Ben Bolstad
| Snapshot Date: 2025-12-14 13:40 -0500 (Sun, 14 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 2025-12-15 11:35 -0500 (Mon, 15 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" | 4583 |
| 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: 2025-12-14 18:48:35 -0500 (Sun, 14 Dec 2025) |
| EndedAt: 2025-12-14 18:48:56 -0500 (Sun, 14 Dec 2025) |
| EllapsedTime: 21.3 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
0.146 0.061 0.205
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] "Sun Dec 14 18:48:48 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 Dec 14 18:48:48 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: 0x6000007a0420>
>
>
>
> 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 Dec 14 18:48:49 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 Dec 14 18:48:49 2025"
>
> ColMode(tmp2)
<pointer: 0x6000007a0420>
>
>
>
> ### 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,] 100.8110011 1.481255 -1.0630620 1.57234569
[2,] -1.1336129 -2.529999 -0.5223571 -1.18441750
[3,] 0.7319146 -1.478885 0.5579713 0.30515096
[4,] 1.1347226 -1.992240 0.9712324 0.05911967
> 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,] 100.8110011 1.481255 1.0630620 1.57234569
[2,] 1.1336129 2.529999 0.5223571 1.18441750
[3,] 0.7319146 1.478885 0.5579713 0.30515096
[4,] 1.1347226 1.992240 0.9712324 0.05911967
> 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,] 10.0404682 1.217068 1.0310490 1.2539321
[2,] 1.0647126 1.590597 0.7227428 1.0883095
[3,] 0.8555201 1.216094 0.7469747 0.5524047
[4,] 1.0652336 1.411467 0.9855112 0.2431454
>
> 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,] 226.21568 38.65194 36.37355 39.11167
[2,] 36.78074 43.43597 32.74978 37.06751
[3,] 34.28712 38.63983 33.02772 30.82920
[4,] 36.78706 41.10691 35.82634 27.49057
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x6000007ac0c0>
> exp(tmp5)
<pointer: 0x6000007ac0c0>
> log(tmp5,2)
<pointer: 0x6000007ac0c0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 470.8383
> Min(tmp5)
[1] 53.32119
> mean(tmp5)
[1] 72.04856
> Sum(tmp5)
[1] 14409.71
> Var(tmp5)
[1] 869.6787
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.11029 71.11314 68.77098 72.15005 67.22567 71.32849 69.47870 68.92359
[9] 71.64750 70.73713
> rowSums(tmp5)
[1] 1782.206 1422.263 1375.420 1443.001 1344.513 1426.570 1389.574 1378.472
[9] 1432.950 1414.743
> rowVars(tmp5)
[1] 8126.16556 48.15541 29.64930 103.79992 100.32631 79.22607
[7] 59.52198 58.98310 87.05031 52.95798
> rowSd(tmp5)
[1] 90.145247 6.939410 5.445117 10.188225 10.016302 8.900903 7.715049
[8] 7.680046 9.330076 7.277223
> rowMax(tmp5)
[1] 470.83831 90.40628 80.42373 93.58132 97.66826 88.39189 88.06198
[8] 80.46705 91.08301 84.82987
> rowMin(tmp5)
[1] 56.47071 62.19584 59.77529 56.24559 53.43320 57.83484 59.78242 53.32119
[9] 57.49851 56.87248
>
> colMeans(tmp5)
[1] 114.98440 75.43083 69.78895 69.16217 70.80115 66.21044 69.06137
[8] 69.73201 69.79265 70.39375 70.80061 66.46960 73.06975 70.83593
[15] 65.76716 68.13961 69.54913 68.44885 70.49077 72.04196
> colSums(tmp5)
[1] 1149.8440 754.3083 697.8895 691.6217 708.0115 662.1044 690.6137
[8] 697.3201 697.9265 703.9375 708.0061 664.6960 730.6975 708.3593
[15] 657.6716 681.3961 695.4913 684.4885 704.9077 720.4196
> colVars(tmp5)
[1] 15659.31923 148.70177 37.98681 91.42872 44.83337 21.63915
[7] 75.62146 32.45985 72.71355 73.36703 124.35685 18.94190
[13] 90.48095 38.35982 106.15629 21.74065 134.95505 70.20528
[19] 84.42103 17.78234
> colSd(tmp5)
[1] 125.137202 12.194333 6.163344 9.561837 6.695772 4.651790
[7] 8.696060 5.697354 8.527224 8.565456 11.151540 4.352229
[13] 9.512147 6.193531 10.303217 4.662687 11.617015 8.378859
[19] 9.188092 4.216912
> colMax(tmp5)
[1] 470.83831 91.08301 77.61867 81.40581 86.26681 73.77275 87.50029
[8] 78.83647 83.19174 82.36891 97.66826 72.42582 93.58132 78.40245
[15] 88.06198 76.66932 87.37258 81.45738 88.39189 77.84074
> colMin(tmp5)
[1] 66.43281 56.87248 58.49916 57.21803 62.63563 59.78242 60.16637 61.94089
[9] 56.47071 56.24559 59.82306 59.77529 63.99787 58.33075 53.32119 61.59182
[17] 55.82740 57.51016 57.49851 63.56858
>
>
> ### 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] NA 71.11314 68.77098 72.15005 67.22567 71.32849 69.47870 68.92359
[9] 71.64750 70.73713
> rowSums(tmp5)
[1] NA 1422.263 1375.420 1443.001 1344.513 1426.570 1389.574 1378.472
[9] 1432.950 1414.743
> rowVars(tmp5)
[1] 8565.99768 48.15541 29.64930 103.79992 100.32631 79.22607
[7] 59.52198 58.98310 87.05031 52.95798
> rowSd(tmp5)
[1] 92.552675 6.939410 5.445117 10.188225 10.016302 8.900903 7.715049
[8] 7.680046 9.330076 7.277223
> rowMax(tmp5)
[1] NA 90.40628 80.42373 93.58132 97.66826 88.39189 88.06198 80.46705
[9] 91.08301 84.82987
> rowMin(tmp5)
[1] NA 62.19584 59.77529 56.24559 53.43320 57.83484 59.78242 53.32119
[9] 57.49851 56.87248
>
> colMeans(tmp5)
[1] 114.98440 75.43083 69.78895 69.16217 70.80115 66.21044 69.06137
[8] 69.73201 69.79265 70.39375 70.80061 66.46960 73.06975 70.83593
[15] 65.76716 68.13961 69.54913 68.44885 NA 72.04196
> colSums(tmp5)
[1] 1149.8440 754.3083 697.8895 691.6217 708.0115 662.1044 690.6137
[8] 697.3201 697.9265 703.9375 708.0061 664.6960 730.6975 708.3593
[15] 657.6716 681.3961 695.4913 684.4885 NA 720.4196
> colVars(tmp5)
[1] 15659.31923 148.70177 37.98681 91.42872 44.83337 21.63915
[7] 75.62146 32.45985 72.71355 73.36703 124.35685 18.94190
[13] 90.48095 38.35982 106.15629 21.74065 134.95505 70.20528
[19] NA 17.78234
> colSd(tmp5)
[1] 125.137202 12.194333 6.163344 9.561837 6.695772 4.651790
[7] 8.696060 5.697354 8.527224 8.565456 11.151540 4.352229
[13] 9.512147 6.193531 10.303217 4.662687 11.617015 8.378859
[19] NA 4.216912
> colMax(tmp5)
[1] 470.83831 91.08301 77.61867 81.40581 86.26681 73.77275 87.50029
[8] 78.83647 83.19174 82.36891 97.66826 72.42582 93.58132 78.40245
[15] 88.06198 76.66932 87.37258 81.45738 NA 77.84074
> colMin(tmp5)
[1] 66.43281 56.87248 58.49916 57.21803 62.63563 59.78242 60.16637 61.94089
[9] 56.47071 56.24559 59.82306 59.77529 63.99787 58.33075 53.32119 61.59182
[17] 55.82740 57.51016 NA 63.56858
>
> Max(tmp5,na.rm=TRUE)
[1] 470.8383
> Min(tmp5,na.rm=TRUE)
[1] 53.32119
> mean(tmp5,na.rm=TRUE)
[1] 72.03366
> Sum(tmp5,na.rm=TRUE)
[1] 14334.7
> Var(tmp5,na.rm=TRUE)
[1] 874.0264
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.85224 71.11314 68.77098 72.15005 67.22567 71.32849 69.47870 68.92359
[9] 71.64750 70.73713
> rowSums(tmp5,na.rm=TRUE)
[1] 1707.193 1422.263 1375.420 1443.001 1344.513 1426.570 1389.574 1378.472
[9] 1432.950 1414.743
> rowVars(tmp5,na.rm=TRUE)
[1] 8565.99768 48.15541 29.64930 103.79992 100.32631 79.22607
[7] 59.52198 58.98310 87.05031 52.95798
> rowSd(tmp5,na.rm=TRUE)
[1] 92.552675 6.939410 5.445117 10.188225 10.016302 8.900903 7.715049
[8] 7.680046 9.330076 7.277223
> rowMax(tmp5,na.rm=TRUE)
[1] 470.83831 90.40628 80.42373 93.58132 97.66826 88.39189 88.06198
[8] 80.46705 91.08301 84.82987
> rowMin(tmp5,na.rm=TRUE)
[1] 56.47071 62.19584 59.77529 56.24559 53.43320 57.83484 59.78242 53.32119
[9] 57.49851 56.87248
>
> colMeans(tmp5,na.rm=TRUE)
[1] 114.98440 75.43083 69.78895 69.16217 70.80115 66.21044 69.06137
[8] 69.73201 69.79265 70.39375 70.80061 66.46960 73.06975 70.83593
[15] 65.76716 68.13961 69.54913 68.44885 69.98828 72.04196
> colSums(tmp5,na.rm=TRUE)
[1] 1149.8440 754.3083 697.8895 691.6217 708.0115 662.1044 690.6137
[8] 697.3201 697.9265 703.9375 708.0061 664.6960 730.6975 708.3593
[15] 657.6716 681.3961 695.4913 684.4885 629.8945 720.4196
> colVars(tmp5,na.rm=TRUE)
[1] 15659.31923 148.70177 37.98681 91.42872 44.83337 21.63915
[7] 75.62146 32.45985 72.71355 73.36703 124.35685 18.94190
[13] 90.48095 38.35982 106.15629 21.74065 134.95505 70.20528
[19] 92.13306 17.78234
> colSd(tmp5,na.rm=TRUE)
[1] 125.137202 12.194333 6.163344 9.561837 6.695772 4.651790
[7] 8.696060 5.697354 8.527224 8.565456 11.151540 4.352229
[13] 9.512147 6.193531 10.303217 4.662687 11.617015 8.378859
[19] 9.598597 4.216912
> colMax(tmp5,na.rm=TRUE)
[1] 470.83831 91.08301 77.61867 81.40581 86.26681 73.77275 87.50029
[8] 78.83647 83.19174 82.36891 97.66826 72.42582 93.58132 78.40245
[15] 88.06198 76.66932 87.37258 81.45738 88.39189 77.84074
> colMin(tmp5,na.rm=TRUE)
[1] 66.43281 56.87248 58.49916 57.21803 62.63563 59.78242 60.16637 61.94089
[9] 56.47071 56.24559 59.82306 59.77529 63.99787 58.33075 53.32119 61.59182
[17] 55.82740 57.51016 57.49851 63.56858
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] NaN 71.11314 68.77098 72.15005 67.22567 71.32849 69.47870 68.92359
[9] 71.64750 70.73713
> rowSums(tmp5,na.rm=TRUE)
[1] 0.000 1422.263 1375.420 1443.001 1344.513 1426.570 1389.574 1378.472
[9] 1432.950 1414.743
> rowVars(tmp5,na.rm=TRUE)
[1] NA 48.15541 29.64930 103.79992 100.32631 79.22607 59.52198
[8] 58.98310 87.05031 52.95798
> rowSd(tmp5,na.rm=TRUE)
[1] NA 6.939410 5.445117 10.188225 10.016302 8.900903 7.715049
[8] 7.680046 9.330076 7.277223
> rowMax(tmp5,na.rm=TRUE)
[1] NA 90.40628 80.42373 93.58132 97.66826 88.39189 88.06198 80.46705
[9] 91.08301 84.82987
> rowMin(tmp5,na.rm=TRUE)
[1] NA 62.19584 59.77529 56.24559 53.43320 57.83484 59.78242 53.32119
[9] 57.49851 56.87248
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 75.44507 74.87326 69.13142 67.80177 70.94102 66.30701 69.72823 70.59769
[9] 71.27286 69.91718 72.02034 65.80780 73.38343 70.97303 65.18313 68.86714
[17] 69.68966 69.66426 NaN 71.46357
> colSums(tmp5,na.rm=TRUE)
[1] 679.0057 673.8593 622.1827 610.2159 638.4692 596.7631 627.5541 635.3792
[9] 641.4558 629.2546 648.1831 592.2702 660.4509 638.7573 586.6482 619.8043
[17] 627.2069 626.9783 0.0000 643.1721
> colVars(tmp5,na.rm=TRUE)
[1] 28.95585 163.79206 37.87117 82.03695 50.21746 24.23912 80.07121
[8] 28.08655 57.15356 79.98277 123.16441 16.38235 100.68416 42.94336
[15] 115.58855 18.50358 151.60227 62.36220 NA 16.24161
> colSd(tmp5,na.rm=TRUE)
[1] 5.381064 12.798127 6.153956 9.057425 7.086428 4.923324 8.948252
[8] 5.299675 7.559997 8.943308 11.097946 4.047511 10.034150 6.553118
[15] 10.751211 4.301578 12.312687 7.896974 NA 4.030087
> colMax(tmp5,na.rm=TRUE)
[1] 85.53253 91.08301 77.61867 80.48722 86.26681 73.77275 87.50029 78.83647
[9] 83.19174 82.36891 97.66826 70.80718 93.58132 78.40245 88.06198 76.66932
[17] 87.37258 81.45738 -Inf 77.84074
> colMin(tmp5,na.rm=TRUE)
[1] 66.43281 56.87248 58.49916 57.21803 62.63563 59.78242 60.16637 63.24188
[9] 60.61103 56.24559 62.29315 59.77529 63.99787 58.33075 53.32119 62.90103
[17] 55.82740 58.78996 Inf 63.56858
>
>
>
>
> 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] 308.5910 210.2275 157.3528 167.7677 298.9676 259.0139 247.7140 179.5021
[9] 215.5148 180.3668
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 308.5910 210.2275 157.3528 167.7677 298.9676 259.0139 247.7140 179.5021
[9] 215.5148 180.3668
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 2.842171e-14 1.136868e-13 0.000000e+00 0.000000e+00 5.684342e-14
[6] 1.136868e-13 -5.684342e-14 -1.989520e-13 -2.842171e-14 5.684342e-14
[11] 0.000000e+00 -5.684342e-14 5.684342e-14 1.705303e-13 0.000000e+00
[16] 0.000000e+00 -1.136868e-13 -1.989520e-13 2.557954e-13 2.842171e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
4 15
1 4
6 7
5 16
2 13
6 2
7 17
6 4
9 11
5 15
4 19
9 12
6 9
5 12
7 20
10 4
3 17
4 11
5 20
1 20
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 3.156405
> Min(tmp)
[1] -1.896114
> mean(tmp)
[1] -0.0931147
> Sum(tmp)
[1] -9.31147
> Var(tmp)
[1] 1.024881
>
> rowMeans(tmp)
[1] -0.0931147
> rowSums(tmp)
[1] -9.31147
> rowVars(tmp)
[1] 1.024881
> rowSd(tmp)
[1] 1.012364
> rowMax(tmp)
[1] 3.156405
> rowMin(tmp)
[1] -1.896114
>
> colMeans(tmp)
[1] 1.342186071 0.405476290 0.143423631 -0.428192758 -1.198507530
[6] -0.671285263 -0.591225655 -1.240711471 1.451828887 1.893710789
[11] -0.874588599 -0.516782151 1.035513541 -1.896114031 0.163446642
[16] -1.356069159 -0.253496715 0.144070348 1.077437629 -0.630622400
[21] 0.678939400 -0.479561395 -0.756501512 -0.997142235 -0.184925351
[26] -0.025596298 -1.189825378 1.254692398 0.261064766 -0.365016295
[31] -1.078765258 0.713831505 0.962757584 -0.957813646 0.248019051
[36] -1.159799220 0.188590545 -1.509893067 -0.381099274 0.728201930
[41] -0.035145259 1.231859260 0.464337852 -0.473693281 -0.496704936
[46] -1.071423170 -1.579018492 0.612677002 0.874966540 -1.104611502
[51] -1.390690896 -0.578023426 -1.513807621 -1.051852374 -0.373451859
[56] -0.035739866 -0.056600763 -1.064829678 0.767941282 1.199334945
[61] 0.558857979 -0.084890846 -0.192267326 0.822602788 -0.084530733
[66] 1.325080556 -1.334641559 -1.153032354 -0.332711891 -0.891193564
[71] -0.370029591 -0.919839633 -1.028558576 -0.009733944 -0.299643814
[76] 0.915545067 -0.732803312 2.316032198 -0.203097034 -1.260982567
[81] -0.330209916 0.876544180 1.386560681 0.281441037 -0.830886034
[86] 0.458462630 1.252193558 -0.656102701 -1.557706225 -0.896642253
[91] -0.421324243 -0.144120513 3.156404999 -1.052954376 1.591355001
[96] 2.441406655 -1.076923781 -1.179765754 1.275725206 0.799730341
> colSums(tmp)
[1] 1.342186071 0.405476290 0.143423631 -0.428192758 -1.198507530
[6] -0.671285263 -0.591225655 -1.240711471 1.451828887 1.893710789
[11] -0.874588599 -0.516782151 1.035513541 -1.896114031 0.163446642
[16] -1.356069159 -0.253496715 0.144070348 1.077437629 -0.630622400
[21] 0.678939400 -0.479561395 -0.756501512 -0.997142235 -0.184925351
[26] -0.025596298 -1.189825378 1.254692398 0.261064766 -0.365016295
[31] -1.078765258 0.713831505 0.962757584 -0.957813646 0.248019051
[36] -1.159799220 0.188590545 -1.509893067 -0.381099274 0.728201930
[41] -0.035145259 1.231859260 0.464337852 -0.473693281 -0.496704936
[46] -1.071423170 -1.579018492 0.612677002 0.874966540 -1.104611502
[51] -1.390690896 -0.578023426 -1.513807621 -1.051852374 -0.373451859
[56] -0.035739866 -0.056600763 -1.064829678 0.767941282 1.199334945
[61] 0.558857979 -0.084890846 -0.192267326 0.822602788 -0.084530733
[66] 1.325080556 -1.334641559 -1.153032354 -0.332711891 -0.891193564
[71] -0.370029591 -0.919839633 -1.028558576 -0.009733944 -0.299643814
[76] 0.915545067 -0.732803312 2.316032198 -0.203097034 -1.260982567
[81] -0.330209916 0.876544180 1.386560681 0.281441037 -0.830886034
[86] 0.458462630 1.252193558 -0.656102701 -1.557706225 -0.896642253
[91] -0.421324243 -0.144120513 3.156404999 -1.052954376 1.591355001
[96] 2.441406655 -1.076923781 -1.179765754 1.275725206 0.799730341
> 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] 1.342186071 0.405476290 0.143423631 -0.428192758 -1.198507530
[6] -0.671285263 -0.591225655 -1.240711471 1.451828887 1.893710789
[11] -0.874588599 -0.516782151 1.035513541 -1.896114031 0.163446642
[16] -1.356069159 -0.253496715 0.144070348 1.077437629 -0.630622400
[21] 0.678939400 -0.479561395 -0.756501512 -0.997142235 -0.184925351
[26] -0.025596298 -1.189825378 1.254692398 0.261064766 -0.365016295
[31] -1.078765258 0.713831505 0.962757584 -0.957813646 0.248019051
[36] -1.159799220 0.188590545 -1.509893067 -0.381099274 0.728201930
[41] -0.035145259 1.231859260 0.464337852 -0.473693281 -0.496704936
[46] -1.071423170 -1.579018492 0.612677002 0.874966540 -1.104611502
[51] -1.390690896 -0.578023426 -1.513807621 -1.051852374 -0.373451859
[56] -0.035739866 -0.056600763 -1.064829678 0.767941282 1.199334945
[61] 0.558857979 -0.084890846 -0.192267326 0.822602788 -0.084530733
[66] 1.325080556 -1.334641559 -1.153032354 -0.332711891 -0.891193564
[71] -0.370029591 -0.919839633 -1.028558576 -0.009733944 -0.299643814
[76] 0.915545067 -0.732803312 2.316032198 -0.203097034 -1.260982567
[81] -0.330209916 0.876544180 1.386560681 0.281441037 -0.830886034
[86] 0.458462630 1.252193558 -0.656102701 -1.557706225 -0.896642253
[91] -0.421324243 -0.144120513 3.156404999 -1.052954376 1.591355001
[96] 2.441406655 -1.076923781 -1.179765754 1.275725206 0.799730341
> colMin(tmp)
[1] 1.342186071 0.405476290 0.143423631 -0.428192758 -1.198507530
[6] -0.671285263 -0.591225655 -1.240711471 1.451828887 1.893710789
[11] -0.874588599 -0.516782151 1.035513541 -1.896114031 0.163446642
[16] -1.356069159 -0.253496715 0.144070348 1.077437629 -0.630622400
[21] 0.678939400 -0.479561395 -0.756501512 -0.997142235 -0.184925351
[26] -0.025596298 -1.189825378 1.254692398 0.261064766 -0.365016295
[31] -1.078765258 0.713831505 0.962757584 -0.957813646 0.248019051
[36] -1.159799220 0.188590545 -1.509893067 -0.381099274 0.728201930
[41] -0.035145259 1.231859260 0.464337852 -0.473693281 -0.496704936
[46] -1.071423170 -1.579018492 0.612677002 0.874966540 -1.104611502
[51] -1.390690896 -0.578023426 -1.513807621 -1.051852374 -0.373451859
[56] -0.035739866 -0.056600763 -1.064829678 0.767941282 1.199334945
[61] 0.558857979 -0.084890846 -0.192267326 0.822602788 -0.084530733
[66] 1.325080556 -1.334641559 -1.153032354 -0.332711891 -0.891193564
[71] -0.370029591 -0.919839633 -1.028558576 -0.009733944 -0.299643814
[76] 0.915545067 -0.732803312 2.316032198 -0.203097034 -1.260982567
[81] -0.330209916 0.876544180 1.386560681 0.281441037 -0.830886034
[86] 0.458462630 1.252193558 -0.656102701 -1.557706225 -0.896642253
[91] -0.421324243 -0.144120513 3.156404999 -1.052954376 1.591355001
[96] 2.441406655 -1.076923781 -1.179765754 1.275725206 0.799730341
> colMedians(tmp)
[1] 1.342186071 0.405476290 0.143423631 -0.428192758 -1.198507530
[6] -0.671285263 -0.591225655 -1.240711471 1.451828887 1.893710789
[11] -0.874588599 -0.516782151 1.035513541 -1.896114031 0.163446642
[16] -1.356069159 -0.253496715 0.144070348 1.077437629 -0.630622400
[21] 0.678939400 -0.479561395 -0.756501512 -0.997142235 -0.184925351
[26] -0.025596298 -1.189825378 1.254692398 0.261064766 -0.365016295
[31] -1.078765258 0.713831505 0.962757584 -0.957813646 0.248019051
[36] -1.159799220 0.188590545 -1.509893067 -0.381099274 0.728201930
[41] -0.035145259 1.231859260 0.464337852 -0.473693281 -0.496704936
[46] -1.071423170 -1.579018492 0.612677002 0.874966540 -1.104611502
[51] -1.390690896 -0.578023426 -1.513807621 -1.051852374 -0.373451859
[56] -0.035739866 -0.056600763 -1.064829678 0.767941282 1.199334945
[61] 0.558857979 -0.084890846 -0.192267326 0.822602788 -0.084530733
[66] 1.325080556 -1.334641559 -1.153032354 -0.332711891 -0.891193564
[71] -0.370029591 -0.919839633 -1.028558576 -0.009733944 -0.299643814
[76] 0.915545067 -0.732803312 2.316032198 -0.203097034 -1.260982567
[81] -0.330209916 0.876544180 1.386560681 0.281441037 -0.830886034
[86] 0.458462630 1.252193558 -0.656102701 -1.557706225 -0.896642253
[91] -0.421324243 -0.144120513 3.156404999 -1.052954376 1.591355001
[96] 2.441406655 -1.076923781 -1.179765754 1.275725206 0.799730341
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 1.342186 0.4054763 0.1434236 -0.4281928 -1.198508 -0.6712853 -0.5912257
[2,] 1.342186 0.4054763 0.1434236 -0.4281928 -1.198508 -0.6712853 -0.5912257
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.240711 1.451829 1.893711 -0.8745886 -0.5167822 1.035514 -1.896114
[2,] -1.240711 1.451829 1.893711 -0.8745886 -0.5167822 1.035514 -1.896114
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.1634466 -1.356069 -0.2534967 0.1440703 1.077438 -0.6306224 0.6789394
[2,] 0.1634466 -1.356069 -0.2534967 0.1440703 1.077438 -0.6306224 0.6789394
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.4795614 -0.7565015 -0.9971422 -0.1849254 -0.0255963 -1.189825 1.254692
[2,] -0.4795614 -0.7565015 -0.9971422 -0.1849254 -0.0255963 -1.189825 1.254692
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.2610648 -0.3650163 -1.078765 0.7138315 0.9627576 -0.9578136 0.2480191
[2,] 0.2610648 -0.3650163 -1.078765 0.7138315 0.9627576 -0.9578136 0.2480191
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.159799 0.1885905 -1.509893 -0.3810993 0.7282019 -0.03514526 1.231859
[2,] -1.159799 0.1885905 -1.509893 -0.3810993 0.7282019 -0.03514526 1.231859
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.4643379 -0.4736933 -0.4967049 -1.071423 -1.579018 0.612677 0.8749665
[2,] 0.4643379 -0.4736933 -0.4967049 -1.071423 -1.579018 0.612677 0.8749665
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.104612 -1.390691 -0.5780234 -1.513808 -1.051852 -0.3734519 -0.03573987
[2,] -1.104612 -1.390691 -0.5780234 -1.513808 -1.051852 -0.3734519 -0.03573987
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.05660076 -1.06483 0.7679413 1.199335 0.558858 -0.08489085 -0.1922673
[2,] -0.05660076 -1.06483 0.7679413 1.199335 0.558858 -0.08489085 -0.1922673
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.8226028 -0.08453073 1.325081 -1.334642 -1.153032 -0.3327119 -0.8911936
[2,] 0.8226028 -0.08453073 1.325081 -1.334642 -1.153032 -0.3327119 -0.8911936
[,71] [,72] [,73] [,74] [,75] [,76]
[1,] -0.3700296 -0.9198396 -1.028559 -0.009733944 -0.2996438 0.9155451
[2,] -0.3700296 -0.9198396 -1.028559 -0.009733944 -0.2996438 0.9155451
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] -0.7328033 2.316032 -0.203097 -1.260983 -0.3302099 0.8765442 1.386561
[2,] -0.7328033 2.316032 -0.203097 -1.260983 -0.3302099 0.8765442 1.386561
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] 0.281441 -0.830886 0.4584626 1.252194 -0.6561027 -1.557706 -0.8966423
[2,] 0.281441 -0.830886 0.4584626 1.252194 -0.6561027 -1.557706 -0.8966423
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] -0.4213242 -0.1441205 3.156405 -1.052954 1.591355 2.441407 -1.076924
[2,] -0.4213242 -0.1441205 3.156405 -1.052954 1.591355 2.441407 -1.076924
[,98] [,99] [,100]
[1,] -1.179766 1.275725 0.7997303
[2,] -1.179766 1.275725 0.7997303
>
>
> Max(tmp2)
[1] 2.614981
> Min(tmp2)
[1] -2.137145
> mean(tmp2)
[1] 0.01069387
> Sum(tmp2)
[1] 1.069387
> Var(tmp2)
[1] 0.7594051
>
> rowMeans(tmp2)
[1] -0.13002443 -0.25814740 0.47354531 -0.26194947 -0.91270887 0.15990690
[7] 0.09012328 -0.22423922 -0.13113738 0.55106054 0.91826042 1.87405340
[13] -0.02252850 -0.34083228 0.33273975 0.29545588 0.74044667 -0.84452942
[19] 0.19815508 -0.90489049 0.61336678 0.55300563 -0.09551172 -1.68509379
[25] 1.22131331 0.07216297 0.51336844 0.05647291 -1.23662047 1.45754807
[31] -1.87102955 -0.93382329 1.04242673 -1.67901262 -0.72815716 -0.89077773
[37] 0.49288142 0.40672527 0.15262280 -0.40662654 0.91942759 -0.34680989
[43] 2.00848072 -1.27086803 -0.41137592 0.43267158 -0.31905534 0.97542870
[49] -0.24227801 -0.53494700 -0.10584613 -0.79813476 -0.79830509 -0.22951864
[55] -0.34106835 -1.14653803 -0.21343390 -0.31220541 -1.19295102 0.32067242
[61] 0.24056237 0.06785225 2.61498074 0.48703321 -0.08270527 0.03390582
[67] -1.12548804 0.89028124 -2.13714533 -0.95867846 0.07768064 -1.37212171
[73] 0.55897186 -0.31167682 0.90691054 -0.86689852 1.52412871 -0.34254322
[79] -0.18138014 -0.66711651 -0.27547686 0.07480019 -0.12336662 0.25431115
[85] 0.72206374 0.34319532 -0.26893069 0.78147242 0.27734149 -0.61910276
[91] 2.28834163 2.10900177 -0.09590038 0.74121952 0.25442614 0.15749183
[97] -0.79080500 0.65317199 0.02633120 0.15190113
> rowSums(tmp2)
[1] -0.13002443 -0.25814740 0.47354531 -0.26194947 -0.91270887 0.15990690
[7] 0.09012328 -0.22423922 -0.13113738 0.55106054 0.91826042 1.87405340
[13] -0.02252850 -0.34083228 0.33273975 0.29545588 0.74044667 -0.84452942
[19] 0.19815508 -0.90489049 0.61336678 0.55300563 -0.09551172 -1.68509379
[25] 1.22131331 0.07216297 0.51336844 0.05647291 -1.23662047 1.45754807
[31] -1.87102955 -0.93382329 1.04242673 -1.67901262 -0.72815716 -0.89077773
[37] 0.49288142 0.40672527 0.15262280 -0.40662654 0.91942759 -0.34680989
[43] 2.00848072 -1.27086803 -0.41137592 0.43267158 -0.31905534 0.97542870
[49] -0.24227801 -0.53494700 -0.10584613 -0.79813476 -0.79830509 -0.22951864
[55] -0.34106835 -1.14653803 -0.21343390 -0.31220541 -1.19295102 0.32067242
[61] 0.24056237 0.06785225 2.61498074 0.48703321 -0.08270527 0.03390582
[67] -1.12548804 0.89028124 -2.13714533 -0.95867846 0.07768064 -1.37212171
[73] 0.55897186 -0.31167682 0.90691054 -0.86689852 1.52412871 -0.34254322
[79] -0.18138014 -0.66711651 -0.27547686 0.07480019 -0.12336662 0.25431115
[85] 0.72206374 0.34319532 -0.26893069 0.78147242 0.27734149 -0.61910276
[91] 2.28834163 2.10900177 -0.09590038 0.74121952 0.25442614 0.15749183
[97] -0.79080500 0.65317199 0.02633120 0.15190113
> 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] -0.13002443 -0.25814740 0.47354531 -0.26194947 -0.91270887 0.15990690
[7] 0.09012328 -0.22423922 -0.13113738 0.55106054 0.91826042 1.87405340
[13] -0.02252850 -0.34083228 0.33273975 0.29545588 0.74044667 -0.84452942
[19] 0.19815508 -0.90489049 0.61336678 0.55300563 -0.09551172 -1.68509379
[25] 1.22131331 0.07216297 0.51336844 0.05647291 -1.23662047 1.45754807
[31] -1.87102955 -0.93382329 1.04242673 -1.67901262 -0.72815716 -0.89077773
[37] 0.49288142 0.40672527 0.15262280 -0.40662654 0.91942759 -0.34680989
[43] 2.00848072 -1.27086803 -0.41137592 0.43267158 -0.31905534 0.97542870
[49] -0.24227801 -0.53494700 -0.10584613 -0.79813476 -0.79830509 -0.22951864
[55] -0.34106835 -1.14653803 -0.21343390 -0.31220541 -1.19295102 0.32067242
[61] 0.24056237 0.06785225 2.61498074 0.48703321 -0.08270527 0.03390582
[67] -1.12548804 0.89028124 -2.13714533 -0.95867846 0.07768064 -1.37212171
[73] 0.55897186 -0.31167682 0.90691054 -0.86689852 1.52412871 -0.34254322
[79] -0.18138014 -0.66711651 -0.27547686 0.07480019 -0.12336662 0.25431115
[85] 0.72206374 0.34319532 -0.26893069 0.78147242 0.27734149 -0.61910276
[91] 2.28834163 2.10900177 -0.09590038 0.74121952 0.25442614 0.15749183
[97] -0.79080500 0.65317199 0.02633120 0.15190113
> rowMin(tmp2)
[1] -0.13002443 -0.25814740 0.47354531 -0.26194947 -0.91270887 0.15990690
[7] 0.09012328 -0.22423922 -0.13113738 0.55106054 0.91826042 1.87405340
[13] -0.02252850 -0.34083228 0.33273975 0.29545588 0.74044667 -0.84452942
[19] 0.19815508 -0.90489049 0.61336678 0.55300563 -0.09551172 -1.68509379
[25] 1.22131331 0.07216297 0.51336844 0.05647291 -1.23662047 1.45754807
[31] -1.87102955 -0.93382329 1.04242673 -1.67901262 -0.72815716 -0.89077773
[37] 0.49288142 0.40672527 0.15262280 -0.40662654 0.91942759 -0.34680989
[43] 2.00848072 -1.27086803 -0.41137592 0.43267158 -0.31905534 0.97542870
[49] -0.24227801 -0.53494700 -0.10584613 -0.79813476 -0.79830509 -0.22951864
[55] -0.34106835 -1.14653803 -0.21343390 -0.31220541 -1.19295102 0.32067242
[61] 0.24056237 0.06785225 2.61498074 0.48703321 -0.08270527 0.03390582
[67] -1.12548804 0.89028124 -2.13714533 -0.95867846 0.07768064 -1.37212171
[73] 0.55897186 -0.31167682 0.90691054 -0.86689852 1.52412871 -0.34254322
[79] -0.18138014 -0.66711651 -0.27547686 0.07480019 -0.12336662 0.25431115
[85] 0.72206374 0.34319532 -0.26893069 0.78147242 0.27734149 -0.61910276
[91] 2.28834163 2.10900177 -0.09590038 0.74121952 0.25442614 0.15749183
[97] -0.79080500 0.65317199 0.02633120 0.15190113
>
> colMeans(tmp2)
[1] 0.01069387
> colSums(tmp2)
[1] 1.069387
> colVars(tmp2)
[1] 0.7594051
> colSd(tmp2)
[1] 0.8714385
> colMax(tmp2)
[1] 2.614981
> colMin(tmp2)
[1] -2.137145
> colMedians(tmp2)
[1] 0.001901348
> colRanges(tmp2)
[,1]
[1,] -2.137145
[2,] 2.614981
>
> 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] -0.8152502 4.7082813 1.7287692 -3.3266602 2.1335096 0.7206044
[7] -3.8494696 2.3468110 3.8707600 -1.8162136
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.1888914
[2,] -0.4126422
[3,] -0.1530904
[4,] 0.2516697
[5,] 1.1195723
>
> rowApply(tmp,sum)
[1] 6.4930067 2.7715804 3.7535116 -2.0968814 -3.1178205 3.5308230
[7] -0.9548240 -0.6415183 -0.5369104 -3.4998251
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 2 3 9 7 6 5 7 1 3
[2,] 3 10 9 6 3 4 9 6 2 7
[3,] 4 7 10 1 4 5 10 2 5 8
[4,] 5 3 6 2 1 8 7 8 3 5
[5,] 8 4 8 10 2 3 4 9 7 10
[6,] 9 5 2 3 9 7 8 1 4 6
[7,] 1 1 5 4 10 2 1 10 9 1
[8,] 6 6 7 8 5 10 3 4 6 2
[9,] 10 8 4 5 6 9 2 3 10 9
[10,] 2 9 1 7 8 1 6 5 8 4
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.41539362 -2.19448382 -1.27210451 -0.35535019 2.56834307 -2.98447503
[7] 0.07784473 -5.77158669 -2.69543768 -2.72458939 1.69782884 0.78904782
[13] -1.96722383 2.66949609 3.64035475 -2.94922501 -4.08737179 0.19650196
[19] 1.70274695 -0.06737703
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.2604277
[2,] -1.1340189
[3,] -0.1755192
[4,] 0.2261302
[5,] 0.9284420
>
> rowApply(tmp,sum)
[1] -12.1139761 -0.4015511 0.1295677 0.2113549 -3.9678498
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 14 4 10 14 1
[2,] 8 14 2 12 11
[3,] 3 13 12 20 3
[4,] 19 9 4 4 18
[5,] 6 16 7 19 17
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.1755192 -0.7932540 -1.7851274 0.6093828 -1.1825196 -0.8990787
[2,] -1.1340189 0.3485424 0.1756472 -0.3407186 0.7258731 0.6281967
[3,] 0.2261302 -1.7494036 0.3245267 -1.0180380 -0.2292904 -2.4110125
[4,] 0.9284420 0.1922683 1.7990489 -1.3078280 1.6867958 1.0404469
[5,] -2.2604277 -0.1926370 -1.7861999 1.7018516 1.5674842 -1.3430274
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.3667918 -0.5484237 -2.44720005 -0.6905046 -0.5351389 -0.4216299
[2,] -1.1998716 -1.4925068 -0.23582437 -0.6933370 1.1638051 -0.4149211
[3,] 1.2272470 -0.5432812 0.52120328 0.4629890 -0.4383188 0.3057002
[4,] 1.3887925 -1.8567551 -0.58114825 -0.6471412 0.5581203 -0.5399838
[5,] -0.9715314 -1.3306199 0.04753172 -1.1565956 0.9493610 1.8598825
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.2244148 0.3001414 0.6491275 -1.39219476 -1.80730124 0.5045073
[2,] -1.3547508 2.0197467 -0.8708172 -0.63552006 0.05378536 0.1647884
[3,] 0.7374330 0.6379179 0.3919468 0.10152355 1.08596781 -1.0342521
[4,] -1.3604273 -0.8231540 1.3266833 -0.97559034 -1.58991262 1.3799917
[5,] -0.2138934 0.5348441 2.1434143 -0.04744341 -1.82991109 -0.8185334
[,19] [,20]
[1,] 0.007690469 -1.3645565
[2,] 1.349235556 1.3411148
[3,] 1.338634234 0.1919445
[4,] -0.284885483 -0.1224087
[5,] -0.707927820 -0.1134711
>
>
> 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 : 563 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-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 2.171059 -2.413856 -0.9235876 0.6196686 0.1275446 1.038135 -0.8095386
col8 col9 col10 col11 col12 col13 col14
row1 0.9801068 -1.024938 -0.03707671 -0.3228543 1.408282 1.661765 0.4571003
col15 col16 col17 col18 col19 col20
row1 -0.8267638 -2.570602 0.7988902 0.6563176 -0.851568 0.06341582
> tmp[,"col10"]
col10
row1 -0.03707671
row2 -0.49263872
row3 1.29556201
row4 -1.41815466
row5 -1.21396436
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 2.171059 -2.4138560 -0.92358762 0.619668636 0.1275446 1.0381346
row5 1.963940 -0.5588693 0.02230326 -0.006004083 0.7790919 -0.1077628
col7 col8 col9 col10 col11 col12 col13
row1 -0.8095386 0.9801068 -1.0249381 -0.03707671 -0.3228543 1.4082821 1.6617648
row5 0.3404395 0.3393409 0.6907754 -1.21396436 1.1350557 0.6837736 0.1833921
col14 col15 col16 col17 col18 col19 col20
row1 0.4571003 -0.8267638 -2.570602 0.7988902 0.6563176 -0.851568 0.06341582
row5 0.6757700 0.2417631 -1.286259 -0.8928982 1.1826362 1.243497 -1.55124161
> tmp[,c("col6","col20")]
col6 col20
row1 1.03813459 0.06341582
row2 0.03115066 -0.38868707
row3 0.94698575 0.16551075
row4 0.31827011 -0.80172073
row5 -0.10776283 -1.55124161
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 1.0381346 0.06341582
row5 -0.1077628 -1.55124161
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.23933 51.08978 49.06182 49.80412 51.24361 103.7719 50.61719 50.97961
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.76202 51.49776 50.74337 50.91162 50.01894 50.17812 48.94738 50.35515
col17 col18 col19 col20
row1 50.36903 47.24925 50.06849 103.4344
> tmp[,"col10"]
col10
row1 51.49776
row2 30.97341
row3 30.73427
row4 29.87367
row5 50.30139
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.23933 51.08978 49.06182 49.80412 51.24361 103.7719 50.61719 50.97961
row5 51.44909 49.81278 50.27656 50.92459 50.96366 102.7600 50.41635 48.96374
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.76202 51.49776 50.74337 50.91162 50.01894 50.17812 48.94738 50.35515
row5 48.86582 50.30139 49.65961 49.18575 50.67488 50.15293 49.92158 48.82224
col17 col18 col19 col20
row1 50.36903 47.24925 50.06849 103.4344
row5 50.26546 49.92092 50.20098 104.8622
> tmp[,c("col6","col20")]
col6 col20
row1 103.77188 103.43437
row2 74.77467 74.38765
row3 75.57184 75.58832
row4 74.00705 75.40541
row5 102.75995 104.86221
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.7719 103.4344
row5 102.7600 104.8622
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.7719 103.4344
row5 102.7600 104.8622
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.7011745
[2,] 0.9255115
[3,] -0.8490669
[4,] -2.5370561
[5,] -0.4425829
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.32005322 0.66265695
[2,] -0.54526413 -1.72138082
[3,] 2.35532829 0.62318859
[4,] 0.04041298 -0.55979262
[5,] 0.65757379 -0.04612161
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.8967309 1.8367309
[2,] -1.0477250 -0.8567533
[3,] 1.0534434 -1.3325481
[4,] 0.2119678 2.3319693
[5,] 1.6751792 0.5696110
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.8967309
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.8967309
[2,] -1.0477250
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -0.6142798 -1.4732863 0.56191950 0.7997741 -0.1622376 -0.4877832
row1 -2.4149039 -0.5770603 0.07179334 -1.1755786 -0.4281657 0.2942033
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 0.1212236 1.255964 1.3738945 1.6419834 0.06367854 0.08553279 1.200565
row1 0.4215175 1.571407 -0.7122881 -0.3628237 -0.09151942 -1.18998584 1.510799
[,14] [,15] [,16] [,17] [,18] [,19]
row3 -0.06181995 -0.18160644 -1.588009 0.128168 0.2896022 0.5879082
row1 -1.69402237 -0.06817295 -1.252819 -0.736782 -0.3341686 0.5968263
[,20]
row3 0.1302014
row1 -0.6179223
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.3248256 0.1894585 0.2618598 0.1856213 -1.398823 1.39981 -0.2249799
[,8] [,9] [,10]
row2 0.4877474 0.305588 0.4150744
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.2606892 -0.2946451 0.06188595 -1.44609 0.4010695 -0.09234726 -0.7361287
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.9263684 -1.747332 0.4895562 0.6443372 -0.1080067 0.8819117 -0.0694434
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.007278831 0.1672184 -0.5034705 0.7452215 1.181952 -1.498671
>
>
> 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: 0x6000007a0660>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f159f7b703"
[2] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f11610541a"
[3] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f1a018247"
[4] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f169100872"
[5] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f11b9aaa41"
[6] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f1471f9f8f"
[7] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f16d2489c3"
[8] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f179d0992f"
[9] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f16df91b23"
[10] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f17d64cf3c"
[11] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f16561ac74"
[12] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f16f8127ab"
[13] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f185384be"
[14] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f1232fda37"
[15] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM33f11a9f62ed"
>
>
> ### 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: 0x6000007a8240>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6000007a8240>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6000007a8240>
> rowMedians(tmp)
[1] -0.320720823 0.009843841 0.363779331 0.566097339 -0.079381372
[6] 0.465412783 0.110292491 -0.194465974 -0.030050490 -0.028105446
[11] 0.133399847 -0.380060084 0.172020431 0.084816908 -0.710613953
[16] -0.283268168 0.426381281 0.101504830 0.454853598 -0.222052452
[21] -0.461216020 -0.022438151 0.342979011 0.101745206 0.458010241
[26] 0.065339381 0.140638310 -0.591966010 0.262107935 0.558343916
[31] 0.027773417 0.352322679 0.751900976 0.070618134 0.211596896
[36] -0.076730683 -0.567065122 -0.537139618 0.549901142 0.294336519
[41] 0.184433369 -0.250002467 -0.383709443 -0.136736935 0.436115991
[46] 0.303168175 -0.173088620 -0.008196378 0.030937495 0.022592869
[51] 0.171584619 0.169295649 0.134116385 -0.233003274 0.284759454
[56] 0.622714099 -0.315384038 -0.447846278 -0.258901210 -0.556786046
[61] -0.063234946 -0.206808638 -0.379798958 -0.204497169 0.300321096
[66] -0.176729160 -0.073800881 -0.526003506 0.062566534 -0.104062300
[71] 0.681990816 -0.117226299 0.227636568 0.101930076 -0.040995407
[76] -0.294098579 -0.020524403 -0.538477164 -0.129813940 -0.090439125
[81] 0.138577172 -0.560812110 -0.319296868 -0.070902275 0.383998632
[86] 0.166523475 -0.101310358 0.017449723 0.055087349 -0.391809233
[91] -0.334691720 0.286598384 0.260654158 -0.049227018 -0.110581154
[96] 0.071963481 -0.126350503 0.677341907 0.408551590 -0.407644065
[101] 0.110478100 -0.446369983 -0.203345981 0.095111268 -0.295151879
[106] -0.234779212 0.488400323 -0.460025468 -0.273175856 0.101510350
[111] 0.184606454 -0.095659864 -0.215685374 -0.083096635 -0.185398294
[116] -0.227665209 0.064566995 -0.497718101 -0.304001897 0.007667961
[121] 0.504239567 0.040381232 0.035038057 -0.153079330 0.593313124
[126] -0.214691783 0.390540535 0.153811474 -0.148113861 0.159170273
[131] 0.477875738 -0.580106869 -0.482817396 0.133867401 -0.562396982
[136] -0.184218498 -0.130353815 0.068513837 -0.514450189 0.285896202
[141] 0.129935936 -0.206186715 0.237075579 -0.380644367 0.202115950
[146] 0.595042652 0.330253979 0.276179384 -0.178839625 0.115585547
[151] -0.254024176 -0.876414809 0.045797428 0.437319623 -0.136119863
[156] -0.545589356 -0.069658644 0.098342782 0.020958493 0.036661373
[161] -0.232186215 0.182244686 -0.235364026 0.217803462 -0.449150803
[166] 0.285509565 0.116511275 0.114177166 0.354810300 0.317192294
[171] -0.318318835 -0.267349099 0.103976523 -0.354483847 -0.269111924
[176] 0.283131715 0.217701326 0.612900875 0.034351611 0.026542691
[181] 0.649137194 -0.427735641 0.273877596 0.125601326 -0.109600597
[186] 0.017344020 0.310250741 -0.286643245 0.229727179 0.383550295
[191] 0.137311966 0.359289492 -0.182673304 0.012423916 0.460259623
[196] -0.247302278 0.281289743 -0.358124954 0.030077342 0.484944289
[201] -0.257611716 -0.555600243 0.293392742 -0.470876202 0.024471642
[206] -0.010625174 -0.178402643 -0.456548325 0.091899307 0.033759038
[211] 0.850079086 -0.077668909 0.084699148 0.553518382 0.105299660
[216] 0.408519825 -0.162020520 -0.071139681 0.080596525 0.618101423
[221] -0.315975186 0.277218669 0.215257731 -0.039726851 0.095428785
[226] 0.317695541 -0.490397470 -0.207863385 -0.074188789 -0.490248458
>
> proc.time()
user system elapsed
0.732 3.689 4.987
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: 0x6000031c0660>
> .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: 0x6000031c0660>
> .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: 0x6000031c0660>
> .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: 0x6000031c0660>
> 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: 0x6000031d8000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031d8000>
> .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: 0x6000031d8000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031d8000>
> .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: 0x6000031d8000>
> 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: 0x6000031d8180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031d8180>
> .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: 0x6000031d8180>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000031d8180>
> .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: 0x6000031d8180>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x6000031d8180>
> .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: 0x6000031d8180>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x6000031d8180>
> .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: 0x6000031d8180>
> 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: 0x6000031d8360>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x6000031d8360>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031d8360>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031d8360>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile36e43926238f" "BufferedMatrixFile36e476e89e98"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile36e43926238f" "BufferedMatrixFile36e476e89e98"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031d8600>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031d8600>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000031d8600>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000031d8600>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6000031d8600>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6000031d8600>
> .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: 0x6000031d87e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031d87e0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000031d87e0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x6000031d87e0>
> 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: 0x6000031d89c0>
> .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: 0x6000031d89c0>
> rm(P)
>
> proc.time()
user system elapsed
0.115 0.052 0.168
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
0.145 0.044 0.188