15320 61.98201 55.19753 60.77750
>
> Max(tmp5,na.rm=TRUE)
[1] 470.1027
> Min(tmp5,na.rm=TRUE)
[1] 54.47073
> mean(tmp5,na.rm=TRUE)
[1] 72.30285
> Sum(tmp5,na.rm=TRUE)
[1] 14388.27
> Var(tmp5,na.rm=TRUE)
[1] 867.5585
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.77208 72.33771 69.32146 69.01892 69.08248 70.02420 70.07333 69.99181
[9] 69.52834 72.71399
> rowSums(tmp5,na.rm=TRUE)
[1] 1815.442 1446.754 1386.429 1311.359 1381.650 1400.484 1401.467 1399.836
[9] 1390.567 1454.280
> rowVars(tmp5,na.rm=TRUE)
[1] 8015.75940 38.65641 83.31350 56.79215 46.92809 62.12651
[7] 72.01803 119.33751 55.28848 78.91674
> rowSd(tmp5,na.rm=TRUE)
[1] 89.530773 6.217428 9.127623 7.536056 6.850408 7.882037 8.486344
[8] 10.924171 7.435623 8.883510
> rowMax(tmp5,na.rm=TRUE)
[1] 470.10269 82.15172 87.29822 82.47816 86.07281 82.86271 86.97874
[8] 95.03129 82.30404 91.57048
> rowMin(tmp5,na.rm=TRUE)
[1] 57.45126 59.23182 56.19639 59.08973 59.53333 54.47073 56.63028 54.80907
[9] 57.33317 58.84697
>
> colMeans(tmp5,na.rm=TRUE)
[1] 115.04696 70.82235 68.36748 69.65932 67.29718 68.56457 69.64929
[8] 74.17278 68.59959 71.38645 73.02963 72.21871 73.86555 70.62272
[15] 71.48865 71.18234 69.86742 71.00383 64.20275 69.28391
> colSums(tmp5,na.rm=TRUE)
[1] 1035.4226 708.2235 683.6748 696.5932 672.9718 685.6457 696.4929
[8] 741.7278 685.9959 713.8645 730.2963 722.1871 738.6555 706.2272
[15] 714.8865 711.8234 698.6742 710.0383 642.0275 692.8391
> colVars(tmp5,na.rm=TRUE)
[1] 17786.62751 50.36828 19.79015 39.83034 55.23069 62.37159
[7] 61.23144 83.91781 72.70554 72.45551 118.54209 76.05350
[13] 66.84047 63.65893 83.67227 104.55714 53.04353 83.75595
[19] 44.74546 37.39609
> colSd(tmp5,na.rm=TRUE)
[1] 133.366516 7.097061 4.448612 6.311128 7.431735 7.897568
[7] 7.825052 9.160666 8.526754 8.512080 10.887704 8.720866
[13] 8.175602 7.978655 9.147255 10.225318 7.283099 9.151828
[19] 6.689204 6.115234
> colMax(tmp5,na.rm=TRUE)
[1] 470.10269 79.24606 74.64722 78.93880 77.85751 79.28466 82.02821
[8] 87.29822 81.82593 85.76878 95.03129 84.69206 91.57048 80.81882
[15] 86.97874 91.43265 79.62766 86.37377 75.76115 82.30404
> colMin(tmp5,na.rm=TRUE)
[1] 58.84697 54.80907 62.64018 59.48277 54.47073 56.63028 57.45126 57.99813
[9] 57.33317 56.19639 59.08973 58.81818 63.43074 57.82249 59.23182 59.53912
[17] 58.15320 61.98201 55.19753 60.77750
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.77208 72.33771 69.32146 NaN 69.08248 70.02420 70.07333 69.99181
[9] 69.52834 72.71399
> rowSums(tmp5,na.rm=TRUE)
[1] 1815.442 1446.754 1386.429 0.000 1381.650 1400.484 1401.467 1399.836
[9] 1390.567 1454.280
> rowVars(tmp5,na.rm=TRUE)
[1] 8015.75940 38.65641 83.31350 NA 46.92809 62.12651
[7] 72.01803 119.33751 55.28848 78.91674
> rowSd(tmp5,na.rm=TRUE)
[1] 89.530773 6.217428 9.127623 NA 6.850408 7.882037 8.486344
[8] 10.924171 7.435623 8.883510
> rowMax(tmp5,na.rm=TRUE)
[1] 470.10269 82.15172 87.29822 NA 86.07281 82.86271 86.97874
[8] 95.03129 82.30404 91.57048
> rowMin(tmp5,na.rm=TRUE)
[1] 57.45126 59.23182 56.19639 NA 59.53333 54.47073 56.63028 54.80907
[9] 57.33317 58.84697
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] NaN 70.49458 68.93383 70.79005 67.69902 67.41733 69.63829 73.24996
[9] 68.22951 71.36370 74.57851 71.59467 74.16638 71.65756 71.27552 72.47603
[17] 68.78295 71.16780 64.19811 70.22906
> colSums(tmp5,na.rm=TRUE)
[1] 0.0000 634.4512 620.4045 637.1105 609.2912 606.7560 626.7446 659.2496
[9] 614.0656 642.2733 671.2066 644.3520 667.4974 644.9180 641.4796 652.2843
[17] 619.0466 640.5102 577.7830 632.0616
> colVars(tmp5,na.rm=TRUE)
[1] NA 55.45569 18.65542 30.42550 60.31785 55.36135 68.88400
[8] 84.82706 80.25290 81.50663 106.37084 81.17906 74.17745 59.56876
[15] 93.62024 98.79836 46.44312 93.92296 50.33840 32.02074
> colSd(tmp5,na.rm=TRUE)
[1] NA 7.446858 4.319192 5.515932 7.766457 7.440521 8.299639
[8] 9.210161 8.958398 9.028102 10.313624 9.009943 8.612633 7.718080
[15] 9.675755 9.939736 6.814919 9.691386 7.094956 5.658687
> colMax(tmp5,na.rm=TRUE)
[1] -Inf 79.24606 74.64722 78.93880 77.85751 79.28466 82.02821 87.29822
[9] 81.82593 85.76878 95.03129 84.69206 91.57048 80.81882 86.97874 91.43265
[17] 76.46371 86.37377 75.76115 82.30404
> colMin(tmp5,na.rm=TRUE)
[1] Inf 54.80907 62.64018 61.05878 54.47073 56.63028 57.45126 57.99813
[9] 57.33317 56.19639 62.60800 58.81818 63.43074 57.82249 59.23182 62.95105
[17] 58.15320 61.98201 55.19753 62.42229
>
>
>
>
> 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] 222.52827 228.66846 183.54021 199.26610 211.91300 85.45867 211.76556
[8] 342.52743 232.63894 270.62403
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 222.52827 228.66846 183.54021 199.26610 211.91300 85.45867 211.76556
[8] 342.52743 232.63894 270.62403
>
>
>
> 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 1.136868e-13 -1.421085e-13 0.000000e+00 -7.105427e-14
[6] 1.136868e-13 2.842171e-14 1.847411e-13 -1.136868e-13 1.136868e-13
[11] 8.526513e-14 -2.842171e-13 -1.136868e-13 -5.684342e-14 5.684342e-14
[16] 5.684342e-14 1.136868e-13 5.684342e-14 2.842171e-14 1.989520e-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)
+ }
6 15
4 20
1 6
6 1
4 1
7 8
1 6
4 7
5 12
10 12
4 16
6 6
9 15
7 14
3 2
7 10
1 12
8 20
5 15
2 13
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] 2.633172
> Min(tmp)
[1] -2.544778
> mean(tmp)
[1] 0.03161238
> Sum(tmp)
[1] 3.161238
> Var(tmp)
[1] 1.002766
>
> rowMeans(tmp)
[1] 0.03161238
> rowSums(tmp)
[1] 3.161238
> rowVars(tmp)
[1] 1.002766
> rowSd(tmp)
[1] 1.001382
> rowMax(tmp)
[1] 2.633172
> rowMin(tmp)
[1] -2.544778
>
> colMeans(tmp)
[1] -1.078428231 -0.295706844 -1.231170312 -0.281995629 0.204138557
[6] 0.064730876 -1.151647951 0.612920109 0.783469954 -1.661534344
[11] 0.696328160 1.491271733 -0.470248420 0.214316803 -0.843380678
[16] 0.275564976 -1.268938903 -0.592346537 0.391338279 -1.599121686
[21] -0.193646903 0.726838956 2.253821978 2.633171578 -0.367147070
[26] 0.692544853 -0.695558640 0.099239118 0.084027123 -0.997525919
[31] 0.667223846 -0.129348247 0.628830779 -0.903521412 0.381397649
[36] 0.944570114 0.460068936 -0.005869595 -0.794891241 0.435117889
[41] 0.221111380 0.045056706 2.385410359 0.234089014 0.187210520
[46] 0.238901166 0.853467298 -0.930988954 -0.180366083 0.342039289
[51] 0.933244406 1.110753441 -0.210476950 -0.369332104 -0.621001846
[56] -0.119531514 -1.124238551 0.453658338 -0.375726134 0.937320785
[61] -0.701201334 -1.621015854 -2.544777970 0.719140243 -1.073919618
[66] -0.433506867 -0.108352603 -1.180470970 -1.550393697 0.001035741
[71] -0.383449148 0.714597103 -0.012230185 -1.014876857 0.197760318
[76] -1.327998238 0.499447638 1.155080697 0.972329529 -0.850837738
[81] 2.090982757 -0.127671703 -0.255798634 1.078502121 1.112369895
[86] -0.950706890 -2.443297732 1.012035865 -1.951633826 2.237419356
[91] -0.001022704 -0.328427662 0.583605368 0.869017417 0.973084761
[96] 0.105770686 1.307880446 1.400701086 0.385132060 0.417431071
> colSums(tmp)
[1] -1.078428231 -0.295706844 -1.231170312 -0.281995629 0.204138557
[6] 0.064730876 -1.151647951 0.612920109 0.783469954 -1.661534344
[11] 0.696328160 1.491271733 -0.470248420 0.214316803 -0.843380678
[16] 0.275564976 -1.268938903 -0.592346537 0.391338279 -1.599121686
[21] -0.193646903 0.726838956 2.253821978 2.633171578 -0.367147070
[26] 0.692544853 -0.695558640 0.099239118 0.084027123 -0.997525919
[31] 0.667223846 -0.129348247 0.628830779 -0.903521412 0.381397649
[36] 0.944570114 0.460068936 -0.005869595 -0.794891241 0.435117889
[41] 0.221111380 0.045056706 2.385410359 0.234089014 0.187210520
[46] 0.238901166 0.853467298 -0.930988954 -0.180366083 0.342039289
[51] 0.933244406 1.110753441 -0.210476950 -0.369332104 -0.621001846
[56] -0.119531514 -1.124238551 0.453658338 -0.375726134 0.937320785
[61] -0.701201334 -1.621015854 -2.544777970 0.719140243 -1.073919618
[66] -0.433506867 -0.108352603 -1.180470970 -1.550393697 0.001035741
[71] -0.383449148 0.714597103 -0.012230185 -1.014876857 0.197760318
[76] -1.327998238 0.499447638 1.155080697 0.972329529 -0.850837738
[81] 2.090982757 -0.127671703 -0.255798634 1.078502121 1.112369895
[86] -0.950706890 -2.443297732 1.012035865 -1.951633826 2.237419356
[91] -0.001022704 -0.328427662 0.583605368 0.869017417 0.973084761
[96] 0.105770686 1.307880446 1.400701086 0.385132060 0.417431071
> 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] -1.078428231 -0.295706844 -1.231170312 -0.281995629 0.204138557
[6] 0.064730876 -1.151647951 0.612920109 0.783469954 -1.661534344
[11] 0.696328160 1.491271733 -0.470248420 0.214316803 -0.843380678
[16] 0.275564976 -1.268938903 -0.592346537 0.391338279 -1.599121686
[21] -0.193646903 0.726838956 2.253821978 2.633171578 -0.367147070
[26] 0.692544853 -0.695558640 0.099239118 0.084027123 -0.997525919
[31] 0.667223846 -0.129348247 0.628830779 -0.903521412 0.381397649
[36] 0.944570114 0.460068936 -0.005869595 -0.794891241 0.435117889
[41] 0.221111380 0.045056706 2.385410359 0.234089014 0.187210520
[46] 0.238901166 0.853467298 -0.930988954 -0.180366083 0.342039289
[51] 0.933244406 1.110753441 -0.210476950 -0.369332104 -0.621001846
[56] -0.119531514 -1.124238551 0.453658338 -0.375726134 0.937320785
[61] -0.701201334 -1.621015854 -2.544777970 0.719140243 -1.073919618
[66] -0.433506867 -0.108352603 -1.180470970 -1.550393697 0.001035741
[71] -0.383449148 0.714597103 -0.012230185 -1.014876857 0.197760318
[76] -1.327998238 0.499447638 1.155080697 0.972329529 -0.850837738
[81] 2.090982757 -0.127671703 -0.255798634 1.078502121 1.112369895
[86] -0.950706890 -2.443297732 1.012035865 -1.951633826 2.237419356
[91] -0.001022704 -0.328427662 0.583605368 0.869017417 0.973084761
[96] 0.105770686 1.307880446 1.400701086 0.385132060 0.417431071
> colMin(tmp)
[1] -1.078428231 -0.295706844 -1.231170312 -0.281995629 0.204138557
[6] 0.064730876 -1.151647951 0.612920109 0.783469954 -1.661534344
[11] 0.696328160 1.491271733 -0.470248420 0.214316803 -0.843380678
[16] 0.275564976 -1.268938903 -0.592346537 0.391338279 -1.599121686
[21] -0.193646903 0.726838956 2.253821978 2.633171578 -0.367147070
[26] 0.692544853 -0.695558640 0.099239118 0.084027123 -0.997525919
[31] 0.667223846 -0.129348247 0.628830779 -0.903521412 0.381397649
[36] 0.944570114 0.460068936 -0.005869595 -0.794891241 0.435117889
[41] 0.221111380 0.045056706 2.385410359 0.234089014 0.187210520
[46] 0.238901166 0.853467298 -0.930988954 -0.180366083 0.342039289
[51] 0.933244406 1.110753441 -0.210476950 -0.369332104 -0.621001846
[56] -0.119531514 -1.124238551 0.453658338 -0.375726134 0.937320785
[61] -0.701201334 -1.621015854 -2.544777970 0.719140243 -1.073919618
[66] -0.433506867 -0.108352603 -1.180470970 -1.550393697 0.001035741
[71] -0.383449148 0.714597103 -0.012230185 -1.014876857 0.197760318
[76] -1.327998238 0.499447638 1.155080697 0.972329529 -0.850837738
[81] 2.090982757 -0.127671703 -0.255798634 1.078502121 1.112369895
[86] -0.950706890 -2.443297732 1.012035865 -1.951633826 2.237419356
[91] -0.001022704 -0.328427662 0.583605368 0.869017417 0.973084761
[96] 0.105770686 1.307880446 1.400701086 0.385132060 0.417431071
> colMedians(tmp)
[1] -1.078428231 -0.295706844 -1.231170312 -0.281995629 0.204138557
[6] 0.064730876 -1.151647951 0.612920109 0.783469954 -1.661534344
[11] 0.696328160 1.491271733 -0.470248420 0.214316803 -0.843380678
[16] 0.275564976 -1.268938903 -0.592346537 0.391338279 -1.599121686
[21] -0.193646903 0.726838956 2.253821978 2.633171578 -0.367147070
[26] 0.692544853 -0.695558640 0.099239118 0.084027123 -0.997525919
[31] 0.667223846 -0.129348247 0.628830779 -0.903521412 0.381397649
[36] 0.944570114 0.460068936 -0.005869595 -0.794891241 0.435117889
[41] 0.221111380 0.045056706 2.385410359 0.234089014 0.187210520
[46] 0.238901166 0.853467298 -0.930988954 -0.180366083 0.342039289
[51] 0.933244406 1.110753441 -0.210476950 -0.369332104 -0.621001846
[56] -0.119531514 -1.124238551 0.453658338 -0.375726134 0.937320785
[61] -0.701201334 -1.621015854 -2.544777970 0.719140243 -1.073919618
[66] -0.433506867 -0.108352603 -1.180470970 -1.550393697 0.001035741
[71] -0.383449148 0.714597103 -0.012230185 -1.014876857 0.197760318
[76] -1.327998238 0.499447638 1.155080697 0.972329529 -0.850837738
[81] 2.090982757 -0.127671703 -0.255798634 1.078502121 1.112369895
[86] -0.950706890 -2.443297732 1.012035865 -1.951633826 2.237419356
[91] -0.001022704 -0.328427662 0.583605368 0.869017417 0.973084761
[96] 0.105770686 1.307880446 1.400701086 0.385132060 0.417431071
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.078428 -0.2957068 -1.23117 -0.2819956 0.2041386 0.06473088 -1.151648
[2,] -1.078428 -0.2957068 -1.23117 -0.2819956 0.2041386 0.06473088 -1.151648
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.6129201 0.78347 -1.661534 0.6963282 1.491272 -0.4702484 0.2143168
[2,] 0.6129201 0.78347 -1.661534 0.6963282 1.491272 -0.4702484 0.2143168
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.8433807 0.275565 -1.268939 -0.5923465 0.3913383 -1.599122 -0.1936469
[2,] -0.8433807 0.275565 -1.268939 -0.5923465 0.3913383 -1.599122 -0.1936469
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.726839 2.253822 2.633172 -0.3671471 0.6925449 -0.6955586 0.09923912
[2,] 0.726839 2.253822 2.633172 -0.3671471 0.6925449 -0.6955586 0.09923912
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.08402712 -0.9975259 0.6672238 -0.1293482 0.6288308 -0.9035214 0.3813976
[2,] 0.08402712 -0.9975259 0.6672238 -0.1293482 0.6288308 -0.9035214 0.3813976
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.9445701 0.4600689 -0.005869595 -0.7948912 0.4351179 0.2211114 0.04505671
[2,] 0.9445701 0.4600689 -0.005869595 -0.7948912 0.4351179 0.2211114 0.04505671
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 2.38541 0.234089 0.1872105 0.2389012 0.8534673 -0.930989 -0.1803661
[2,] 2.38541 0.234089 0.1872105 0.2389012 0.8534673 -0.930989 -0.1803661
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.3420393 0.9332444 1.110753 -0.210477 -0.3693321 -0.6210018 -0.1195315
[2,] 0.3420393 0.9332444 1.110753 -0.210477 -0.3693321 -0.6210018 -0.1195315
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.124239 0.4536583 -0.3757261 0.9373208 -0.7012013 -1.621016 -2.544778
[2,] -1.124239 0.4536583 -0.3757261 0.9373208 -0.7012013 -1.621016 -2.544778
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.7191402 -1.07392 -0.4335069 -0.1083526 -1.180471 -1.550394 0.001035741
[2,] 0.7191402 -1.07392 -0.4335069 -0.1083526 -1.180471 -1.550394 0.001035741
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.3834491 0.7145971 -0.01223019 -1.014877 0.1977603 -1.327998 0.4994476
[2,] -0.3834491 0.7145971 -0.01223019 -1.014877 0.1977603 -1.327998 0.4994476
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 1.155081 0.9723295 -0.8508377 2.090983 -0.1276717 -0.2557986 1.078502
[2,] 1.155081 0.9723295 -0.8508377 2.090983 -0.1276717 -0.2557986 1.078502
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 1.11237 -0.9507069 -2.443298 1.012036 -1.951634 2.237419 -0.001022704
[2,] 1.11237 -0.9507069 -2.443298 1.012036 -1.951634 2.237419 -0.001022704
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.3284277 0.5836054 0.8690174 0.9730848 0.1057707 1.30788 1.400701
[2,] -0.3284277 0.5836054 0.8690174 0.9730848 0.1057707 1.30788 1.400701
[,99] [,100]
[1,] 0.3851321 0.4174311
[2,] 0.3851321 0.4174311
>
>
> Max(tmp2)
[1] 2.874546
> Min(tmp2)
[1] -2.293641
> mean(tmp2)
[1] 0.03519269
> Sum(tmp2)
[1] 3.519269
> Var(tmp2)
[1] 0.9813101
>
> rowMeans(tmp2)
[1] -0.134302506 0.032245192 0.249745479 2.121401177 -1.572452664
[6] 0.365822583 0.357409760 -0.280846232 -1.082731498 0.116823831
[11] -1.507422835 -0.101763697 -1.313311512 2.079770558 -0.411373711
[16] 0.041296484 -0.435111564 -1.961683575 -0.116444276 1.566845622
[21] 1.800318255 1.071296915 -1.323077511 0.228092532 -0.348928228
[26] 0.451275589 -0.695107684 0.462453481 0.052523789 -0.920676806
[31] -2.293640650 -1.473581526 1.799053523 0.242828073 -0.494526564
[36] -0.323283820 1.055380047 -0.684377790 2.874546199 -0.047243093
[41] -0.202840578 -1.615269309 -1.966730943 -0.920327018 0.192852982
[46] -0.286236770 1.879892883 -1.273291047 1.570254070 0.605579668
[51] -0.330140400 -0.541002092 0.909138521 0.001235552 0.969198491
[56] -0.798066062 -0.408726562 -0.912088128 1.432543460 0.619790881
[61] 1.247474807 0.356658777 -0.952081463 -0.866886333 0.279636117
[66] 0.210891753 0.330590222 0.563517410 -1.025762143 0.877936612
[71] -0.573560379 0.476063808 0.094348778 0.334729968 0.133210811
[76] 0.485755017 0.054531040 0.169819674 1.095240346 1.560794385
[81] 0.375705515 0.238665605 -0.942101642 0.052226579 -0.473283563
[86] -0.185580675 -0.320347784 0.648643973 1.462590460 -0.746807637
[91] 0.316605925 -0.439251697 -0.134051323 -0.618845884 -0.379904908
[96] 0.614023075 0.820908137 1.983367162 -0.588303478 -1.390906871
> rowSums(tmp2)
[1] -0.134302506 0.032245192 0.249745479 2.121401177 -1.572452664
[6] 0.365822583 0.357409760 -0.280846232 -1.082731498 0.116823831
[11] -1.507422835 -0.101763697 -1.313311512 2.079770558 -0.411373711
[16] 0.041296484 -0.435111564 -1.961683575 -0.116444276 1.566845622
[21] 1.800318255 1.071296915 -1.323077511 0.228092532 -0.348928228
[26] 0.451275589 -0.695107684 0.462453481 0.052523789 -0.920676806
[31] -2.293640650 -1.473581526 1.799053523 0.242828073 -0.494526564
[36] -0.323283820 1.055380047 -0.684377790 2.874546199 -0.047243093
[41] -0.202840578 -1.615269309 -1.966730943 -0.920327018 0.192852982
[46] -0.286236770 1.879892883 -1.273291047 1.570254070 0.605579668
[51] -0.330140400 -0.541002092 0.909138521 0.001235552 0.969198491
[56] -0.798066062 -0.408726562 -0.912088128 1.432543460 0.619790881
[61] 1.247474807 0.356658777 -0.952081463 -0.866886333 0.279636117
[66] 0.210891753 0.330590222 0.563517410 -1.025762143 0.877936612
[71] -0.573560379 0.476063808 0.094348778 0.334729968 0.133210811
[76] 0.485755017 0.054531040 0.169819674 1.095240346 1.560794385
[81] 0.375705515 0.238665605 -0.942101642 0.052226579 -0.473283563
[86] -0.185580675 -0.320347784 0.648643973 1.462590460 -0.746807637
[91] 0.316605925 -0.439251697 -0.134051323 -0.618845884 -0.379904908
[96] 0.614023075 0.820908137 1.983367162 -0.588303478 -1.390906871
> 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] -0.134302506 0.032245192 0.249745479 2.121401177 -1.572452664
[6] 0.365822583 0.357409760 -0.280846232 -1.082731498 0.116823831
[11] -1.507422835 -0.101763697 -1.313311512 2.079770558 -0.411373711
[16] 0.041296484 -0.435111564 -1.961683575 -0.116444276 1.566845622
[21] 1.800318255 1.071296915 -1.323077511 0.228092532 -0.348928228
[26] 0.451275589 -0.695107684 0.462453481 0.052523789 -0.920676806
[31] -2.293640650 -1.473581526 1.799053523 0.242828073 -0.494526564
[36] -0.323283820 1.055380047 -0.684377790 2.874546199 -0.047243093
[41] -0.202840578 -1.615269309 -1.966730943 -0.920327018 0.192852982
[46] -0.286236770 1.879892883 -1.273291047 1.570254070 0.605579668
[51] -0.330140400 -0.541002092 0.909138521 0.001235552 0.969198491
[56] -0.798066062 -0.408726562 -0.912088128 1.432543460 0.619790881
[61] 1.247474807 0.356658777 -0.952081463 -0.866886333 0.279636117
[66] 0.210891753 0.330590222 0.563517410 -1.025762143 0.877936612
[71] -0.573560379 0.476063808 0.094348778 0.334729968 0.133210811
[76] 0.485755017 0.054531040 0.169819674 1.095240346 1.560794385
[81] 0.375705515 0.238665605 -0.942101642 0.052226579 -0.473283563
[86] -0.185580675 -0.320347784 0.648643973 1.462590460 -0.746807637
[91] 0.316605925 -0.439251697 -0.134051323 -0.618845884 -0.379904908
[96] 0.614023075 0.820908137 1.983367162 -0.588303478 -1.390906871
> rowMin(tmp2)
[1] -0.134302506 0.032245192 0.249745479 2.121401177 -1.572452664
[6] 0.365822583 0.357409760 -0.280846232 -1.082731498 0.116823831
[11] -1.507422835 -0.101763697 -1.313311512 2.079770558 -0.411373711
[16] 0.041296484 -0.435111564 -1.961683575 -0.116444276 1.566845622
[21] 1.800318255 1.071296915 -1.323077511 0.228092532 -0.348928228
[26] 0.451275589 -0.695107684 0.462453481 0.052523789 -0.920676806
[31] -2.293640650 -1.473581526 1.799053523 0.242828073 -0.494526564
[36] -0.323283820 1.055380047 -0.684377790 2.874546199 -0.047243093
[41] -0.202840578 -1.615269309 -1.966730943 -0.920327018 0.192852982
[46] -0.286236770 1.879892883 -1.273291047 1.570254070 0.605579668
[51] -0.330140400 -0.541002092 0.909138521 0.001235552 0.969198491
[56] -0.798066062 -0.408726562 -0.912088128 1.432543460 0.619790881
[61] 1.247474807 0.356658777 -0.952081463 -0.866886333 0.279636117
[66] 0.210891753 0.330590222 0.563517410 -1.025762143 0.877936612
[71] -0.573560379 0.476063808 0.094348778 0.334729968 0.133210811
[76] 0.485755017 0.054531040 0.169819674 1.095240346 1.560794385
[81] 0.375705515 0.238665605 -0.942101642 0.052226579 -0.473283563
[86] -0.185580675 -0.320347784 0.648643973 1.462590460 -0.746807637
[91] 0.316605925 -0.439251697 -0.134051323 -0.618845884 -0.379904908
[96] 0.614023075 0.820908137 1.983367162 -0.588303478 -1.390906871
>
> colMeans(tmp2)
[1] 0.03519269
> colSums(tmp2)
[1] 3.519269
> colVars(tmp2)
[1] 0.9813101
> colSd(tmp2)
[1] 0.9906109
> colMax(tmp2)
[1] 2.874546
> colMin(tmp2)
[1] -2.293641
> colMedians(tmp2)
[1] 0.04676153
> colRanges(tmp2)
[,1]
[1,] -2.293641
[2,] 2.874546
>
> 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] 2.641829395 -1.613826158 6.387837924 0.443041674 1.391654390
[6] 1.936140787 3.492901036 0.857797897 -0.003905297 2.460936470
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.1673634
[2,] -0.1152124
[3,] 0.3729497
[4,] 0.5365341
[5,] 1.7190295
>
> rowApply(tmp,sum)
[1] 0.91556333 0.25549088 -0.53380079 1.53099135 1.65185631 1.94811354
[7] -0.08959754 -0.91725732 6.18522944 7.04781892
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 7 10 3 1 9 6 8 4 4
[2,] 9 3 4 1 5 4 2 3 8 8
[3,] 2 4 8 10 9 1 10 6 9 5
[4,] 3 9 2 7 3 7 9 1 1 10
[5,] 1 8 9 5 10 2 7 10 3 3
[6,] 8 2 5 8 2 8 8 4 7 6
[7,] 10 10 1 9 6 3 5 2 6 7
[8,] 5 6 7 2 4 10 3 9 5 1
[9,] 6 5 3 4 7 6 1 7 2 9
[10,] 4 1 6 6 8 5 4 5 10 2
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.2146309 -1.0320031 2.9939568 -0.1273940 -1.7941328 -1.8723989
[7] -2.0124529 -1.3200015 0.2087764 0.1518135 3.6635734 1.4078540
[13] -4.2091199 -0.6787083 0.9143236 -3.4857030 2.7874057 -3.3584211
[19] 0.9468316 4.0663543
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.4692862
[2,] -1.1182109
[3,] -0.9537655
[4,] 0.1286551
[5,] 1.1979767
>
> rowApply(tmp,sum)
[1] -2.3373008 -4.4878693 -0.7830652 3.7029383 -1.0587803
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 4 3 1 18 12
[2,] 12 13 2 8 7
[3,] 11 10 14 20 20
[4,] 7 9 16 17 4
[5,] 6 5 9 4 18
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.1182109 0.07222466 -0.1949753 -0.5164046 -1.0001806 0.5820639
[2,] -0.9537655 0.16810692 -0.4559901 -0.5038274 -0.7317156 -0.6085255
[3,] -1.4692862 -0.79105587 0.2175319 0.5593145 -0.3570345 -0.5965364
[4,] 1.1979767 0.03301642 2.3078603 1.1035371 -0.5868139 -1.4052777
[5,] 0.1286551 -0.51429523 1.1195300 -0.7700135 0.8816118 0.1558768
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -1.0347955 -0.2085290 -0.2008968 -0.45387935 0.6635734 0.10988689
[2,] 0.3252359 -1.1734370 -0.5883517 1.06758777 1.1425963 -0.36635337
[3,] -0.4415036 1.4289927 0.4885561 -0.08198489 0.8736781 0.86018696
[4,] 0.3877426 -0.3409497 -0.1856622 0.06047419 0.4063939 0.74131662
[5,] -1.2491324 -1.0260786 0.6951310 -0.44038420 0.5773319 0.06281685
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.3019441 0.072693963 0.81574728 -2.29653062 2.5474319 -1.3126723
[2,] -2.0096860 0.578421335 0.46465109 -0.90109609 0.5333784 -0.2637463
[3,] -0.6198203 -0.009192759 0.13759267 -0.65569161 -0.4439503 -0.6321976
[4,] -1.3273316 -2.002275890 0.08929494 0.46246188 0.8619011 0.3845829
[5,] 1.0496622 0.681645010 -0.59296241 -0.09484655 -0.7113554 -1.5343878
[,19] [,20]
[1,] 1.00811671 1.42997961
[2,] -0.51819131 0.30683915
[3,] 0.71246433 0.03687154
[4,] -0.05836284 1.57305361
[5,] -0.19719528 0.71961038
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-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-3.23-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-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 562 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-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 -2.528359 0.9515295 -0.1692881 1.646751 0.07955058 0.5756586 -1.42897
col8 col9 col10 col11 col12 col13 col14
row1 0.1180732 0.07266767 0.3502781 1.447909 0.1485258 1.609858 -2.617071
col15 col16 col17 col18 col19 col20
row1 0.252607 0.2381179 -2.261885 -0.9585365 0.5161008 0.07447615
> tmp[,"col10"]
col10
row1 0.3502781
row2 0.7460217
row3 -0.3279991
row4 1.0071954
row5 -1.0220311
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -2.5283587 0.9515295 -0.1692881 1.64675103 0.07955058 0.5756586
row5 -0.2930071 -0.5636343 2.0814746 0.07228302 -0.39406999 0.1458400
col7 col8 col9 col10 col11 col12
row1 -1.4289701 0.1180732 0.07266767 0.3502781 1.4479087 0.1485258
row5 -0.1947559 -1.0566031 -1.22729548 -1.0220311 0.4423508 -0.3423257
col13 col14 col15 col16 col17 col18
row1 1.6098576 -2.6170710 0.25260698 0.2381179 -2.26188461 -0.9585365
row5 0.4435472 0.5905384 -0.03867182 -0.8575110 0.08521314 -0.3837405
col19 col20
row1 0.5161008 0.07447615
row5 -0.6180669 -1.20955041
> tmp[,c("col6","col20")]
col6 col20
row1 0.5756586 0.07447615
row2 -0.5359509 -1.92329126
row3 1.2073179 -0.43801350
row4 -0.9748757 -0.73668518
row5 0.1458400 -1.20955041
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.5756586 0.07447615
row5 0.1458400 -1.20955041
>
>
>
>
> 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 51.11435 48.86509 49.96625 50.29454 50.81792 103.9524 49.39332 48.89968
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.23825 50.84648 50.35108 50.07241 49.9548 50.09732 50.5598 50.02313
col17 col18 col19 col20
row1 51.0145 49.05828 50.09431 105.6033
> tmp[,"col10"]
col10
row1 50.84648
row2 29.65291
row3 30.89511
row4 29.78484
row5 49.09694
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.11435 48.86509 49.96625 50.29454 50.81792 103.9524 49.39332 48.89968
row5 50.26828 49.59945 49.45853 49.99278 50.86953 105.8324 49.97437 48.74160
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.23825 50.84648 50.35108 50.07241 49.95480 50.09732 50.5598 50.02313
row5 50.25340 49.09694 49.84770 50.77338 49.15257 48.99183 49.9670 49.13342
col17 col18 col19 col20
row1 51.01450 49.05828 50.09431 105.6033
row5 49.66348 51.69244 49.77176 105.0314
> tmp[,c("col6","col20")]
col6 col20
row1 103.95243 105.60330
row2 74.39979 75.15494
row3 75.12034 75.13070
row4 74.62295 74.23408
row5 105.83244 105.03138
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.9524 105.6033
row5 105.8324 105.0314
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.9524 105.6033
row5 105.8324 105.0314
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.6950290
[2,] 1.0931417
[3,] -0.2753882
[4,] -0.1888743
[5,] 0.4065686
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.4251960 0.63625985
[2,] -1.9834105 0.03115183
[3,] -0.8753429 1.55867661
[4,] -1.0726191 -0.76744893
[5,] 0.3216395 -0.22664765
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.9978657 -0.4046276
[2,] 0.2232023 0.7591316
[3,] -0.6983987 0.2286466
[4,] 2.0135472 -0.4349915
[5,] 0.5768352 1.0311637
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.9978657
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.9978657
[2,] 0.2232023
>
>
>
> 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 1.2252099 -1.057260 -1.175126 -0.5230219 -0.01056389 -1.13186071
row1 -0.3990555 1.275973 1.393940 -1.4479972 -0.30255735 -0.08882799
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 0.6840044 0.1545002 0.5530625 0.2143576 -0.04968484 1.147636 -0.6867479
row1 0.2595561 0.9646168 -1.1284994 2.1136128 1.81819766 -2.389135 -1.6901624
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.6274210 0.6005382 0.01418588 0.5353607 1.7295153 -0.7347559 -1.078273
row1 -0.3687025 0.7273430 1.70547571 -1.2348421 -0.5739034 -1.0586230 1.207035
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.02705444 0.2077993 -1.136802 0.8096796 0.07775417 -0.1258068 2.300156
[,8] [,9] [,10]
row2 0.801877 -0.5874766 0.05577221
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.4435958 1.231757 0.1488511 0.2416317 0.8556406 1.374548 1.789644
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.8453274 0.192476 0.4644306 0.4295661 -0.3778197 0.6370017 -0.6195156
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.491607 0.3310083 -0.6693998 -1.411784 0.1759572 -1.05104
>
>
> 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: 0x6000002c4480>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d13dad768"
[2] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d473f707"
[3] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d595eeed9"
[4] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d67931665"
[5] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d69a37602"
[6] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d6a98b37c"
[7] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d4f2fc890"
[8] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d4a188e8d"
[9] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d1236f0fc"
[10] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d550739bb"
[11] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d4d5f4f99"
[12] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d2c62ed7e"
[13] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d12d601f6"
[14] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d201ac723"
[15] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM242d3e07db4c"
>
>
> ### 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: 0x6000002c44e0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6000002c44e0>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6000002c44e0>
> rowMedians(tmp)
[1] -0.587124699 0.293526775 0.033221850 0.255086952 -0.363523066
[6] 0.139030365 -0.267672792 0.140117622 0.021743042 -0.197027182
[11] 0.109821731 -0.375326159 -0.033202592 -0.263917327 0.058401032
[16] -0.075862200 0.380802654 -0.253598250 0.073760187 -0.198724088
[21] 0.389852119 -0.033678897 0.360371145 -0.141030526 0.335472922
[26] -0.406571416 0.067148973 -0.361909340 0.178971061 -0.562928618
[31] 0.006674893 -0.072468558 -0.108663686 -0.080079935 0.882336970
[36] 0.018304922 -0.716187364 0.059933479 -0.127546701 0.501012806
[41] 0.122134741 0.132765577 -0.072084174 0.070664315 -0.206134928
[46] -0.019450012 -0.179024617 0.859135362 -0.138405855 0.628488398
[51] 0.005628280 0.145069477 0.430843087 -0.325883382 0.045411377
[56] -0.025282910 -0.146740017 -0.203445267 0.168118441 -0.283818551
[61] 0.191696590 0.257472841 0.038573504 0.311960590 0.120730612
[66] 0.279309808 -0.426716537 -0.041666416 -0.658269605 0.212600250
[71] -0.056866237 0.125591895 -0.323881517 -0.034893047 0.275349588
[76] 0.333004573 0.062862729 -0.278005370 0.075510034 -0.064296219
[81] -0.003456735 -0.281984578 -0.182570934 0.124276831 0.399153228
[86] -0.005508120 0.106382703 0.599315808 0.173847960 0.419706455
[91] 0.401735619 -0.352591509 -0.327210426 0.051266663 0.158307833
[96] -0.133623611 -0.292457161 -0.361220502 -0.709800932 -0.072547914
[101] 0.017902403 -0.110573907 -0.011920118 0.301024394 0.511603636
[106] 0.003749968 0.373573239 0.208653082 0.027415436 0.441332619
[111] 0.407744612 -0.155487250 0.197091295 -0.156665004 -0.337184145
[116] 0.182487020 0.151293113 -0.236162909 -0.196927948 -0.133978061
[121] -0.459291741 -0.264327079 -0.203188634 -0.390665944 -0.456578818
[126] 0.259287236 0.194162538 0.136826164 0.550301256 0.174683750
[131] 0.314329947 0.433174758 -0.138761211 -0.222429639 -0.143437245
[136] 0.202022561 0.412400701 -0.163357933 -0.109770458 0.033999789
[141] 0.280792776 -0.487782085 0.365005656 0.031034473 0.124615126
[146] -0.379846621 0.175258930 0.246014326 -0.395566702 0.523070316
[151] 0.123867352 0.117892163 0.003224361 0.355591967 -0.056325198
[156] 0.053038926 0.449635310 -0.029808905 0.028194851 0.014959635
[161] 0.035336818 -0.498382600 -0.540284260 0.134114341 0.360598053
[166] -0.178414558 0.131954483 0.363706631 0.692818957 -0.623956451
[171] 0.055566657 -0.306439382 0.050011258 -0.358708860 -0.121486844
[176] 0.335038231 0.237541622 -0.067576611 -0.258721772 -0.407188748
[181] 0.658892598 0.009187468 0.500384914 -0.679501405 0.333324911
[186] 0.516363087 -0.167765174 0.120876535 0.452704391 -0.338043007
[191] -0.042445498 0.238730483 0.204187606 0.158191304 0.888738475
[196] -0.084676205 0.156544077 0.052242725 -0.281781388 0.896219670
[201] -0.014280281 0.218672305 0.348948817 -0.293670551 0.169205949
[206] -0.400016182 -0.527719122 0.718291857 -0.360229495 -0.046213763
[211] -0.084893658 0.139535011 0.402194747 0.480370045 0.272415429
[216] 0.170595683 0.056490590 0.022219921 -0.271668926 0.211820295
[221] 0.121985169 0.513138699 -0.167156923 -0.237864362 0.066321523
[226] 0.191565377 0.735032078 0.190595822 -0.318387812 0.856667312
>
> proc.time()
user system elapsed
0.720 3.608 4.834
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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: 0x600003bfc000>
> .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: 0x600003bfc000>
> .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: 0x600003bfc000>
> .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: 0x600003bfc000>
> 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: 0x600003bfc0c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003bfc0c0>
> .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: 0x600003bfc0c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003bfc0c0>
> .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: 0x600003bfc0c0>
> 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: 0x600003bfc2a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003bfc2a0>
> .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: 0x600003bfc2a0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003bfc2a0>
> .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: 0x600003bfc2a0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600003bfc2a0>
> .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: 0x600003bfc2a0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600003bfc2a0>
> .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: 0x600003bfc2a0>
> 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: 0x600003bfc480>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600003bfc480>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003bfc480>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003bfc480>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile288e26dee068" "BufferedMatrixFile288e725edfc7"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile288e26dee068" "BufferedMatrixFile288e725edfc7"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003bfc720>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003bfc720>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003bfc720>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003bfc720>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600003bfc720>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600003bfc720>
> .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: 0x600003bfc900>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003bfc900>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003bfc900>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x600003bfc900>
> 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: 0x600003bfcae0>
> .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: 0x600003bfcae0>
> rm(P)
>
> proc.time()
user system elapsed
0.155 0.056 0.208
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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
0.112 0.029 0.149