Ben Bolstad
| Snapshot Date: 2026-03-26 13:40 -0400 (Thu, 26 Mar 2026) |
| 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-27 11:33 -0400 (Fri, 27 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4880 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4577 |
| 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 258/2372 | 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 | ERROR | |||||||||
| See other builds for BufferedMatrix in R Universe. | ||||||||||||||
|
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: 2026-03-26 18:32:04 -0400 (Thu, 26 Mar 2026) |
| EndedAt: 2026-03-26 18:32:24 -0400 (Thu, 26 Mar 2026) |
| EllapsedTime: 20.2 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) (2026-03-20 r89666)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-26 22:32:04 UTC
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -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=gnu23 -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]
1580 | if (!(Matrix->readonly) & setting){
| ^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
1580 | if (!(Matrix->readonly) & setting){
| ^
| ( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
1580 | if (!(Matrix->readonly) & setting){
| ^
| ( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
2 warnings generated.
clang -arch arm64 -std=gnu23 -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=gnu23 -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=gnu23 -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/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) (2026-03-20 r89666) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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
0.147 0.058 0.206
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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 484118 25.9 1067182 57 NA 632022 33.8
Vcells 896941 6.9 8388608 64 196608 2112082 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] "Thu Mar 26 18:32:14 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Thu Mar 26 18:32:14 2026"
>
>
> 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: 0x73c688000>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Thu Mar 26 18:32:16 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Thu Mar 26 18:32:16 2026"
>
> ColMode(tmp2)
<pointer: 0x73c688000>
>
>
>
> ### 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,] 101.2806049 0.07778239 -0.02188613 0.30483546
[2,] 0.7097335 -0.41450763 0.59674154 0.04347912
[3,] -0.7164600 1.39866245 -0.59776231 0.70225486
[4,] -1.7343594 -0.64425334 1.01062261 -0.53476676
> 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,] 101.2806049 0.07778239 0.02188613 0.30483546
[2,] 0.7097335 0.41450763 0.59674154 0.04347912
[3,] 0.7164600 1.39866245 0.59776231 0.70225486
[4,] 1.7343594 0.64425334 1.01062261 0.53476676
> 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,] 10.0638266 0.2788950 0.1479396 0.5521191
[2,] 0.8424568 0.6438227 0.7724905 0.2085165
[3,] 0.8464396 1.1826506 0.7731509 0.8380065
[4,] 1.3169508 0.8026539 1.0052973 0.7312775
>
> 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,] 226.91887 27.86673 26.50128 30.82603
[2,] 34.13430 31.85273 33.32165 27.12864
[3,] 34.18086 38.22517 33.32927 34.08232
[4,] 39.90387 33.67079 36.06360 32.84754
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x73c6880c0>
> exp(tmp5)
<pointer: 0x73c6880c0>
> log(tmp5,2)
<pointer: 0x73c6880c0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 472.3019
> Min(tmp5)
[1] 53.40831
> mean(tmp5)
[1] 73.35721
> Sum(tmp5)
[1] 14671.44
> Var(tmp5)
[1] 874.7635
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.15612 67.16384 73.17479 71.12445 70.17676 72.11762 68.46089 73.90862
[9] 73.07804 75.21099
> rowSums(tmp5)
[1] 1783.122 1343.277 1463.496 1422.489 1403.535 1442.352 1369.218 1478.172
[9] 1461.561 1504.220
> rowVars(tmp5)
[1] 8210.71320 41.84494 58.50234 63.23257 64.22811 43.96586
[7] 57.33718 104.70816 80.65091 86.89152
> rowSd(tmp5)
[1] 90.612986 6.468766 7.648682 7.951891 8.014244 6.630675 7.572132
[8] 10.232701 8.980585 9.321562
> rowMax(tmp5)
[1] 472.30190 77.30393 85.33355 83.05467 81.76007 85.79099 81.41463
[8] 92.74917 95.60583 90.32253
> rowMin(tmp5)
[1] 55.15895 56.46472 57.41185 53.41290 54.14685 63.86262 53.40831 54.01368
[9] 53.85847 55.37148
>
> colMeans(tmp5)
[1] 112.06301 67.76967 69.26615 66.33402 72.79915 72.27509 67.36278
[8] 71.41448 66.22708 75.60342 68.33603 73.88530 75.68695 72.19632
[15] 70.86777 75.87649 73.59365 70.78245 69.87908 74.92531
> colSums(tmp5)
[1] 1120.6301 677.6967 692.6615 663.3402 727.9915 722.7509 673.6278
[8] 714.1448 662.2708 756.0342 683.3603 738.8530 756.8695 721.9632
[15] 708.6777 758.7649 735.9365 707.8245 698.7908 749.2531
> colVars(tmp5)
[1] 16073.68792 53.84263 153.15555 30.09911 75.87020 108.99958
[7] 70.56043 78.15966 84.34269 62.12932 70.57833 35.03471
[13] 64.15765 55.79055 61.72167 60.45076 61.79404 70.24069
[19] 80.17252 37.26357
> colSd(tmp5)
[1] 126.782049 7.337754 12.375603 5.486265 8.710350 10.440287
[7] 8.400026 8.840795 9.183828 7.882216 8.401091 5.919012
[13] 8.009847 7.469307 7.856314 7.775008 7.860918 8.380972
[19] 8.953911 6.104389
> colMax(tmp5)
[1] 472.30190 79.56068 95.60583 75.17225 85.33355 85.79099 80.30402
[8] 85.12625 80.48394 90.32253 78.53745 81.76007 87.84639 84.06712
[15] 81.55017 92.74917 82.91806 85.48575 81.41463 83.34537
> colMin(tmp5)
[1] 61.42307 56.34987 53.40831 56.46472 59.93417 58.85346 54.01368 58.20086
[9] 53.85847 59.94983 54.14685 64.61415 64.09979 60.70457 53.41290 62.78856
[17] 60.53099 59.83903 55.37148 63.56076
>
>
> ### 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] 89.15612 NA 73.17479 71.12445 70.17676 72.11762 68.46089 73.90862
[9] 73.07804 75.21099
> rowSums(tmp5)
[1] 1783.122 NA 1463.496 1422.489 1403.535 1442.352 1369.218 1478.172
[9] 1461.561 1504.220
> rowVars(tmp5)
[1] 8210.71320 44.12574 58.50234 63.23257 64.22811 43.96586
[7] 57.33718 104.70816 80.65091 86.89152
> rowSd(tmp5)
[1] 90.612986 6.642721 7.648682 7.951891 8.014244 6.630675 7.572132
[8] 10.232701 8.980585 9.321562
> rowMax(tmp5)
[1] 472.30190 NA 85.33355 83.05467 81.76007 85.79099 81.41463
[8] 92.74917 95.60583 90.32253
> rowMin(tmp5)
[1] 55.15895 NA 57.41185 53.41290 54.14685 63.86262 53.40831 54.01368
[9] 53.85847 55.37148
>
> colMeans(tmp5)
[1] 112.06301 NA 69.26615 66.33402 72.79915 72.27509 67.36278
[8] 71.41448 66.22708 75.60342 68.33603 73.88530 75.68695 72.19632
[15] 70.86777 75.87649 73.59365 70.78245 69.87908 74.92531
> colSums(tmp5)
[1] 1120.6301 NA 692.6615 663.3402 727.9915 722.7509 673.6278
[8] 714.1448 662.2708 756.0342 683.3603 738.8530 756.8695 721.9632
[15] 708.6777 758.7649 735.9365 707.8245 698.7908 749.2531
> colVars(tmp5)
[1] 16073.68792 NA 153.15555 30.09911 75.87020 108.99958
[7] 70.56043 78.15966 84.34269 62.12932 70.57833 35.03471
[13] 64.15765 55.79055 61.72167 60.45076 61.79404 70.24069
[19] 80.17252 37.26357
> colSd(tmp5)
[1] 126.782049 NA 12.375603 5.486265 8.710350 10.440287
[7] 8.400026 8.840795 9.183828 7.882216 8.401091 5.919012
[13] 8.009847 7.469307 7.856314 7.775008 7.860918 8.380972
[19] 8.953911 6.104389
> colMax(tmp5)
[1] 472.30190 NA 95.60583 75.17225 85.33355 85.79099 80.30402
[8] 85.12625 80.48394 90.32253 78.53745 81.76007 87.84639 84.06712
[15] 81.55017 92.74917 82.91806 85.48575 81.41463 83.34537
> colMin(tmp5)
[1] 61.42307 NA 53.40831 56.46472 59.93417 58.85346 54.01368 58.20086
[9] 53.85847 59.94983 54.14685 64.61415 64.09979 60.70457 53.41290 62.78856
[17] 60.53099 59.83903 55.37148 63.56076
>
> Max(tmp5,na.rm=TRUE)
[1] 472.3019
> Min(tmp5,na.rm=TRUE)
[1] 53.40831
> mean(tmp5,na.rm=TRUE)
[1] 73.39269
> Sum(tmp5,na.rm=TRUE)
[1] 14605.14
> Var(tmp5,na.rm=TRUE)
[1] 878.9285
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.15612 67.20944 73.17479 71.12445 70.17676 72.11762 68.46089 73.90862
[9] 73.07804 75.21099
> rowSums(tmp5,na.rm=TRUE)
[1] 1783.122 1276.979 1463.496 1422.489 1403.535 1442.352 1369.218 1478.172
[9] 1461.561 1504.220
> rowVars(tmp5,na.rm=TRUE)
[1] 8210.71320 44.12574 58.50234 63.23257 64.22811 43.96586
[7] 57.33718 104.70816 80.65091 86.89152
> rowSd(tmp5,na.rm=TRUE)
[1] 90.612986 6.642721 7.648682 7.951891 8.014244 6.630675 7.572132
[8] 10.232701 8.980585 9.321562
> rowMax(tmp5,na.rm=TRUE)
[1] 472.30190 77.30393 85.33355 83.05467 81.76007 85.79099 81.41463
[8] 92.74917 95.60583 90.32253
> rowMin(tmp5,na.rm=TRUE)
[1] 55.15895 56.46472 57.41185 53.41290 54.14685 63.86262 53.40831 54.01368
[9] 53.85847 55.37148
>
> colMeans(tmp5,na.rm=TRUE)
[1] 112.06301 67.93326 69.26615 66.33402 72.79915 72.27509 67.36278
[8] 71.41448 66.22708 75.60342 68.33603 73.88530 75.68695 72.19632
[15] 70.86777 75.87649 73.59365 70.78245 69.87908 74.92531
> colSums(tmp5,na.rm=TRUE)
[1] 1120.6301 611.3994 692.6615 663.3402 727.9915 722.7509 673.6278
[8] 714.1448 662.2708 756.0342 683.3603 738.8530 756.8695 721.9632
[15] 708.6777 758.7649 735.9365 707.8245 698.7908 749.2531
> colVars(tmp5,na.rm=TRUE)
[1] 16073.68792 60.27186 153.15555 30.09911 75.87020 108.99958
[7] 70.56043 78.15966 84.34269 62.12932 70.57833 35.03471
[13] 64.15765 55.79055 61.72167 60.45076 61.79404 70.24069
[19] 80.17252 37.26357
> colSd(tmp5,na.rm=TRUE)
[1] 126.782049 7.763495 12.375603 5.486265 8.710350 10.440287
[7] 8.400026 8.840795 9.183828 7.882216 8.401091 5.919012
[13] 8.009847 7.469307 7.856314 7.775008 7.860918 8.380972
[19] 8.953911 6.104389
> colMax(tmp5,na.rm=TRUE)
[1] 472.30190 79.56068 95.60583 75.17225 85.33355 85.79099 80.30402
[8] 85.12625 80.48394 90.32253 78.53745 81.76007 87.84639 84.06712
[15] 81.55017 92.74917 82.91806 85.48575 81.41463 83.34537
> colMin(tmp5,na.rm=TRUE)
[1] 61.42307 56.34987 53.40831 56.46472 59.93417 58.85346 54.01368 58.20086
[9] 53.85847 59.94983 54.14685 64.61415 64.09979 60.70457 53.41290 62.78856
[17] 60.53099 59.83903 55.37148 63.56076
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.15612 NaN 73.17479 71.12445 70.17676 72.11762 68.46089 73.90862
[9] 73.07804 75.21099
> rowSums(tmp5,na.rm=TRUE)
[1] 1783.122 0.000 1463.496 1422.489 1403.535 1442.352 1369.218 1478.172
[9] 1461.561 1504.220
> rowVars(tmp5,na.rm=TRUE)
[1] 8210.71320 NA 58.50234 63.23257 64.22811 43.96586
[7] 57.33718 104.70816 80.65091 86.89152
> rowSd(tmp5,na.rm=TRUE)
[1] 90.612986 NA 7.648682 7.951891 8.014244 6.630675 7.572132
[8] 10.232701 8.980585 9.321562
> rowMax(tmp5,na.rm=TRUE)
[1] 472.30190 NA 85.33355 83.05467 81.76007 85.79099 81.41463
[8] 92.74917 95.60583 90.32253
> rowMin(tmp5,na.rm=TRUE)
[1] 55.15895 NA 57.41185 53.41290 54.14685 63.86262 53.40831 54.01368
[9] 53.85847 55.37148
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.62045 NaN 69.25632 67.43061 74.12687 72.51988 68.17491
[8] 71.86025 65.70750 75.41448 67.72845 73.75742 76.97441 73.20680
[15] 71.36750 75.83963 73.47331 71.99838 71.32878 76.18804
> colSums(tmp5,na.rm=TRUE)
[1] 1049.5840 0.0000 623.3069 606.8755 667.1418 652.6789 613.5742
[8] 646.7423 591.3675 678.7303 609.5561 663.8167 692.7697 658.8612
[15] 642.3075 682.5567 661.2598 647.9854 641.9591 685.6923
> colVars(tmp5,na.rm=TRUE)
[1] 17849.23376 NA 172.29891 20.33328 65.52211 121.95041
[7] 71.96047 85.69414 91.84850 69.49386 75.24765 39.23007
[13] 53.52980 51.27735 66.62735 67.99182 69.35537 62.38768
[19] 66.55076 23.98359
> colSd(tmp5,na.rm=TRUE)
[1] 133.601025 NA 13.126268 4.509243 8.094573 11.043116
[7] 8.482952 9.257113 9.583762 8.336298 8.674540 6.263392
[13] 7.316407 7.160820 8.162558 8.245715 8.327987 7.898587
[19] 8.157865 4.897304
> colMax(tmp5,na.rm=TRUE)
[1] 472.30190 -Inf 95.60583 75.17225 85.33355 85.79099 80.30402
[8] 85.12625 80.48394 90.32253 78.53745 81.76007 87.84639 84.06712
[15] 81.55017 92.74917 82.91806 85.48575 81.41463 83.34537
> colMin(tmp5,na.rm=TRUE)
[1] 61.42307 Inf 53.40831 61.50698 59.93417 58.85346 54.01368 58.20086
[9] 53.85847 59.94983 54.14685 64.61415 66.40189 60.70457 53.41290 62.78856
[17] 60.53099 61.17377 55.37148 69.00184
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 222.3025 170.8665 213.4771 182.9969 245.1824 300.3475 169.8427 145.0702
[9] 347.2708 190.9888
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 222.3025 170.8665 213.4771 182.9969 245.1824 300.3475 169.8427 145.0702
[9] 347.2708 190.9888
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 1.421085e-14 0.000000e+00 -1.136868e-13 -8.526513e-14 -2.842171e-13
[6] -1.421085e-13 1.136868e-13 0.000000e+00 1.136868e-13 -8.526513e-14
[11] 5.684342e-14 1.705303e-13 5.684342e-14 5.684342e-14 -1.136868e-13
[16] 0.000000e+00 0.000000e+00 0.000000e+00 -5.684342e-14 -5.684342e-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 1
7 5
5 17
8 10
1 19
5 6
10 13
8 16
1 8
3 3
3 3
9 20
8 4
7 4
8 1
6 2
9 1
5 11
3 12
9 9
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.065425
> Min(tmp)
[1] -2.713186
> mean(tmp)
[1] -0.1353397
> Sum(tmp)
[1] -13.53397
> Var(tmp)
[1] 1.076754
>
> rowMeans(tmp)
[1] -0.1353397
> rowSums(tmp)
[1] -13.53397
> rowVars(tmp)
[1] 1.076754
> rowSd(tmp)
[1] 1.037667
> rowMax(tmp)
[1] 2.065425
> rowMin(tmp)
[1] -2.713186
>
> colMeans(tmp)
[1] -1.92708460 0.43652198 -0.09198876 -0.17471333 -2.13129551 -0.33460850
[7] -0.44671550 -0.45839121 -0.75622553 0.61747086 -0.47153794 -0.34015701
[13] 0.65594608 -0.24156415 -1.37873563 -0.58306999 -0.15497172 -0.25770762
[19] 1.89242544 1.87216937 -0.12892754 -0.05653233 -1.51544730 -0.87669820
[25] 0.18392924 -2.71318566 -0.51194916 1.35606051 -0.17570633 -0.04326803
[31] 0.71948000 -1.70589189 -0.27805124 -1.26644960 -0.47933764 0.50833715
[37] -0.13725479 0.62435134 -0.29995610 -0.91204420 0.98156917 1.98625135
[43] -0.61005389 -0.92743507 -1.53487723 -1.58171370 -0.04061732 -0.78739949
[49] 0.27681208 -0.17702909 2.05903296 0.79848417 0.43950367 0.04998294
[55] -1.04520063 -1.52578667 -2.21127729 -0.67649606 -0.17670059 -1.00410293
[61] -0.31513547 -0.01880843 0.49442046 0.77483339 -0.16476019 -1.12477502
[67] -0.94008523 1.05354156 -0.15667173 -0.05009219 1.07100848 -0.91042803
[73] -0.31839400 2.06542482 0.18602188 -0.52186378 1.59721817 0.49843069
[79] 1.18966959 -0.86981912 -1.10041195 1.18618064 -0.19244696 0.16524666
[85] -0.93189193 -0.68916346 0.58800950 -0.03094793 -0.35866968 -2.50488406
[91] -1.89940093 -0.62614809 1.86897330 1.25257858 1.06769723 0.69980751
[97] 1.53984548 -0.07540385 1.36221856 -0.70506173
> colSums(tmp)
[1] -1.92708460 0.43652198 -0.09198876 -0.17471333 -2.13129551 -0.33460850
[7] -0.44671550 -0.45839121 -0.75622553 0.61747086 -0.47153794 -0.34015701
[13] 0.65594608 -0.24156415 -1.37873563 -0.58306999 -0.15497172 -0.25770762
[19] 1.89242544 1.87216937 -0.12892754 -0.05653233 -1.51544730 -0.87669820
[25] 0.18392924 -2.71318566 -0.51194916 1.35606051 -0.17570633 -0.04326803
[31] 0.71948000 -1.70589189 -0.27805124 -1.26644960 -0.47933764 0.50833715
[37] -0.13725479 0.62435134 -0.29995610 -0.91204420 0.98156917 1.98625135
[43] -0.61005389 -0.92743507 -1.53487723 -1.58171370 -0.04061732 -0.78739949
[49] 0.27681208 -0.17702909 2.05903296 0.79848417 0.43950367 0.04998294
[55] -1.04520063 -1.52578667 -2.21127729 -0.67649606 -0.17670059 -1.00410293
[61] -0.31513547 -0.01880843 0.49442046 0.77483339 -0.16476019 -1.12477502
[67] -0.94008523 1.05354156 -0.15667173 -0.05009219 1.07100848 -0.91042803
[73] -0.31839400 2.06542482 0.18602188 -0.52186378 1.59721817 0.49843069
[79] 1.18966959 -0.86981912 -1.10041195 1.18618064 -0.19244696 0.16524666
[85] -0.93189193 -0.68916346 0.58800950 -0.03094793 -0.35866968 -2.50488406
[91] -1.89940093 -0.62614809 1.86897330 1.25257858 1.06769723 0.69980751
[97] 1.53984548 -0.07540385 1.36221856 -0.70506173
> 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] -1.92708460 0.43652198 -0.09198876 -0.17471333 -2.13129551 -0.33460850
[7] -0.44671550 -0.45839121 -0.75622553 0.61747086 -0.47153794 -0.34015701
[13] 0.65594608 -0.24156415 -1.37873563 -0.58306999 -0.15497172 -0.25770762
[19] 1.89242544 1.87216937 -0.12892754 -0.05653233 -1.51544730 -0.87669820
[25] 0.18392924 -2.71318566 -0.51194916 1.35606051 -0.17570633 -0.04326803
[31] 0.71948000 -1.70589189 -0.27805124 -1.26644960 -0.47933764 0.50833715
[37] -0.13725479 0.62435134 -0.29995610 -0.91204420 0.98156917 1.98625135
[43] -0.61005389 -0.92743507 -1.53487723 -1.58171370 -0.04061732 -0.78739949
[49] 0.27681208 -0.17702909 2.05903296 0.79848417 0.43950367 0.04998294
[55] -1.04520063 -1.52578667 -2.21127729 -0.67649606 -0.17670059 -1.00410293
[61] -0.31513547 -0.01880843 0.49442046 0.77483339 -0.16476019 -1.12477502
[67] -0.94008523 1.05354156 -0.15667173 -0.05009219 1.07100848 -0.91042803
[73] -0.31839400 2.06542482 0.18602188 -0.52186378 1.59721817 0.49843069
[79] 1.18966959 -0.86981912 -1.10041195 1.18618064 -0.19244696 0.16524666
[85] -0.93189193 -0.68916346 0.58800950 -0.03094793 -0.35866968 -2.50488406
[91] -1.89940093 -0.62614809 1.86897330 1.25257858 1.06769723 0.69980751
[97] 1.53984548 -0.07540385 1.36221856 -0.70506173
> colMin(tmp)
[1] -1.92708460 0.43652198 -0.09198876 -0.17471333 -2.13129551 -0.33460850
[7] -0.44671550 -0.45839121 -0.75622553 0.61747086 -0.47153794 -0.34015701
[13] 0.65594608 -0.24156415 -1.37873563 -0.58306999 -0.15497172 -0.25770762
[19] 1.89242544 1.87216937 -0.12892754 -0.05653233 -1.51544730 -0.87669820
[25] 0.18392924 -2.71318566 -0.51194916 1.35606051 -0.17570633 -0.04326803
[31] 0.71948000 -1.70589189 -0.27805124 -1.26644960 -0.47933764 0.50833715
[37] -0.13725479 0.62435134 -0.29995610 -0.91204420 0.98156917 1.98625135
[43] -0.61005389 -0.92743507 -1.53487723 -1.58171370 -0.04061732 -0.78739949
[49] 0.27681208 -0.17702909 2.05903296 0.79848417 0.43950367 0.04998294
[55] -1.04520063 -1.52578667 -2.21127729 -0.67649606 -0.17670059 -1.00410293
[61] -0.31513547 -0.01880843 0.49442046 0.77483339 -0.16476019 -1.12477502
[67] -0.94008523 1.05354156 -0.15667173 -0.05009219 1.07100848 -0.91042803
[73] -0.31839400 2.06542482 0.18602188 -0.52186378 1.59721817 0.49843069
[79] 1.18966959 -0.86981912 -1.10041195 1.18618064 -0.19244696 0.16524666
[85] -0.93189193 -0.68916346 0.58800950 -0.03094793 -0.35866968 -2.50488406
[91] -1.89940093 -0.62614809 1.86897330 1.25257858 1.06769723 0.69980751
[97] 1.53984548 -0.07540385 1.36221856 -0.70506173
> colMedians(tmp)
[1] -1.92708460 0.43652198 -0.09198876 -0.17471333 -2.13129551 -0.33460850
[7] -0.44671550 -0.45839121 -0.75622553 0.61747086 -0.47153794 -0.34015701
[13] 0.65594608 -0.24156415 -1.37873563 -0.58306999 -0.15497172 -0.25770762
[19] 1.89242544 1.87216937 -0.12892754 -0.05653233 -1.51544730 -0.87669820
[25] 0.18392924 -2.71318566 -0.51194916 1.35606051 -0.17570633 -0.04326803
[31] 0.71948000 -1.70589189 -0.27805124 -1.26644960 -0.47933764 0.50833715
[37] -0.13725479 0.62435134 -0.29995610 -0.91204420 0.98156917 1.98625135
[43] -0.61005389 -0.92743507 -1.53487723 -1.58171370 -0.04061732 -0.78739949
[49] 0.27681208 -0.17702909 2.05903296 0.79848417 0.43950367 0.04998294
[55] -1.04520063 -1.52578667 -2.21127729 -0.67649606 -0.17670059 -1.00410293
[61] -0.31513547 -0.01880843 0.49442046 0.77483339 -0.16476019 -1.12477502
[67] -0.94008523 1.05354156 -0.15667173 -0.05009219 1.07100848 -0.91042803
[73] -0.31839400 2.06542482 0.18602188 -0.52186378 1.59721817 0.49843069
[79] 1.18966959 -0.86981912 -1.10041195 1.18618064 -0.19244696 0.16524666
[85] -0.93189193 -0.68916346 0.58800950 -0.03094793 -0.35866968 -2.50488406
[91] -1.89940093 -0.62614809 1.86897330 1.25257858 1.06769723 0.69980751
[97] 1.53984548 -0.07540385 1.36221856 -0.70506173
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.927085 0.436522 -0.09198876 -0.1747133 -2.131296 -0.3346085 -0.4467155
[2,] -1.927085 0.436522 -0.09198876 -0.1747133 -2.131296 -0.3346085 -0.4467155
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.4583912 -0.7562255 0.6174709 -0.4715379 -0.340157 0.6559461 -0.2415641
[2,] -0.4583912 -0.7562255 0.6174709 -0.4715379 -0.340157 0.6559461 -0.2415641
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.378736 -0.58307 -0.1549717 -0.2577076 1.892425 1.872169 -0.1289275
[2,] -1.378736 -0.58307 -0.1549717 -0.2577076 1.892425 1.872169 -0.1289275
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.05653233 -1.515447 -0.8766982 0.1839292 -2.713186 -0.5119492 1.356061
[2,] -0.05653233 -1.515447 -0.8766982 0.1839292 -2.713186 -0.5119492 1.356061
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.1757063 -0.04326803 0.71948 -1.705892 -0.2780512 -1.26645 -0.4793376
[2,] -0.1757063 -0.04326803 0.71948 -1.705892 -0.2780512 -1.26645 -0.4793376
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.5083371 -0.1372548 0.6243513 -0.2999561 -0.9120442 0.9815692 1.986251
[2,] 0.5083371 -0.1372548 0.6243513 -0.2999561 -0.9120442 0.9815692 1.986251
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.6100539 -0.9274351 -1.534877 -1.581714 -0.04061732 -0.7873995 0.2768121
[2,] -0.6100539 -0.9274351 -1.534877 -1.581714 -0.04061732 -0.7873995 0.2768121
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.1770291 2.059033 0.7984842 0.4395037 0.04998294 -1.045201 -1.525787
[2,] -0.1770291 2.059033 0.7984842 0.4395037 0.04998294 -1.045201 -1.525787
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -2.211277 -0.6764961 -0.1767006 -1.004103 -0.3151355 -0.01880843 0.4944205
[2,] -2.211277 -0.6764961 -0.1767006 -1.004103 -0.3151355 -0.01880843 0.4944205
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.7748334 -0.1647602 -1.124775 -0.9400852 1.053542 -0.1566717 -0.05009219
[2,] 0.7748334 -0.1647602 -1.124775 -0.9400852 1.053542 -0.1566717 -0.05009219
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 1.071008 -0.910428 -0.318394 2.065425 0.1860219 -0.5218638 1.597218
[2,] 1.071008 -0.910428 -0.318394 2.065425 0.1860219 -0.5218638 1.597218
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.4984307 1.18967 -0.8698191 -1.100412 1.186181 -0.192447 0.1652467
[2,] 0.4984307 1.18967 -0.8698191 -1.100412 1.186181 -0.192447 0.1652467
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.9318919 -0.6891635 0.5880095 -0.03094793 -0.3586697 -2.504884 -1.899401
[2,] -0.9318919 -0.6891635 0.5880095 -0.03094793 -0.3586697 -2.504884 -1.899401
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.6261481 1.868973 1.252579 1.067697 0.6998075 1.539845 -0.07540385
[2,] -0.6261481 1.868973 1.252579 1.067697 0.6998075 1.539845 -0.07540385
[,99] [,100]
[1,] 1.362219 -0.7050617
[2,] 1.362219 -0.7050617
>
>
> Max(tmp2)
[1] 2.28625
> Min(tmp2)
[1] -2.88352
> mean(tmp2)
[1] -0.04923391
> Sum(tmp2)
[1] -4.923391
> Var(tmp2)
[1] 1.017156
>
> rowMeans(tmp2)
[1] 0.109221410 0.004892961 -0.623960382 2.105975839 -0.838926766
[6] 0.580249407 0.667853109 0.204328446 -0.765033272 -1.306647990
[11] -0.572255047 0.817816332 -0.489044283 -1.029151073 -0.138801394
[16] -2.883520326 -0.243925611 -0.199111491 -0.753445109 1.821653693
[21] -0.446912540 -2.271810107 0.177156577 -0.296781461 0.366460822
[26] -0.288880926 0.485159426 -0.108791979 0.835791202 0.445435140
[31] 0.018272825 2.286250260 -1.223742264 -0.388838695 -2.577008509
[36] -1.193183881 -0.603552355 1.424009891 1.378529971 -0.420838056
[41] -0.192346301 0.601078229 -0.344906028 -0.777762240 1.752276985
[46] 0.582941424 -0.827928856 -1.397807211 -0.050173680 1.425825213
[51] 0.651432081 0.258669958 1.507790202 -0.441585419 -0.298365586
[56] 0.513689151 0.998275829 -0.892262831 0.138315686 0.622198739
[61] 0.380790958 -1.823495373 0.435469830 -1.289517326 0.720548869
[66] 0.107687302 1.299232465 -0.664332949 0.296658515 -0.910994363
[71] 1.152479850 0.308176869 1.431127899 -1.155767307 0.651157623
[76] -2.094357697 -0.192475003 -1.317171740 -1.546816298 -0.391458894
[81] -0.354856755 0.641739374 1.117034838 -0.833534610 0.047498903
[86] 0.598075828 -0.162845749 -0.025144746 0.701423004 1.794868181
[91] -0.408708957 1.189658890 0.563390049 -1.031520669 -0.618401429
[96] -0.073321307 -0.423840033 -1.301431044 1.180133286 -0.814800011
> rowSums(tmp2)
[1] 0.109221410 0.004892961 -0.623960382 2.105975839 -0.838926766
[6] 0.580249407 0.667853109 0.204328446 -0.765033272 -1.306647990
[11] -0.572255047 0.817816332 -0.489044283 -1.029151073 -0.138801394
[16] -2.883520326 -0.243925611 -0.199111491 -0.753445109 1.821653693
[21] -0.446912540 -2.271810107 0.177156577 -0.296781461 0.366460822
[26] -0.288880926 0.485159426 -0.108791979 0.835791202 0.445435140
[31] 0.018272825 2.286250260 -1.223742264 -0.388838695 -2.577008509
[36] -1.193183881 -0.603552355 1.424009891 1.378529971 -0.420838056
[41] -0.192346301 0.601078229 -0.344906028 -0.777762240 1.752276985
[46] 0.582941424 -0.827928856 -1.397807211 -0.050173680 1.425825213
[51] 0.651432081 0.258669958 1.507790202 -0.441585419 -0.298365586
[56] 0.513689151 0.998275829 -0.892262831 0.138315686 0.622198739
[61] 0.380790958 -1.823495373 0.435469830 -1.289517326 0.720548869
[66] 0.107687302 1.299232465 -0.664332949 0.296658515 -0.910994363
[71] 1.152479850 0.308176869 1.431127899 -1.155767307 0.651157623
[76] -2.094357697 -0.192475003 -1.317171740 -1.546816298 -0.391458894
[81] -0.354856755 0.641739374 1.117034838 -0.833534610 0.047498903
[86] 0.598075828 -0.162845749 -0.025144746 0.701423004 1.794868181
[91] -0.408708957 1.189658890 0.563390049 -1.031520669 -0.618401429
[96] -0.073321307 -0.423840033 -1.301431044 1.180133286 -0.814800011
> 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] 0.109221410 0.004892961 -0.623960382 2.105975839 -0.838926766
[6] 0.580249407 0.667853109 0.204328446 -0.765033272 -1.306647990
[11] -0.572255047 0.817816332 -0.489044283 -1.029151073 -0.138801394
[16] -2.883520326 -0.243925611 -0.199111491 -0.753445109 1.821653693
[21] -0.446912540 -2.271810107 0.177156577 -0.296781461 0.366460822
[26] -0.288880926 0.485159426 -0.108791979 0.835791202 0.445435140
[31] 0.018272825 2.286250260 -1.223742264 -0.388838695 -2.577008509
[36] -1.193183881 -0.603552355 1.424009891 1.378529971 -0.420838056
[41] -0.192346301 0.601078229 -0.344906028 -0.777762240 1.752276985
[46] 0.582941424 -0.827928856 -1.397807211 -0.050173680 1.425825213
[51] 0.651432081 0.258669958 1.507790202 -0.441585419 -0.298365586
[56] 0.513689151 0.998275829 -0.892262831 0.138315686 0.622198739
[61] 0.380790958 -1.823495373 0.435469830 -1.289517326 0.720548869
[66] 0.107687302 1.299232465 -0.664332949 0.296658515 -0.910994363
[71] 1.152479850 0.308176869 1.431127899 -1.155767307 0.651157623
[76] -2.094357697 -0.192475003 -1.317171740 -1.546816298 -0.391458894
[81] -0.354856755 0.641739374 1.117034838 -0.833534610 0.047498903
[86] 0.598075828 -0.162845749 -0.025144746 0.701423004 1.794868181
[91] -0.408708957 1.189658890 0.563390049 -1.031520669 -0.618401429
[96] -0.073321307 -0.423840033 -1.301431044 1.180133286 -0.814800011
> rowMin(tmp2)
[1] 0.109221410 0.004892961 -0.623960382 2.105975839 -0.838926766
[6] 0.580249407 0.667853109 0.204328446 -0.765033272 -1.306647990
[11] -0.572255047 0.817816332 -0.489044283 -1.029151073 -0.138801394
[16] -2.883520326 -0.243925611 -0.199111491 -0.753445109 1.821653693
[21] -0.446912540 -2.271810107 0.177156577 -0.296781461 0.366460822
[26] -0.288880926 0.485159426 -0.108791979 0.835791202 0.445435140
[31] 0.018272825 2.286250260 -1.223742264 -0.388838695 -2.577008509
[36] -1.193183881 -0.603552355 1.424009891 1.378529971 -0.420838056
[41] -0.192346301 0.601078229 -0.344906028 -0.777762240 1.752276985
[46] 0.582941424 -0.827928856 -1.397807211 -0.050173680 1.425825213
[51] 0.651432081 0.258669958 1.507790202 -0.441585419 -0.298365586
[56] 0.513689151 0.998275829 -0.892262831 0.138315686 0.622198739
[61] 0.380790958 -1.823495373 0.435469830 -1.289517326 0.720548869
[66] 0.107687302 1.299232465 -0.664332949 0.296658515 -0.910994363
[71] 1.152479850 0.308176869 1.431127899 -1.155767307 0.651157623
[76] -2.094357697 -0.192475003 -1.317171740 -1.546816298 -0.391458894
[81] -0.354856755 0.641739374 1.117034838 -0.833534610 0.047498903
[86] 0.598075828 -0.162845749 -0.025144746 0.701423004 1.794868181
[91] -0.408708957 1.189658890 0.563390049 -1.031520669 -0.618401429
[96] -0.073321307 -0.423840033 -1.301431044 1.180133286 -0.814800011
>
> colMeans(tmp2)
[1] -0.04923391
> colSums(tmp2)
[1] -4.923391
> colVars(tmp2)
[1] 1.017156
> colSd(tmp2)
[1] 1.008542
> colMax(tmp2)
[1] 2.28625
> colMin(tmp2)
[1] -2.88352
> colMedians(tmp2)
[1] -0.09105664
> colRanges(tmp2)
[,1]
[1,] -2.88352
[2,] 2.28625
>
> 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] -1.03215359 6.68521570 0.88261167 3.22483046 1.05550781 -1.02018049
[7] -4.24079986 3.52814356 -0.06313567 -0.13143505
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.5459159
[2,] -0.3754859
[3,] -0.2074063
[4,] 0.3141381
[5,] 1.4015302
>
> rowApply(tmp,sum)
[1] 1.4896780 0.3025167 -1.6596803 2.1654397 1.5311280 4.6735776
[7] 2.6556990 -0.6111282 -6.1629474 4.5043212
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 8 5 4 5 7 6 9 3 3
[2,] 5 7 9 9 10 2 7 2 7 10
[3,] 4 5 1 5 9 3 2 5 6 9
[4,] 6 6 7 7 8 9 5 7 4 7
[5,] 9 10 10 6 3 5 1 8 5 1
[6,] 10 4 2 1 7 8 8 6 1 5
[7,] 3 2 8 3 1 4 9 1 2 8
[8,] 7 9 3 8 2 10 4 3 9 4
[9,] 8 3 6 2 4 1 10 10 10 2
[10,] 2 1 4 10 6 6 3 4 8 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.007277685 2.579170969 -2.125958644 0.143561311 1.660084181
[6] 2.920160809 2.585460305 -1.174375640 -3.134922784 -3.982926982
[11] -0.331285376 -0.402607934 0.565841617 -3.460029956 -1.650455775
[16] 5.430917665 1.330585239 -0.568706361 -5.562261899 -0.987438427
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.6270586
[2,] -0.8465345
[3,] -0.4507401
[4,] 0.3889601
[5,] 2.5280955
>
> rowApply(tmp,sum)
[1] 0.5863789 -5.6206815 -3.2669336 3.3280843 -1.1993134
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 20 5 8 11 3
[2,] 5 20 16 8 17
[3,] 1 2 5 20 11
[4,] 12 9 14 16 6
[5,] 14 1 6 18 20
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 2.5280955 -0.8163519 -1.5254237 0.1247566 0.4457697 0.2321241
[2,] -0.8465345 1.6572595 -1.6188948 -0.4041233 -1.7234833 0.7151396
[3,] -0.4507401 0.6185805 -0.8266621 0.2234651 -0.7036514 0.3279822
[4,] 0.3889601 -0.2632231 1.9209055 0.9569033 1.2546956 1.0294131
[5,] -1.6270586 1.3829060 -0.0758836 -0.7574404 2.3867536 0.6155018
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.1053529 -0.7587709 -0.5075216 -1.2211214 -0.5372134 0.12404736
[2,] -0.5399381 -1.5861438 0.5851872 -0.2504911 -0.1253138 -0.05695599
[3,] 2.0890293 -0.1191696 -1.1803191 -1.4008743 -0.4767654 0.80662432
[4,] 0.4188448 -1.0190892 0.3544054 -1.0080933 0.9493975 -0.41962840
[5,] -0.4878286 2.3087977 -2.3866746 -0.1023469 -0.1413902 -0.85669523
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.18999354 -0.3434511 1.1576129 1.4940751 0.61518348 0.9365329
[2,] -0.59183248 -0.1541330 -1.5408267 0.8264059 0.83328984 -0.4173218
[3,] -0.43213715 -0.2374754 -1.3446515 0.8051225 -0.26858416 -1.1416669
[4,] 1.76465593 -1.7605873 0.6067275 0.5108307 0.22383827 -0.3768725
[5,] 0.01514885 -0.9643832 -0.5293180 1.7944834 -0.07314219 0.4306219
[,19] [,20]
[1,] -1.2743716 -1.00295239
[2,] -0.1839890 -0.19798198
[3,] -0.1771016 0.62206125
[4,] -1.7655593 -0.43844033
[5,] -2.1612404 0.02987502
>
>
> 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 0.7575222 -0.547884 -0.8980927 -1.141028 1.438828 -0.6315742 -1.952092
col8 col9 col10 col11 col12 col13 col14
row1 -1.180905 -0.8696037 1.839613 1.680805 0.57574 -0.4286232 -0.1013919
col15 col16 col17 col18 col19 col20
row1 -0.5715493 -0.1125195 1.5427 2.241126 1.730735 0.05186934
> tmp[,"col10"]
col10
row1 1.8396126
row2 2.2135871
row3 0.9352943
row4 -0.9622329
row5 0.7349883
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.75752219 -0.547884 -0.8980927 -1.141028 1.4388282 -0.6315742 -1.9520922
row5 0.03864379 -1.567577 2.4797326 1.155027 -0.8602758 -1.2968733 -0.5668958
col8 col9 col10 col11 col12 col13 col14
row1 -1.1809052 -0.8696037 1.8396126 1.680805 0.5757400 -0.4286232 -0.1013919
row5 0.1479011 -1.6555753 0.7349883 -1.919721 0.3025985 -0.8733976 -0.2033715
col15 col16 col17 col18 col19 col20
row1 -0.5715493 -0.1125195 1.542700 2.241126 1.7307348 0.05186934
row5 -0.5542347 0.6795747 1.333254 1.112398 -0.6296391 -2.17906476
> tmp[,c("col6","col20")]
col6 col20
row1 -0.6315742 0.05186934
row2 -0.4737414 0.30645355
row3 -0.5136889 1.50835897
row4 -0.2917197 0.78964341
row5 -1.2968733 -2.17906476
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.6315742 0.05186934
row5 -1.2968733 -2.17906476
>
>
>
>
> 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 48.96476 50.9727 49.44412 49.88429 51.13399 104.9686 49.58452 49.73236
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.23713 50.68831 51.23959 48.15856 50.53548 50.87642 50.09722 50.51711
col17 col18 col19 col20
row1 48.94383 49.87917 47.86027 105.9387
> tmp[,"col10"]
col10
row1 50.68831
row2 31.32019
row3 28.89002
row4 29.50804
row5 49.55817
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 48.96476 50.9727 49.44412 49.88429 51.13399 104.9686 49.58452 49.73236
row5 49.34681 48.6247 49.61621 50.31571 50.60773 105.7917 50.31019 49.08229
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.23713 50.68831 51.23959 48.15856 50.53548 50.87642 50.09722 50.51711
row5 50.20662 49.55817 49.91138 52.06579 49.57410 50.69314 50.70905 48.61371
col17 col18 col19 col20
row1 48.94383 49.87917 47.86027 105.9387
row5 50.23857 47.95408 50.63809 105.5244
> tmp[,c("col6","col20")]
col6 col20
row1 104.96856 105.93870
row2 75.12095 76.76533
row3 74.53364 74.69893
row4 74.80535 74.50090
row5 105.79168 105.52439
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.9686 105.9387
row5 105.7917 105.5244
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.9686 105.9387
row5 105.7917 105.5244
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.7988414
[2,] -0.4266212
[3,] 0.3072276
[4,] 0.3803972
[5,] 0.6463769
> tmp[,c("col17","col7")]
col17 col7
[1,] -1.2405442 -0.6816797
[2,] 0.8204293 -0.1320680
[3,] -2.2179427 0.7357367
[4,] 0.7074126 -0.5466424
[5,] -0.7787243 2.1375781
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 1.8751444 -0.8606867
[2,] -0.4242150 2.2070748
[3,] -0.2427456 -0.4821830
[4,] -0.2328280 1.0220914
[5,] -1.9465602 0.8203809
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 1.875144
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 1.875144
[2,] -0.424215
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 1.291718 0.4771221 -0.3334167 0.2424392 -0.2467677 -1.7975581 0.6912939
row1 2.152252 2.3748123 0.8355913 0.3883997 -0.9678673 0.2274081 -1.0878038
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 1.156503 0.770312 0.1881188 -0.6959527 -1.0259428 0.8492165 -0.4433727
row1 -2.220986 -1.740959 1.2662813 0.9744726 0.1152931 1.7614653 0.9131258
[,15] [,16] [,17] [,18] [,19] [,20]
row3 1.269244 -0.6105179 -0.01695262 -0.1872482 1.1139038 0.5251493
row1 1.277910 0.9990055 -0.06305953 -0.6833585 -0.5988196 -0.3012867
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.79421 1.355018 0.3170163 0.980694 -0.2672952 0.912612 0.4666049
[,8] [,9] [,10]
row2 -0.8662282 -1.147698 -0.2378837
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.521852 -1.315939 -1.004205 -0.1130856 0.03862755 -0.582997 0.01133259
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.5560505 -0.5072315 -1.290167 0.6438806 -0.6790241 2.279285 0.06685183
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.4053619 -1.036911 -0.5892394 0.6738821 -0.5977364 1.57628
>
>
> 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: 0x73c6886c0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83623a2c7bf0"
[2] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83623e7ce766"
[3] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83627a3bf996"
[4] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM8362777f258b"
[5] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83623c7a05f7"
[6] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83626f1dba25"
[7] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83628a80c21"
[8] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM836250b44ef7"
[9] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83626dac6385"
[10] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM836250b9e903"
[11] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83625d70ed5c"
[12] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM836220ef62f1"
[13] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM83624448cd1b"
[14] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM8362791caa3"
[15] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM8362748e9736"
>
>
> ### 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: 0x73c689320>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x73c689320>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x73c689320>
> rowMedians(tmp)
[1] 0.314519638 -0.578944702 0.103544523 -0.052395441 0.342727463
[6] -0.346171380 -0.455023045 0.311116153 -0.509458399 0.148914499
[11] -0.276461226 0.083704020 0.616614591 0.212831276 -0.317238818
[16] -0.192745252 -0.193435342 0.131606138 -0.175670007 -0.433488214
[21] -0.612870590 0.433169338 -0.253859372 -0.187257949 -0.100588212
[26] -0.933787333 -0.181345553 0.322369047 -0.085599093 -0.052868062
[31] -0.180194974 0.181524676 -0.353809457 -0.376734468 -0.027536469
[36] -0.321182151 0.046704196 0.288719305 0.314583252 -0.194109912
[41] 0.210174995 -0.038382605 0.187262436 -0.171042772 -0.382518422
[46] -0.225793155 -0.112573792 -0.296085556 0.168449883 -0.262164121
[51] 0.008851575 -0.395294557 -0.054165864 -0.246589867 -0.126093535
[56] 0.387560602 -0.487369834 -0.124236128 0.227533745 0.249913316
[61] -0.497206285 0.182510166 -0.048832535 -0.233977793 -0.434813058
[66] 0.461234997 -0.111438923 0.913728063 -0.378775563 0.191142655
[71] -0.183400480 -0.341913636 -0.180154541 -0.206388084 -0.390508855
[76] 0.205662712 0.010228981 0.089426393 -0.479004245 -0.264755304
[81] -0.088854949 0.058707952 -0.116097527 -0.294290240 0.268185199
[86] 0.063625052 0.622288223 0.251711828 -0.786947764 0.172522055
[91] -0.297099075 0.237707420 -0.137325954 0.550643882 -0.254227444
[96] 0.459144996 0.001622727 -0.071111678 -0.337853887 0.002162932
[101] 0.065898256 -0.435025180 0.105013020 -0.362031324 0.353307204
[106] -0.227583665 -0.017506561 0.405142630 -0.034747203 -0.236297626
[111] -0.231700206 -0.380032578 -0.083767739 0.490732221 0.100685928
[116] 0.272604212 -0.182329715 -0.090488106 0.077394052 -0.196800501
[121] -0.649688814 -0.265378726 0.296635771 0.078336239 0.202930264
[126] -0.498966803 -0.112915589 -0.026497664 0.111345519 0.283524212
[131] 0.021654450 0.004920125 -0.551689593 0.179992903 -0.301310493
[136] -0.247122734 0.665067814 0.146912951 -0.073327498 -0.229855744
[141] 0.042049907 -0.194354314 -0.197171888 -0.345695364 0.011828427
[146] -0.224635089 0.571865743 -0.251859679 0.312422506 -0.391308348
[151] 0.343594385 -0.358380880 -0.180478731 -0.193730448 -0.195494644
[156] -0.156839219 0.066963557 -0.349674811 -0.780099801 0.299738768
[161] 0.355389016 -0.109073140 0.103516425 0.276709446 -0.330667280
[166] 0.359051481 -0.466427817 0.397832523 -0.180331371 -0.507122333
[171] -0.136201196 0.077467483 0.243596351 -0.109712234 -0.006104262
[176] -0.526391588 -0.261688560 -0.728424450 0.377441592 -0.020578992
[181] -0.295475648 -0.726277293 -0.088976741 -0.216353914 0.705671737
[186] 0.077708164 0.274522537 0.438690108 0.191607314 0.090056547
[191] -0.325682897 0.262231865 -0.108736093 -0.035463192 0.106392159
[196] 0.337233992 -0.221426460 0.639977920 0.018050397 -0.093395574
[201] 0.350993603 0.152944963 0.147877352 0.407216636 -0.305356329
[206] 0.371363104 -0.079522693 0.131306444 -0.489035116 -0.182590095
[211] 0.216901597 -0.318961892 0.684461599 0.181037817 -0.451092105
[216] 0.159937554 -0.196781593 0.030783137 -0.146594806 0.316805375
[221] 0.504143630 -0.291290999 -0.222706612 -0.004340578 -0.238898177
[226] 0.036219601 0.044866686 0.043041297 0.630964039 -0.129494919
>
> proc.time()
user system elapsed
0.794 5.089 5.987
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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: 0x103b857b0>
> .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: 0x103b857b0>
> .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: 0x103b857b0>
> .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: 0x103b857b0>
> 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: 0x875c20000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x875c20000>
> .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: 0x875c20000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x875c20000>
> .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: 0x875c20000>
> 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: 0x875c203c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x875c203c0>
> .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: 0x875c203c0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x875c203c0>
> .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: 0x875c203c0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x875c203c0>
> .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: 0x875c203c0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x875c203c0>
> .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: 0x875c203c0>
> 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: 0x875c204e0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x875c204e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x875c204e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x875c204e0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile872155673a62" "BufferedMatrixFile87216c2a23bb"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile872155673a62" "BufferedMatrixFile87216c2a23bb"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x875c20600>
> .Call("R_bm_AddColumn",P)
<pointer: 0x875c20600>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x875c20600>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x875c20600>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x875c20600>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x875c20600>
> .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: 0x875c20780>
> .Call("R_bm_AddColumn",P)
<pointer: 0x875c20780>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x875c20780>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x875c20780>
> 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: 0x875c208a0>
> .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: 0x875c208a0>
> rm(P)
>
> proc.time()
user system elapsed
0.124 0.053 0.175
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences"
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Platform: aarch64-apple-darwin23
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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.
Type 'demo()' for some demos, 'help()' for on-line help, or
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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
0.140 0.033 0.169