Ben Bolstad
| Snapshot Date: 2025-11-21 13:40 -0500 (Fri, 21 Nov 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 2025-11-22 11:39 -0500 (Sat, 22 Nov 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" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4567 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 252/2327 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | 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: 2025-11-21 18:47:54 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 18:48:15 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 21.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### 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
##############################################################################
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###
### 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
0.117 0.045 0.187
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] "Fri Nov 21 18:48:06 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri Nov 21 18:48:06 2025"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x600002f10060>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri Nov 21 18:48:07 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri Nov 21 18:48:08 2025"
>
> ColMode(tmp2)
<pointer: 0x600002f10060>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.59988262 0.64011320 1.2422656 -1.2409613
[2,] 0.28329177 -0.08356476 0.1098194 0.4346209
[3,] 0.73653531 0.42752891 1.2631419 -0.5212862
[4,] 0.04594001 -1.59874409 -0.4121492 0.4758044
> 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,] 99.59988262 0.64011320 1.2422656 1.2409613
[2,] 0.28329177 0.08356476 0.1098194 0.4346209
[3,] 0.73653531 0.42752891 1.2631419 0.5212862
[4,] 0.04594001 1.59874409 0.4121492 0.4758044
> 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,] 9.9799741 0.8000707 1.1145697 1.1139844
[2,] 0.5322516 0.2890757 0.3313901 0.6592578
[3,] 0.8582164 0.6538569 1.1238959 0.7220015
[4,] 0.2143362 1.2644145 0.6419885 0.6897858
>
> 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,] 224.39962 33.64082 37.38796 37.38081
[2,] 30.60581 27.97432 28.42372 32.02720
[3,] 34.31870 31.96610 37.50210 32.74130
[4,] 27.18930 39.24289 31.83203 32.37366
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600002f2c000>
> exp(tmp5)
<pointer: 0x600002f2c000>
> log(tmp5,2)
<pointer: 0x600002f2c000>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 467.0584
> Min(tmp5)
[1] 53.06863
> mean(tmp5)
[1] 72.90127
> Sum(tmp5)
[1] 14580.25
> Var(tmp5)
[1] 860.0851
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.89476 66.16648 69.79431 71.30081 69.70639 71.91394 72.36997 74.15161
[9] 71.53782 72.17661
> rowSums(tmp5)
[1] 1797.895 1323.330 1395.886 1426.016 1394.128 1438.279 1447.399 1483.032
[9] 1430.756 1443.532
> rowVars(tmp5)
[1] 7953.03478 43.81921 72.04197 81.49526 49.41584 65.23881
[7] 84.14739 52.69908 98.52823 127.03597
> rowSd(tmp5)
[1] 89.179789 6.619608 8.487754 9.027473 7.029640 8.077054 9.173189
[8] 7.259413 9.926139 11.271024
> rowMax(tmp5)
[1] 467.05842 77.04879 80.77823 89.28298 79.44679 87.81618 93.14296
[8] 84.77745 101.19437 89.59321
> rowMin(tmp5)
[1] 57.56814 57.02443 54.14181 55.66458 53.06863 54.10333 57.41398 58.77549
[9] 60.18935 54.07888
>
> colMeans(tmp5)
[1] 109.97986 71.52208 70.26195 71.40641 66.24230 68.66953 68.06567
[8] 69.51849 78.65039 71.17514 72.07320 72.79928 68.40959 74.55787
[15] 70.31510 71.93233 68.92124 73.49856 70.98233 69.04408
> colSums(tmp5)
[1] 1099.7986 715.2208 702.6195 714.0641 662.4230 686.6953 680.6567
[8] 695.1849 786.5039 711.7514 720.7320 727.9928 684.0959 745.5787
[15] 703.1510 719.3233 689.2124 734.9856 709.8233 690.4408
> colVars(tmp5)
[1] 15791.81409 68.07923 42.88815 56.38012 59.85438 57.84944
[7] 112.74914 191.80844 85.69469 52.03883 127.31228 53.07028
[13] 74.77391 72.00922 42.52310 63.72988 49.31290 51.48571
[19] 109.02251 93.89236
> colSd(tmp5)
[1] 125.665485 8.251014 6.548905 7.508669 7.736561 7.605882
[7] 10.618340 13.849492 9.257143 7.213795 11.283274 7.284935
[13] 8.647191 8.485825 6.520974 7.983100 7.022314 7.175354
[19] 10.441385 9.689807
> colMax(tmp5)
[1] 467.05842 81.72214 79.17652 85.23394 80.21260 78.87288 86.40319
[8] 101.19437 93.14296 81.34614 88.15926 80.67893 80.69434 86.28734
[15] 79.42847 80.18977 84.08860 82.06023 84.03251 89.28298
> colMin(tmp5)
[1] 56.59097 58.22489 59.16025 63.08613 59.61135 57.56814 54.44037 54.07888
[9] 61.31659 58.79995 54.14181 58.75205 53.06863 57.41398 58.77549 58.78127
[17] 63.10103 63.40214 55.66458 55.40097
>
>
> ### 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] 89.89476 66.16648 69.79431 71.30081 69.70639 71.91394 NA 74.15161
[9] 71.53782 72.17661
> rowSums(tmp5)
[1] 1797.895 1323.330 1395.886 1426.016 1394.128 1438.279 NA 1483.032
[9] 1430.756 1443.532
> rowVars(tmp5)
[1] 7953.03478 43.81921 72.04197 81.49526 49.41584 65.23881
[7] 85.24627 52.69908 98.52823 127.03597
> rowSd(tmp5)
[1] 89.179789 6.619608 8.487754 9.027473 7.029640 8.077054 9.232890
[8] 7.259413 9.926139 11.271024
> rowMax(tmp5)
[1] 467.05842 77.04879 80.77823 89.28298 79.44679 87.81618 NA
[8] 84.77745 101.19437 89.59321
> rowMin(tmp5)
[1] 57.56814 57.02443 54.14181 55.66458 53.06863 54.10333 NA 58.77549
[9] 60.18935 54.07888
>
> colMeans(tmp5)
[1] 109.97986 71.52208 70.26195 71.40641 66.24230 68.66953 68.06567
[8] 69.51849 78.65039 71.17514 72.07320 72.79928 68.40959 74.55787
[15] 70.31510 NA 68.92124 73.49856 70.98233 69.04408
> colSums(tmp5)
[1] 1099.7986 715.2208 702.6195 714.0641 662.4230 686.6953 680.6567
[8] 695.1849 786.5039 711.7514 720.7320 727.9928 684.0959 745.5787
[15] 703.1510 NA 689.2124 734.9856 709.8233 690.4408
> colVars(tmp5)
[1] 15791.81409 68.07923 42.88815 56.38012 59.85438 57.84944
[7] 112.74914 191.80844 85.69469 52.03883 127.31228 53.07028
[13] 74.77391 72.00922 42.52310 NA 49.31290 51.48571
[19] 109.02251 93.89236
> colSd(tmp5)
[1] 125.665485 8.251014 6.548905 7.508669 7.736561 7.605882
[7] 10.618340 13.849492 9.257143 7.213795 11.283274 7.284935
[13] 8.647191 8.485825 6.520974 NA 7.022314 7.175354
[19] 10.441385 9.689807
> colMax(tmp5)
[1] 467.05842 81.72214 79.17652 85.23394 80.21260 78.87288 86.40319
[8] 101.19437 93.14296 81.34614 88.15926 80.67893 80.69434 86.28734
[15] 79.42847 NA 84.08860 82.06023 84.03251 89.28298
> colMin(tmp5)
[1] 56.59097 58.22489 59.16025 63.08613 59.61135 57.56814 54.44037 54.07888
[9] 61.31659 58.79995 54.14181 58.75205 53.06863 57.41398 58.77549 NA
[17] 63.10103 63.40214 55.66458 55.40097
>
> Max(tmp5,na.rm=TRUE)
[1] 467.0584
> Min(tmp5,na.rm=TRUE)
[1] 53.06863
> mean(tmp5,na.rm=TRUE)
[1] 72.86464
> Sum(tmp5,na.rm=TRUE)
[1] 14500.06
> Var(tmp5,na.rm=TRUE)
[1] 864.1593
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.89476 66.16648 69.79431 71.30081 69.70639 71.91394 71.95840 74.15161
[9] 71.53782 72.17661
> rowSums(tmp5,na.rm=TRUE)
[1] 1797.895 1323.330 1395.886 1426.016 1394.128 1438.279 1367.210 1483.032
[9] 1430.756 1443.532
> rowVars(tmp5,na.rm=TRUE)
[1] 7953.03478 43.81921 72.04197 81.49526 49.41584 65.23881
[7] 85.24627 52.69908 98.52823 127.03597
> rowSd(tmp5,na.rm=TRUE)
[1] 89.179789 6.619608 8.487754 9.027473 7.029640 8.077054 9.232890
[8] 7.259413 9.926139 11.271024
> rowMax(tmp5,na.rm=TRUE)
[1] 467.05842 77.04879 80.77823 89.28298 79.44679 87.81618 93.14296
[8] 84.77745 101.19437 89.59321
> rowMin(tmp5,na.rm=TRUE)
[1] 57.56814 57.02443 54.14181 55.66458 53.06863 54.10333 57.41398 58.77549
[9] 60.18935 54.07888
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.97986 71.52208 70.26195 71.40641 66.24230 68.66953 68.06567
[8] 69.51849 78.65039 71.17514 72.07320 72.79928 68.40959 74.55787
[15] 70.31510 71.01484 68.92124 73.49856 70.98233 69.04408
> colSums(tmp5,na.rm=TRUE)
[1] 1099.7986 715.2208 702.6195 714.0641 662.4230 686.6953 680.6567
[8] 695.1849 786.5039 711.7514 720.7320 727.9928 684.0959 745.5787
[15] 703.1510 639.1335 689.2124 734.9856 709.8233 690.4408
> colVars(tmp5,na.rm=TRUE)
[1] 15791.81409 68.07923 42.88815 56.38012 59.85438 57.84944
[7] 112.74914 191.80844 85.69469 52.03883 127.31228 53.07028
[13] 74.77391 72.00922 42.52310 62.22594 49.31290 51.48571
[19] 109.02251 93.89236
> colSd(tmp5,na.rm=TRUE)
[1] 125.665485 8.251014 6.548905 7.508669 7.736561 7.605882
[7] 10.618340 13.849492 9.257143 7.213795 11.283274 7.284935
[13] 8.647191 8.485825 6.520974 7.888342 7.022314 7.175354
[19] 10.441385 9.689807
> colMax(tmp5,na.rm=TRUE)
[1] 467.05842 81.72214 79.17652 85.23394 80.21260 78.87288 86.40319
[8] 101.19437 93.14296 81.34614 88.15926 80.67893 80.69434 86.28734
[15] 79.42847 79.44679 84.08860 82.06023 84.03251 89.28298
> colMin(tmp5,na.rm=TRUE)
[1] 56.59097 58.22489 59.16025 63.08613 59.61135 57.56814 54.44037 54.07888
[9] 61.31659 58.79995 54.14181 58.75205 53.06863 57.41398 58.77549 58.78127
[17] 63.10103 63.40214 55.66458 55.40097
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.89476 66.16648 69.79431 71.30081 69.70639 71.91394 NaN 74.15161
[9] 71.53782 72.17661
> rowSums(tmp5,na.rm=TRUE)
[1] 1797.895 1323.330 1395.886 1426.016 1394.128 1438.279 0.000 1483.032
[9] 1430.756 1443.532
> rowVars(tmp5,na.rm=TRUE)
[1] 7953.03478 43.81921 72.04197 81.49526 49.41584 65.23881
[7] NA 52.69908 98.52823 127.03597
> rowSd(tmp5,na.rm=TRUE)
[1] 89.179789 6.619608 8.487754 9.027473 7.029640 8.077054 NA
[8] 7.259413 9.926139 11.271024
> rowMax(tmp5,na.rm=TRUE)
[1] 467.05842 77.04879 80.77823 89.28298 79.44679 87.81618 NA
[8] 84.77745 101.19437 89.59321
> rowMin(tmp5,na.rm=TRUE)
[1] 57.56814 57.02443 54.14181 55.66458 53.06863 54.10333 NA 58.77549
[9] 60.18935 54.07888
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.67545 70.38874 70.76195 70.26284 66.70934 69.67759 68.56168
[8] 68.34488 77.04011 70.67403 72.82914 71.92376 68.48468 76.46275
[15] 70.20254 NaN 69.15632 72.85301 70.63581 68.54663
> colSums(tmp5,na.rm=TRUE)
[1] 1032.0790 633.4987 636.8575 632.3655 600.3840 627.0983 617.0551
[8] 615.1039 693.3610 636.0663 655.4623 647.3139 616.3622 688.1647
[15] 631.8229 0.0000 622.4068 655.6771 635.7223 616.9197
> colVars(tmp5,na.rm=TRUE)
[1] 17517.74523 62.13897 45.43667 48.71523 64.88227 53.64842
[7] 124.07504 200.28917 67.23507 55.71872 136.79748 51.08062
[13] 84.05721 40.18912 47.69595 NA 54.85534 53.23314
[19] 121.29950 102.84503
> colSd(tmp5,na.rm=TRUE)
[1] 132.354619 7.882827 6.740673 6.979629 8.054953 7.324508
[7] 11.138898 14.152356 8.199699 7.464497 11.696045 7.147071
[13] 9.168272 6.339489 6.906225 NA 7.406439 7.296104
[19] 11.013605 10.141254
> colMax(tmp5,na.rm=TRUE)
[1] 467.05842 81.67893 79.17652 85.23394 80.21260 78.87288 86.40319
[8] 101.19437 89.59321 81.34614 88.15926 79.53841 80.69434 86.28734
[15] 79.42847 -Inf 84.08860 82.06023 84.03251 89.28298
> colMin(tmp5,na.rm=TRUE)
[1] 56.59097 58.22489 59.16025 63.08613 59.61135 57.56814 54.44037 54.07888
[9] 61.31659 58.79995 54.14181 58.75205 53.06863 64.30275 58.77549 Inf
[17] 63.10103 63.40214 55.66458 55.40097
>
>
>
>
> 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] 138.7820 223.6776 302.4201 122.8138 265.1761 262.2337 470.4329 190.3688
[9] 182.8756 164.0837
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 138.7820 223.6776 302.4201 122.8138 265.1761 262.2337 470.4329 190.3688
[9] 182.8756 164.0837
>
>
>
> 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 -2.842171e-14 1.421085e-14 1.421085e-14 5.684342e-14
[6] 1.421085e-13 5.684342e-14 7.105427e-14 -1.847411e-13 1.136868e-13
[11] -9.947598e-14 0.000000e+00 -2.842171e-14 2.842171e-14 7.105427e-14
[16] 5.115908e-13 -1.136868e-13 0.000000e+00 0.000000e+00 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
4 18
5 4
10 12
6 8
9 6
6 5
9 13
7 6
5 5
2 8
2 11
6 15
8 18
3 3
9 2
2 16
8 2
2 1
6 7
8 1
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] 3.000294
> Min(tmp)
[1] -2.509954
> mean(tmp)
[1] 0.01643013
> Sum(tmp)
[1] 1.643013
> Var(tmp)
[1] 0.9284526
>
> rowMeans(tmp)
[1] 0.01643013
> rowSums(tmp)
[1] 1.643013
> rowVars(tmp)
[1] 0.9284526
> rowSd(tmp)
[1] 0.9635625
> rowMax(tmp)
[1] 3.000294
> rowMin(tmp)
[1] -2.509954
>
> colMeans(tmp)
[1] -1.278727805 0.381574889 -1.055807478 0.459458116 -0.057979802
[6] 0.602458127 -1.192007418 -0.032860750 -0.627298594 1.079860560
[11] -1.691780230 0.134527672 0.000124484 1.611647090 1.244193422
[16] 0.710890287 -1.353727366 1.598308279 0.378377202 -0.785414091
[21] -0.715790244 1.535718155 1.464595387 1.874706051 0.353570328
[26] 0.404615642 0.472365134 0.375941730 -0.670159378 -0.932639325
[31] 0.507796637 -1.526511409 -1.007497204 -0.783364344 -0.469695128
[36] -0.414515081 0.665375224 -1.235049760 1.291724442 0.101624974
[41] -0.296129195 -0.241113043 -0.610398934 0.228086031 0.308536848
[46] -0.324526679 0.498380409 -0.169548594 -0.459281825 -0.370421022
[51] 0.223948952 -0.045246475 -0.304653136 0.497727978 -0.363362689
[56] 0.631417796 -1.174866095 -1.519281072 -0.482992799 -2.509954013
[61] 1.090783979 -1.187135597 1.061005211 -0.103468640 -1.271050198
[66] 1.797871668 -0.634820221 -1.689661462 -1.317365866 -1.438298732
[71] 0.450698960 0.101690384 -0.185431376 -0.837037339 0.731302184
[76] -0.366302289 0.433831513 -0.941197317 0.212311964 0.209600027
[81] 1.242302773 0.793283843 0.925812406 -0.466710467 1.350162083
[86] -0.318819840 0.861079380 -1.017971818 -0.182112916 0.301125754
[91] 1.313969273 0.176784458 0.078528493 0.290298086 -0.063919427
[96] 2.237928064 0.211536784 0.145326519 -0.288162321 3.000294479
> colSums(tmp)
[1] -1.278727805 0.381574889 -1.055807478 0.459458116 -0.057979802
[6] 0.602458127 -1.192007418 -0.032860750 -0.627298594 1.079860560
[11] -1.691780230 0.134527672 0.000124484 1.611647090 1.244193422
[16] 0.710890287 -1.353727366 1.598308279 0.378377202 -0.785414091
[21] -0.715790244 1.535718155 1.464595387 1.874706051 0.353570328
[26] 0.404615642 0.472365134 0.375941730 -0.670159378 -0.932639325
[31] 0.507796637 -1.526511409 -1.007497204 -0.783364344 -0.469695128
[36] -0.414515081 0.665375224 -1.235049760 1.291724442 0.101624974
[41] -0.296129195 -0.241113043 -0.610398934 0.228086031 0.308536848
[46] -0.324526679 0.498380409 -0.169548594 -0.459281825 -0.370421022
[51] 0.223948952 -0.045246475 -0.304653136 0.497727978 -0.363362689
[56] 0.631417796 -1.174866095 -1.519281072 -0.482992799 -2.509954013
[61] 1.090783979 -1.187135597 1.061005211 -0.103468640 -1.271050198
[66] 1.797871668 -0.634820221 -1.689661462 -1.317365866 -1.438298732
[71] 0.450698960 0.101690384 -0.185431376 -0.837037339 0.731302184
[76] -0.366302289 0.433831513 -0.941197317 0.212311964 0.209600027
[81] 1.242302773 0.793283843 0.925812406 -0.466710467 1.350162083
[86] -0.318819840 0.861079380 -1.017971818 -0.182112916 0.301125754
[91] 1.313969273 0.176784458 0.078528493 0.290298086 -0.063919427
[96] 2.237928064 0.211536784 0.145326519 -0.288162321 3.000294479
> 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] -1.278727805 0.381574889 -1.055807478 0.459458116 -0.057979802
[6] 0.602458127 -1.192007418 -0.032860750 -0.627298594 1.079860560
[11] -1.691780230 0.134527672 0.000124484 1.611647090 1.244193422
[16] 0.710890287 -1.353727366 1.598308279 0.378377202 -0.785414091
[21] -0.715790244 1.535718155 1.464595387 1.874706051 0.353570328
[26] 0.404615642 0.472365134 0.375941730 -0.670159378 -0.932639325
[31] 0.507796637 -1.526511409 -1.007497204 -0.783364344 -0.469695128
[36] -0.414515081 0.665375224 -1.235049760 1.291724442 0.101624974
[41] -0.296129195 -0.241113043 -0.610398934 0.228086031 0.308536848
[46] -0.324526679 0.498380409 -0.169548594 -0.459281825 -0.370421022
[51] 0.223948952 -0.045246475 -0.304653136 0.497727978 -0.363362689
[56] 0.631417796 -1.174866095 -1.519281072 -0.482992799 -2.509954013
[61] 1.090783979 -1.187135597 1.061005211 -0.103468640 -1.271050198
[66] 1.797871668 -0.634820221 -1.689661462 -1.317365866 -1.438298732
[71] 0.450698960 0.101690384 -0.185431376 -0.837037339 0.731302184
[76] -0.366302289 0.433831513 -0.941197317 0.212311964 0.209600027
[81] 1.242302773 0.793283843 0.925812406 -0.466710467 1.350162083
[86] -0.318819840 0.861079380 -1.017971818 -0.182112916 0.301125754
[91] 1.313969273 0.176784458 0.078528493 0.290298086 -0.063919427
[96] 2.237928064 0.211536784 0.145326519 -0.288162321 3.000294479
> colMin(tmp)
[1] -1.278727805 0.381574889 -1.055807478 0.459458116 -0.057979802
[6] 0.602458127 -1.192007418 -0.032860750 -0.627298594 1.079860560
[11] -1.691780230 0.134527672 0.000124484 1.611647090 1.244193422
[16] 0.710890287 -1.353727366 1.598308279 0.378377202 -0.785414091
[21] -0.715790244 1.535718155 1.464595387 1.874706051 0.353570328
[26] 0.404615642 0.472365134 0.375941730 -0.670159378 -0.932639325
[31] 0.507796637 -1.526511409 -1.007497204 -0.783364344 -0.469695128
[36] -0.414515081 0.665375224 -1.235049760 1.291724442 0.101624974
[41] -0.296129195 -0.241113043 -0.610398934 0.228086031 0.308536848
[46] -0.324526679 0.498380409 -0.169548594 -0.459281825 -0.370421022
[51] 0.223948952 -0.045246475 -0.304653136 0.497727978 -0.363362689
[56] 0.631417796 -1.174866095 -1.519281072 -0.482992799 -2.509954013
[61] 1.090783979 -1.187135597 1.061005211 -0.103468640 -1.271050198
[66] 1.797871668 -0.634820221 -1.689661462 -1.317365866 -1.438298732
[71] 0.450698960 0.101690384 -0.185431376 -0.837037339 0.731302184
[76] -0.366302289 0.433831513 -0.941197317 0.212311964 0.209600027
[81] 1.242302773 0.793283843 0.925812406 -0.466710467 1.350162083
[86] -0.318819840 0.861079380 -1.017971818 -0.182112916 0.301125754
[91] 1.313969273 0.176784458 0.078528493 0.290298086 -0.063919427
[96] 2.237928064 0.211536784 0.145326519 -0.288162321 3.000294479
> colMedians(tmp)
[1] -1.278727805 0.381574889 -1.055807478 0.459458116 -0.057979802
[6] 0.602458127 -1.192007418 -0.032860750 -0.627298594 1.079860560
[11] -1.691780230 0.134527672 0.000124484 1.611647090 1.244193422
[16] 0.710890287 -1.353727366 1.598308279 0.378377202 -0.785414091
[21] -0.715790244 1.535718155 1.464595387 1.874706051 0.353570328
[26] 0.404615642 0.472365134 0.375941730 -0.670159378 -0.932639325
[31] 0.507796637 -1.526511409 -1.007497204 -0.783364344 -0.469695128
[36] -0.414515081 0.665375224 -1.235049760 1.291724442 0.101624974
[41] -0.296129195 -0.241113043 -0.610398934 0.228086031 0.308536848
[46] -0.324526679 0.498380409 -0.169548594 -0.459281825 -0.370421022
[51] 0.223948952 -0.045246475 -0.304653136 0.497727978 -0.363362689
[56] 0.631417796 -1.174866095 -1.519281072 -0.482992799 -2.509954013
[61] 1.090783979 -1.187135597 1.061005211 -0.103468640 -1.271050198
[66] 1.797871668 -0.634820221 -1.689661462 -1.317365866 -1.438298732
[71] 0.450698960 0.101690384 -0.185431376 -0.837037339 0.731302184
[76] -0.366302289 0.433831513 -0.941197317 0.212311964 0.209600027
[81] 1.242302773 0.793283843 0.925812406 -0.466710467 1.350162083
[86] -0.318819840 0.861079380 -1.017971818 -0.182112916 0.301125754
[91] 1.313969273 0.176784458 0.078528493 0.290298086 -0.063919427
[96] 2.237928064 0.211536784 0.145326519 -0.288162321 3.000294479
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.278728 0.3815749 -1.055807 0.4594581 -0.0579798 0.6024581 -1.192007
[2,] -1.278728 0.3815749 -1.055807 0.4594581 -0.0579798 0.6024581 -1.192007
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.03286075 -0.6272986 1.079861 -1.69178 0.1345277 0.000124484 1.611647
[2,] -0.03286075 -0.6272986 1.079861 -1.69178 0.1345277 0.000124484 1.611647
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.244193 0.7108903 -1.353727 1.598308 0.3783772 -0.7854141 -0.7157902
[2,] 1.244193 0.7108903 -1.353727 1.598308 0.3783772 -0.7854141 -0.7157902
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.535718 1.464595 1.874706 0.3535703 0.4046156 0.4723651 0.3759417
[2,] 1.535718 1.464595 1.874706 0.3535703 0.4046156 0.4723651 0.3759417
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.6701594 -0.9326393 0.5077966 -1.526511 -1.007497 -0.7833643 -0.4696951
[2,] -0.6701594 -0.9326393 0.5077966 -1.526511 -1.007497 -0.7833643 -0.4696951
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.4145151 0.6653752 -1.23505 1.291724 0.101625 -0.2961292 -0.241113
[2,] -0.4145151 0.6653752 -1.23505 1.291724 0.101625 -0.2961292 -0.241113
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.6103989 0.228086 0.3085368 -0.3245267 0.4983804 -0.1695486 -0.4592818
[2,] -0.6103989 0.228086 0.3085368 -0.3245267 0.4983804 -0.1695486 -0.4592818
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.370421 0.223949 -0.04524648 -0.3046531 0.497728 -0.3633627 0.6314178
[2,] -0.370421 0.223949 -0.04524648 -0.3046531 0.497728 -0.3633627 0.6314178
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.174866 -1.519281 -0.4829928 -2.509954 1.090784 -1.187136 1.061005
[2,] -1.174866 -1.519281 -0.4829928 -2.509954 1.090784 -1.187136 1.061005
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.1034686 -1.27105 1.797872 -0.6348202 -1.689661 -1.317366 -1.438299
[2,] -0.1034686 -1.27105 1.797872 -0.6348202 -1.689661 -1.317366 -1.438299
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.450699 0.1016904 -0.1854314 -0.8370373 0.7313022 -0.3663023 0.4338315
[2,] 0.450699 0.1016904 -0.1854314 -0.8370373 0.7313022 -0.3663023 0.4338315
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.9411973 0.212312 0.2096 1.242303 0.7932838 0.9258124 -0.4667105
[2,] -0.9411973 0.212312 0.2096 1.242303 0.7932838 0.9258124 -0.4667105
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 1.350162 -0.3188198 0.8610794 -1.017972 -0.1821129 0.3011258 1.313969
[2,] 1.350162 -0.3188198 0.8610794 -1.017972 -0.1821129 0.3011258 1.313969
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.1767845 0.07852849 0.2902981 -0.06391943 2.237928 0.2115368 0.1453265
[2,] 0.1767845 0.07852849 0.2902981 -0.06391943 2.237928 0.2115368 0.1453265
[,99] [,100]
[1,] -0.2881623 3.000294
[2,] -0.2881623 3.000294
>
>
> Max(tmp2)
[1] 1.952026
> Min(tmp2)
[1] -1.445943
> mean(tmp2)
[1] 0.09480391
> Sum(tmp2)
[1] 9.480391
> Var(tmp2)
[1] 0.6629205
>
> rowMeans(tmp2)
[1] 0.426027682 -1.231518568 -0.512796087 -0.170148906 0.984045977
[6] 0.374277805 0.380240412 -0.296205469 0.418071301 1.231525439
[11] 1.503353960 0.230433602 -0.008187005 0.004387731 0.541318613
[16] -0.193193644 -0.654111218 0.643039703 -0.235392340 -0.772234775
[21] -0.041564249 -0.008516580 -0.258931123 -1.445943345 1.669690802
[26] 0.122723520 0.677151151 0.235292553 1.202602770 0.396148926
[31] -0.182174424 -0.906007673 0.851931965 1.281282199 -0.403673296
[36] 1.636735514 0.343412151 -0.390832121 0.226489246 -0.369938563
[41] 1.010157923 1.174967873 0.136104372 -0.307035020 -0.343077659
[46] 0.804720847 0.226749723 -1.049548307 0.982991561 -0.192555124
[51] 0.601394770 1.375653673 1.375450569 0.997900227 0.120720904
[56] -0.514343427 -1.025124888 0.679114001 -0.541273809 0.398613544
[61] 0.041708296 -0.398176036 -0.304015133 -0.339817277 -0.234362081
[66] -1.184535603 1.952025857 -0.537697355 0.113219317 -1.021645536
[71] -0.775056531 -0.490990979 -0.038235172 -0.074860681 -0.787553976
[76] -1.242764618 -0.987834972 -0.287695561 -0.614491080 -0.182730193
[81] 0.990446878 0.311547989 -1.024066757 -0.320553604 -0.083438722
[86] 0.962498694 1.488632775 0.500986169 1.527580527 -1.282988011
[91] -0.214882705 -1.300345950 -0.864429849 0.408901454 0.806925735
[96] 1.749550603 1.158084208 -1.280919889 0.574821156 -0.442845343
> rowSums(tmp2)
[1] 0.426027682 -1.231518568 -0.512796087 -0.170148906 0.984045977
[6] 0.374277805 0.380240412 -0.296205469 0.418071301 1.231525439
[11] 1.503353960 0.230433602 -0.008187005 0.004387731 0.541318613
[16] -0.193193644 -0.654111218 0.643039703 -0.235392340 -0.772234775
[21] -0.041564249 -0.008516580 -0.258931123 -1.445943345 1.669690802
[26] 0.122723520 0.677151151 0.235292553 1.202602770 0.396148926
[31] -0.182174424 -0.906007673 0.851931965 1.281282199 -0.403673296
[36] 1.636735514 0.343412151 -0.390832121 0.226489246 -0.369938563
[41] 1.010157923 1.174967873 0.136104372 -0.307035020 -0.343077659
[46] 0.804720847 0.226749723 -1.049548307 0.982991561 -0.192555124
[51] 0.601394770 1.375653673 1.375450569 0.997900227 0.120720904
[56] -0.514343427 -1.025124888 0.679114001 -0.541273809 0.398613544
[61] 0.041708296 -0.398176036 -0.304015133 -0.339817277 -0.234362081
[66] -1.184535603 1.952025857 -0.537697355 0.113219317 -1.021645536
[71] -0.775056531 -0.490990979 -0.038235172 -0.074860681 -0.787553976
[76] -1.242764618 -0.987834972 -0.287695561 -0.614491080 -0.182730193
[81] 0.990446878 0.311547989 -1.024066757 -0.320553604 -0.083438722
[86] 0.962498694 1.488632775 0.500986169 1.527580527 -1.282988011
[91] -0.214882705 -1.300345950 -0.864429849 0.408901454 0.806925735
[96] 1.749550603 1.158084208 -1.280919889 0.574821156 -0.442845343
> 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] 0.426027682 -1.231518568 -0.512796087 -0.170148906 0.984045977
[6] 0.374277805 0.380240412 -0.296205469 0.418071301 1.231525439
[11] 1.503353960 0.230433602 -0.008187005 0.004387731 0.541318613
[16] -0.193193644 -0.654111218 0.643039703 -0.235392340 -0.772234775
[21] -0.041564249 -0.008516580 -0.258931123 -1.445943345 1.669690802
[26] 0.122723520 0.677151151 0.235292553 1.202602770 0.396148926
[31] -0.182174424 -0.906007673 0.851931965 1.281282199 -0.403673296
[36] 1.636735514 0.343412151 -0.390832121 0.226489246 -0.369938563
[41] 1.010157923 1.174967873 0.136104372 -0.307035020 -0.343077659
[46] 0.804720847 0.226749723 -1.049548307 0.982991561 -0.192555124
[51] 0.601394770 1.375653673 1.375450569 0.997900227 0.120720904
[56] -0.514343427 -1.025124888 0.679114001 -0.541273809 0.398613544
[61] 0.041708296 -0.398176036 -0.304015133 -0.339817277 -0.234362081
[66] -1.184535603 1.952025857 -0.537697355 0.113219317 -1.021645536
[71] -0.775056531 -0.490990979 -0.038235172 -0.074860681 -0.787553976
[76] -1.242764618 -0.987834972 -0.287695561 -0.614491080 -0.182730193
[81] 0.990446878 0.311547989 -1.024066757 -0.320553604 -0.083438722
[86] 0.962498694 1.488632775 0.500986169 1.527580527 -1.282988011
[91] -0.214882705 -1.300345950 -0.864429849 0.408901454 0.806925735
[96] 1.749550603 1.158084208 -1.280919889 0.574821156 -0.442845343
> rowMin(tmp2)
[1] 0.426027682 -1.231518568 -0.512796087 -0.170148906 0.984045977
[6] 0.374277805 0.380240412 -0.296205469 0.418071301 1.231525439
[11] 1.503353960 0.230433602 -0.008187005 0.004387731 0.541318613
[16] -0.193193644 -0.654111218 0.643039703 -0.235392340 -0.772234775
[21] -0.041564249 -0.008516580 -0.258931123 -1.445943345 1.669690802
[26] 0.122723520 0.677151151 0.235292553 1.202602770 0.396148926
[31] -0.182174424 -0.906007673 0.851931965 1.281282199 -0.403673296
[36] 1.636735514 0.343412151 -0.390832121 0.226489246 -0.369938563
[41] 1.010157923 1.174967873 0.136104372 -0.307035020 -0.343077659
[46] 0.804720847 0.226749723 -1.049548307 0.982991561 -0.192555124
[51] 0.601394770 1.375653673 1.375450569 0.997900227 0.120720904
[56] -0.514343427 -1.025124888 0.679114001 -0.541273809 0.398613544
[61] 0.041708296 -0.398176036 -0.304015133 -0.339817277 -0.234362081
[66] -1.184535603 1.952025857 -0.537697355 0.113219317 -1.021645536
[71] -0.775056531 -0.490990979 -0.038235172 -0.074860681 -0.787553976
[76] -1.242764618 -0.987834972 -0.287695561 -0.614491080 -0.182730193
[81] 0.990446878 0.311547989 -1.024066757 -0.320553604 -0.083438722
[86] 0.962498694 1.488632775 0.500986169 1.527580527 -1.282988011
[91] -0.214882705 -1.300345950 -0.864429849 0.408901454 0.806925735
[96] 1.749550603 1.158084208 -1.280919889 0.574821156 -0.442845343
>
> colMeans(tmp2)
[1] 0.09480391
> colSums(tmp2)
[1] 9.480391
> colVars(tmp2)
[1] 0.6629205
> colSd(tmp2)
[1] 0.8141993
> colMax(tmp2)
[1] 1.952026
> colMin(tmp2)
[1] -1.445943
> colMedians(tmp2)
[1] -0.008351792
> colRanges(tmp2)
[,1]
[1,] -1.445943
[2,] 1.952026
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.2247504 -0.4684122 -1.9353726 -1.2060200 -0.1422859 -0.5468189
[7] -0.3172755 5.3397350 -2.9114884 0.8075646
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.5230388
[2,] -0.2133369
[3,] 0.1612683
[4,] 0.5167376
[5,] 0.6288305
>
> rowApply(tmp,sum)
[1] 1.3544468 1.7413314 2.4288362 3.0800225 1.2377851 -2.4451495
[7] -3.3016639 0.9368359 -1.4873278 -3.7007402
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 6 7 3 4 10 8 2 7 7
[2,] 2 8 6 7 1 3 6 8 9 5
[3,] 8 7 5 8 3 1 4 7 3 9
[4,] 3 10 1 2 8 2 3 3 10 2
[5,] 4 2 10 1 7 6 7 10 4 1
[6,] 5 1 9 5 9 8 1 5 6 8
[7,] 7 5 2 9 10 7 5 1 2 3
[8,] 10 9 8 4 5 9 2 9 8 10
[9,] 1 3 3 10 6 4 9 6 1 4
[10,] 9 4 4 6 2 5 10 4 5 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.4609471 2.0900853 1.8783408 2.5440492 1.9511097 1.5840235
[7] -3.3353707 -0.8708678 0.9286090 0.5602109 2.4140561 -0.3381583
[13] 0.7715878 -0.2529029 0.5589055 1.9892569 1.6110021 -0.7741776
[19] 0.2324523 0.2053542
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.51228851
[2,] 0.07558748
[3,] 0.36577068
[4,] 0.64819831
[5,] 0.88367912
>
> rowApply(tmp,sum)
[1] 2.074774 7.058670 3.328000 3.980509 -1.233440
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 14 16 8 16 9
[2,] 17 8 7 4 20
[3,] 12 13 1 18 17
[4,] 11 18 14 19 6
[5,] 15 9 17 17 12
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.36577068 0.699554146 0.2804704 0.1437136 0.41370726 0.6862859
[2,] 0.88367912 0.004567128 0.7130459 1.1766865 0.06976444 1.5192625
[3,] 0.07558748 0.021343368 -1.2839306 0.3032131 0.72424868 0.8918657
[4,] 0.64819831 -0.174829888 0.9362913 1.6682856 0.67700610 0.1544662
[5,] -0.51228851 1.539450518 1.2324639 -0.7478497 0.06638319 -1.6678567
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.3245199 -0.5683751 -0.2489397 -0.06674129 1.50659650 -0.3181488
[2,] -0.5424083 -0.5883977 0.8235664 -0.64141067 0.35187822 -0.3308454
[3,] 0.1040611 0.4046760 -0.5988698 0.82357659 0.27681970 0.2583343
[4,] -1.5098190 0.5742950 0.2870562 0.13963015 -0.08352054 -1.4126658
[5,] -1.0626845 -0.6930659 0.6657960 0.30515613 0.36228224 1.4651673
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 1.00660451 -1.2628574 -0.35378090 0.35808143 -0.3898882 -1.53808622
[2,] 0.82304436 -1.2716987 -0.27754789 2.97883739 0.4473561 -0.41887678
[3,] -0.08900403 0.6572412 -0.49732913 -0.78355088 0.2796000 1.52600694
[4,] 0.43601439 0.2904492 1.67381470 -0.03674292 0.5760793 0.02940973
[5,] -1.40507141 1.3339627 0.01374869 -0.52736815 0.6978549 -0.37263132
[,19] [,20]
[1,] 1.671879086 0.01344769
[2,] 0.417297186 0.92087039
[3,] 0.005280274 0.22883014
[4,] -0.860226658 -0.03268195
[5,] -1.001777597 -0.92511205
>
>
> 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 : 649 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 1.497785 -0.260268 0.209035 -2.063093 0.296552 0.3542374 -1.346915
col8 col9 col10 col11 col12 col13 col14
row1 -1.036554 1.227905 0.2588599 -1.962154 0.8638872 -0.7123287 0.6444892
col15 col16 col17 col18 col19 col20
row1 1.638329 -0.5065461 -0.002100234 -1.121641 -0.7566546 0.538398
> tmp[,"col10"]
col10
row1 0.2588599
row2 0.8967749
row3 -2.2855421
row4 0.6124503
row5 -0.6964733
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.497785 -0.2602680 0.2090350 -2.0630930 0.296552 0.3542374 -1.346915
row5 -1.842081 -0.8148449 -0.6306638 -0.3386689 0.654677 0.8190467 1.436330
col8 col9 col10 col11 col12 col13 col14
row1 -1.0365540 1.227905 0.2588599 -1.9621540 0.8638872 -0.7123287 0.6444892
row5 -0.8408481 1.384689 -0.6964733 0.1306111 -0.6015233 -2.0906030 0.5023484
col15 col16 col17 col18 col19 col20
row1 1.6383293 -0.5065461 -0.002100234 -1.12164079 -0.7566546 0.5383980
row5 0.5368721 1.3086510 -0.953773617 0.08150637 0.2082528 -0.1823897
> tmp[,c("col6","col20")]
col6 col20
row1 0.3542374 0.5383980
row2 0.8720587 -1.9988170
row3 0.4984077 -0.9582173
row4 -0.5638768 -0.9014156
row5 0.8190467 -0.1823897
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.3542374 0.5383980
row5 0.8190467 -0.1823897
>
>
>
>
> 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 48.87765 49.59027 49.45159 47.87427 49.69803 104.9857 51.5394 49.73709
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.36997 49.58359 50.92625 49.61375 49.9786 49.38109 50.6172 49.05537
col17 col18 col19 col20
row1 49.3508 50.34895 48.10701 105.7108
> tmp[,"col10"]
col10
row1 49.58359
row2 30.89589
row3 31.53848
row4 32.05078
row5 50.08552
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 48.87765 49.59027 49.45159 47.87427 49.69803 104.9857 51.53940 49.73709
row5 49.17351 50.22228 49.06867 49.04621 49.90595 104.7112 49.99624 50.12358
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.36997 49.58359 50.92625 49.61375 49.97860 49.38109 50.61720 49.05537
row5 51.22329 50.08552 49.89281 48.83346 50.33499 49.60332 50.34966 50.98003
col17 col18 col19 col20
row1 49.35080 50.34895 48.10701 105.7108
row5 50.03351 49.92063 49.78807 103.9913
> tmp[,c("col6","col20")]
col6 col20
row1 104.98573 105.71084
row2 76.29924 74.11366
row3 73.70343 73.31974
row4 76.71710 75.31926
row5 104.71115 103.99133
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.9857 105.7108
row5 104.7112 103.9913
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.9857 105.7108
row5 104.7112 103.9913
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -1.2438244
[2,] 1.4094919
[3,] -1.1633689
[4,] 0.6547423
[5,] -1.8481138
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.39365477 -2.2053340
[2,] 0.20876627 0.5991568
[3,] 0.02467748 1.3027774
[4,] -0.98243817 -0.7641678
[5,] 1.28384354 -1.2287159
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.1878245 0.7503665
[2,] -0.2299283 1.4929685
[3,] 1.1695041 -0.3048740
[4,] -0.8985394 -0.8573164
[5,] 0.2316163 -1.4329274
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.1878245
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.1878245
[2,] -0.2299283
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 -0.5144754 0.8453392 1.19512986 -0.4410073 -0.9982536 0.441365 -1.3285714
row1 1.0778555 -0.2203428 0.08075863 0.1780158 0.3572649 3.068789 0.3710858
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.3855733 0.1570134 -2.1332811 -0.1702422 0.1081601 -0.2591279 -0.4707967
row1 1.6793192 -0.4636507 0.1265014 0.6578205 0.8607659 -1.2501522 -0.6813456
[,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.7794626 -1.637848 -1.206980 1.5295373 -0.9337346 -1.355982
row1 -1.2961354 1.760763 -1.013143 -0.4470922 -0.2089651 1.581388
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.2991503 0.6835481 -0.6204178 2.071624 -0.1333576 -0.564111 -1.758972
[,8] [,9] [,10]
row2 2.45559 0.04220502 0.1513031
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.187911 -2.160738 2.0559 0.001478202 -1.454824 -0.5107032 -0.8650509
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.7557072 -0.3128687 1.400879 -0.6992655 1.128652 0.5203186 -0.1705088
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.655648 -2.04687 -0.4535548 -0.6459032 -1.04636 1.009758
>
>
> 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: 0x600002f54000>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a532916b28"
[2] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a569122907"
[3] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a52743c075"
[4] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a551105576"
[5] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a575adf8e"
[6] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a55f0ae767"
[7] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a544de4bf0"
[8] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a55e4b9ce2"
[9] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a53628e9cb"
[10] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a5380d2a34"
[11] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a5684dd8ab"
[12] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a54ecbf80c"
[13] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a5310a043e"
[14] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a589c9b99"
[15] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM55a561ab5e39"
>
>
> ### 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: 0x600002f282a0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x600002f282a0>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x600002f282a0>
> rowMedians(tmp)
[1] 0.129872278 -0.409458792 0.087453224 -0.313044756 0.022070248
[6] -0.152829866 0.033062517 -0.293750621 -0.165866358 -0.883146217
[11] 0.335235840 0.009759447 -0.469624378 0.349833891 0.057207010
[16] -0.473716041 0.258572452 -0.314607243 -0.486333109 -0.092189713
[21] 0.434932778 0.342887870 -0.722192503 0.301535604 -0.057517779
[26] -0.898425495 -0.357957349 -0.627672444 -0.401346224 0.205125513
[31] 0.634066876 0.437401984 -0.134814194 0.579971614 -0.424393022
[36] 0.204383641 -0.157112665 0.101981774 0.126595369 -0.093530530
[41] -0.113350881 0.076536224 0.185000950 -0.135733787 0.198200459
[46] -0.461042223 -0.155795803 0.497107475 -0.752682788 -0.223862248
[51] 0.273916096 0.453643864 -0.455710390 0.603160096 0.271837817
[56] -0.096204651 0.064216971 -0.114000422 -0.184734367 -0.448162595
[61] 0.278803112 0.624128571 0.089537212 0.015556501 -0.116222016
[66] 0.133653463 -0.352344891 -0.391214554 -0.001039363 0.326653123
[71] -0.545480783 -0.954851729 -0.393126455 0.133692874 -0.304892902
[76] 0.359567197 -0.266063680 -0.368401794 -0.017765507 -0.274762096
[81] 0.399221817 0.084138255 0.244805933 0.493634685 -0.248708482
[86] 0.552502922 -0.057990965 0.316241843 -0.211558744 -0.045762272
[91] -0.820951120 -0.175596487 0.019848031 -0.024516333 -0.130817319
[96] -0.274964365 0.246180736 0.043038769 -0.268858534 -0.345164593
[101] 0.057350222 0.136966803 -0.457100518 0.351617094 0.461659192
[106] 0.384189700 -0.106321549 0.436250930 -0.400553607 -0.236308329
[111] 0.132138883 -0.094145158 0.459274085 -0.269267339 -0.083266948
[116] 0.265499838 0.553100022 0.302725415 0.150022435 0.120396473
[121] 0.115741697 0.176630286 -0.114343909 0.210563660 0.590992442
[126] 0.238797874 -0.406004810 -0.286668652 -0.264177775 0.399088911
[131] -0.443960582 0.109112507 -0.691307310 0.323862253 0.476782251
[136] 0.407444743 0.445380059 -0.534893374 0.257463807 0.059129559
[141] -0.134239953 0.687167355 -0.155710480 -0.037302166 -0.037262533
[146] 0.371185150 0.542743647 0.404800235 0.396285495 0.496216337
[151] -0.502192768 0.442287587 -0.095198545 -0.385566603 0.567474602
[156] 0.048206554 0.300747599 0.118528018 0.483269852 0.211130673
[161] 0.015770054 0.334245383 0.300739254 -0.180217800 0.040181432
[166] -0.381623807 -0.283735493 0.134482889 0.536939281 -0.124807117
[171] -0.078601817 0.104496825 -0.075595525 -0.420037673 0.259202201
[176] -0.675158698 0.380369307 -0.443438687 0.166798479 0.084407583
[181] -0.258492372 -0.453908214 -0.196131998 -0.366193010 -0.027552314
[186] 0.339803324 0.450797085 0.057802929 0.079724122 1.005288607
[191] -0.211361322 -0.568921956 -0.187743777 0.130394347 -0.188293160
[196] 0.268796980 0.323712057 -0.030177039 0.283363122 0.313893508
[201] 0.492774555 -0.514839587 -0.215032920 -0.395289396 0.181597952
[206] 0.220143111 0.241878658 0.217924698 -0.248269861 -0.083293215
[211] 0.102786344 -0.301364461 0.284385336 0.095428596 -0.319056169
[216] 0.507021378 0.233120128 0.061156934 -0.015974212 0.259990341
[221] 0.091185248 -0.773085724 0.232189222 0.380419812 0.259659165
[226] -0.304396933 0.268257417 -0.091740876 -0.427533526 0.079650552
>
> proc.time()
user system elapsed
0.732 3.781 5.114
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: 0x60000154c000>
> .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: 0x60000154c000>
> .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: 0x60000154c000>
> .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: 0x60000154c000>
> 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: 0x6000015682a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000015682a0>
> .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: 0x6000015682a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000015682a0>
> .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: 0x6000015682a0>
> 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: 0x600001568420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600001568420>
> .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: 0x600001568420>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600001568420>
> .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: 0x600001568420>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600001568420>
> .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: 0x600001568420>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600001568420>
> .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: 0x600001568420>
> 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: 0x60000155c000>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x60000155c000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60000155c000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60000155c000>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile5a0818b50f9f" "BufferedMatrixFile5a08498c47aa"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile5a0818b50f9f" "BufferedMatrixFile5a08498c47aa"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000015441e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000015441e0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000015441e0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000015441e0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6000015441e0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6000015441e0>
> .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: 0x60000154c3c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60000154c3c0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x60000154c3c0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x60000154c3c0>
> 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: 0x60000154c5a0>
> .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: 0x60000154c5a0>
> rm(P)
>
> proc.time()
user system elapsed
0.136 0.059 0.191
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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Platform: aarch64-apple-darwin20
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
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> 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
0.118 0.036 0.181