Ben Bolstad
| Snapshot Date: 2026-02-22 13:40 -0500 (Sun, 22 Feb 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 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-23 11:32 -0500 (Mon, 23 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4871 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 255/2354 | 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 | | ||||||||
| 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2026-02-22 22:05:30 -0500 (Sun, 22 Feb 2026) |
| EndedAt: 2026-02-22 22:05:56 -0500 (Sun, 22 Feb 2026) |
| EllapsedTime: 26.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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’ ...* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
0.247 0.053 0.289
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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] "/home/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) max used (Mb)
Ncells 478920 25.6 1048721 56.1 639242 34.2
Vcells 885815 6.8 8388608 64.0 2083259 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Sun Feb 22 22:05:46 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] "Sun Feb 22 22:05:46 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: 0x5dd0479b9c10>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Sun Feb 22 22:05:46 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] "Sun Feb 22 22:05:47 2026"
>
> ColMode(tmp2)
<pointer: 0x5dd0479b9c10>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.6244411 -1.1516170 -2.2019052 -0.9621340
[2,] 1.7226612 1.0050771 1.1273750 -0.4065552
[3,] 0.3412982 1.1714847 -0.3877138 0.5206165
[4,] 0.3800815 0.1067987 -0.9395654 0.6792245
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.6244411 1.1516170 2.2019052 0.9621340
[2,] 1.7226612 1.0050771 1.1273750 0.4065552
[3,] 0.3412982 1.1714847 0.3877138 0.5206165
[4,] 0.3800815 0.1067987 0.9395654 0.6792245
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0311735 1.0731342 1.4838818 0.9808843
[2,] 1.3125019 1.0025354 1.0617792 0.6376168
[3,] 0.5842073 1.0823515 0.6226667 0.7215376
[4,] 0.6165075 0.3268007 0.9693118 0.8241508
>
> 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: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.93618 36.88296 42.04072 35.77098
[2,] 39.84768 36.03043 36.74517 31.78272
[3,] 31.18337 36.99500 31.61438 32.73599
[4,] 31.54516 28.37481 35.63268 33.92073
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5dd048810ff0>
> exp(tmp5)
<pointer: 0x5dd048810ff0>
> log(tmp5,2)
<pointer: 0x5dd048810ff0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 470.2565
> Min(tmp5)
[1] 52.23979
> mean(tmp5)
[1] 72.03835
> Sum(tmp5)
[1] 14407.67
> Var(tmp5)
[1] 866.6972
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.68134 73.63474 69.59743 68.06824 72.05502 68.59927 66.89047 68.48785
[9] 70.43637 70.93276
> rowSums(tmp5)
[1] 1833.627 1472.695 1391.949 1361.365 1441.100 1371.985 1337.809 1369.757
[9] 1408.727 1418.655
> rowVars(tmp5)
[1] 8000.47908 46.93817 44.09979 74.58186 78.82996 99.07697
[7] 65.76093 49.65529 50.62897 78.15797
> rowSd(tmp5)
[1] 89.445397 6.851144 6.640768 8.636079 8.878624 9.953741 8.109311
[8] 7.046651 7.115404 8.840700
> rowMax(tmp5)
[1] 470.25655 87.52432 81.16837 89.05374 91.87853 91.56124 84.55285
[8] 82.04785 81.45013 83.59874
> rowMin(tmp5)
[1] 57.28468 62.90812 55.90811 55.20710 55.36624 53.93235 52.23979 54.96348
[9] 54.30705 54.33715
>
> colMeans(tmp5)
[1] 107.88295 72.00420 73.17749 70.49730 68.46731 67.00043 71.96435
[8] 69.69203 68.48278 69.85334 66.92856 69.75008 73.68583 70.20900
[15] 72.13860 66.61229 69.33927 69.09056 72.69373 71.29687
> colSums(tmp5)
[1] 1078.8295 720.0420 731.7749 704.9730 684.6731 670.0043 719.6435
[8] 696.9203 684.8278 698.5334 669.2856 697.5008 736.8583 702.0900
[15] 721.3860 666.1229 693.3927 690.9056 726.9373 712.9687
> colVars(tmp5)
[1] 16251.10465 50.48763 105.96756 23.56465 22.98854 50.59699
[7] 93.34540 133.49910 85.49682 103.39683 52.72884 71.81358
[13] 125.42932 56.76702 57.79339 99.24404 61.36006 34.30236
[19] 29.87685 61.22792
> colSd(tmp5)
[1] 127.479821 7.105465 10.294054 4.854343 4.794637 7.113156
[7] 9.661542 11.554181 9.246449 10.168423 7.261463 8.474289
[13] 11.199523 7.534389 7.602196 9.962130 7.833266 5.856821
[19] 5.465972 7.824827
> colMax(tmp5)
[1] 470.25655 79.74835 87.50226 77.11305 73.63355 75.67339 91.56124
[8] 81.63416 87.52432 84.55285 81.16837 83.50245 91.87853 83.59874
[15] 89.05374 82.81489 77.64380 81.40889 79.89241 79.63124
> colMin(tmp5)
[1] 62.09059 59.05844 52.23979 60.00638 57.28468 54.30705 61.32334 54.96348
[9] 56.68621 55.90811 56.04922 56.88274 55.20710 55.36624 62.79749 53.93235
[17] 54.33715 59.85700 64.56728 55.88555
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 91.68134 73.63474 69.59743 68.06824 72.05502 68.59927 66.89047 68.48785
[9] NA 70.93276
> rowSums(tmp5)
[1] 1833.627 1472.695 1391.949 1361.365 1441.100 1371.985 1337.809 1369.757
[9] NA 1418.655
> rowVars(tmp5)
[1] 8000.47908 46.93817 44.09979 74.58186 78.82996 99.07697
[7] 65.76093 49.65529 52.72945 78.15797
> rowSd(tmp5)
[1] 89.445397 6.851144 6.640768 8.636079 8.878624 9.953741 8.109311
[8] 7.046651 7.261505 8.840700
> rowMax(tmp5)
[1] 470.25655 87.52432 81.16837 89.05374 91.87853 91.56124 84.55285
[8] 82.04785 NA 83.59874
> rowMin(tmp5)
[1] 57.28468 62.90812 55.90811 55.20710 55.36624 53.93235 52.23979 54.96348
[9] NA 54.33715
>
> colMeans(tmp5)
[1] 107.88295 72.00420 73.17749 70.49730 68.46731 67.00043 71.96435
[8] 69.69203 68.48278 69.85334 66.92856 69.75008 73.68583 70.20900
[15] 72.13860 66.61229 69.33927 69.09056 72.69373 NA
> colSums(tmp5)
[1] 1078.8295 720.0420 731.7749 704.9730 684.6731 670.0043 719.6435
[8] 696.9203 684.8278 698.5334 669.2856 697.5008 736.8583 702.0900
[15] 721.3860 666.1229 693.3927 690.9056 726.9373 NA
> colVars(tmp5)
[1] 16251.10465 50.48763 105.96756 23.56465 22.98854 50.59699
[7] 93.34540 133.49910 85.49682 103.39683 52.72884 71.81358
[13] 125.42932 56.76702 57.79339 99.24404 61.36006 34.30236
[19] 29.87685 NA
> colSd(tmp5)
[1] 127.479821 7.105465 10.294054 4.854343 4.794637 7.113156
[7] 9.661542 11.554181 9.246449 10.168423 7.261463 8.474289
[13] 11.199523 7.534389 7.602196 9.962130 7.833266 5.856821
[19] 5.465972 NA
> colMax(tmp5)
[1] 470.25655 79.74835 87.50226 77.11305 73.63355 75.67339 91.56124
[8] 81.63416 87.52432 84.55285 81.16837 83.50245 91.87853 83.59874
[15] 89.05374 82.81489 77.64380 81.40889 79.89241 NA
> colMin(tmp5)
[1] 62.09059 59.05844 52.23979 60.00638 57.28468 54.30705 61.32334 54.96348
[9] 56.68621 55.90811 56.04922 56.88274 55.20710 55.36624 62.79749 53.93235
[17] 54.33715 59.85700 64.56728 NA
>
> Max(tmp5,na.rm=TRUE)
[1] 470.2565
> Min(tmp5,na.rm=TRUE)
[1] 52.23979
> mean(tmp5,na.rm=TRUE)
[1] 72.02886
> Sum(tmp5,na.rm=TRUE)
[1] 14333.74
> Var(tmp5,na.rm=TRUE)
[1] 871.0564
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.68134 73.63474 69.59743 68.06824 72.05502 68.59927 66.89047 68.48785
[9] 70.25269 70.93276
> rowSums(tmp5,na.rm=TRUE)
[1] 1833.627 1472.695 1391.949 1361.365 1441.100 1371.985 1337.809 1369.757
[9] 1334.801 1418.655
> rowVars(tmp5,na.rm=TRUE)
[1] 8000.47908 46.93817 44.09979 74.58186 78.82996 99.07697
[7] 65.76093 49.65529 52.72945 78.15797
> rowSd(tmp5,na.rm=TRUE)
[1] 89.445397 6.851144 6.640768 8.636079 8.878624 9.953741 8.109311
[8] 7.046651 7.261505 8.840700
> rowMax(tmp5,na.rm=TRUE)
[1] 470.25655 87.52432 81.16837 89.05374 91.87853 91.56124 84.55285
[8] 82.04785 81.45013 83.59874
> rowMin(tmp5,na.rm=TRUE)
[1] 57.28468 62.90812 55.90811 55.20710 55.36624 53.93235 52.23979 54.96348
[9] 54.30705 54.33715
>
> colMeans(tmp5,na.rm=TRUE)
[1] 107.88295 72.00420 73.17749 70.49730 68.46731 67.00043 71.96435
[8] 69.69203 68.48278 69.85334 66.92856 69.75008 73.68583 70.20900
[15] 72.13860 66.61229 69.33927 69.09056 72.69373 71.00472
> colSums(tmp5,na.rm=TRUE)
[1] 1078.8295 720.0420 731.7749 704.9730 684.6731 670.0043 719.6435
[8] 696.9203 684.8278 698.5334 669.2856 697.5008 736.8583 702.0900
[15] 721.3860 666.1229 693.3927 690.9056 726.9373 639.0425
> colVars(tmp5,na.rm=TRUE)
[1] 16251.10465 50.48763 105.96756 23.56465 22.98854 50.59699
[7] 93.34540 133.49910 85.49682 103.39683 52.72884 71.81358
[13] 125.42932 56.76702 57.79339 99.24404 61.36006 34.30236
[19] 29.87685 67.92119
> colSd(tmp5,na.rm=TRUE)
[1] 127.479821 7.105465 10.294054 4.854343 4.794637 7.113156
[7] 9.661542 11.554181 9.246449 10.168423 7.261463 8.474289
[13] 11.199523 7.534389 7.602196 9.962130 7.833266 5.856821
[19] 5.465972 8.241431
> colMax(tmp5,na.rm=TRUE)
[1] 470.25655 79.74835 87.50226 77.11305 73.63355 75.67339 91.56124
[8] 81.63416 87.52432 84.55285 81.16837 83.50245 91.87853 83.59874
[15] 89.05374 82.81489 77.64380 81.40889 79.89241 79.63124
> colMin(tmp5,na.rm=TRUE)
[1] 62.09059 59.05844 52.23979 60.00638 57.28468 54.30705 61.32334 54.96348
[9] 56.68621 55.90811 56.04922 56.88274 55.20710 55.36624 62.79749 53.93235
[17] 54.33715 59.85700 64.56728 55.88555
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.68134 73.63474 69.59743 68.06824 72.05502 68.59927 66.89047 68.48785
[9] NaN 70.93276
> rowSums(tmp5,na.rm=TRUE)
[1] 1833.627 1472.695 1391.949 1361.365 1441.100 1371.985 1337.809 1369.757
[9] 0.000 1418.655
> rowVars(tmp5,na.rm=TRUE)
[1] 8000.47908 46.93817 44.09979 74.58186 78.82996 99.07697
[7] 65.76093 49.65529 NA 78.15797
> rowSd(tmp5,na.rm=TRUE)
[1] 89.445397 6.851144 6.640768 8.636079 8.878624 9.953741 8.109311
[8] 7.046651 NA 8.840700
> rowMax(tmp5,na.rm=TRUE)
[1] 470.25655 87.52432 81.16837 89.05374 91.87853 91.56124 84.55285
[8] 82.04785 NA 83.59874
> rowMin(tmp5,na.rm=TRUE)
[1] 57.28468 62.90812 55.90811 55.20710 55.36624 53.93235 52.23979 54.96348
[9] NA 54.33715
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 112.32547 71.56859 73.04684 70.42860 68.61084 68.41080 72.84361
[8] 68.64774 67.52625 69.36110 67.27187 70.95454 72.82313 70.10705
[15] 73.17650 66.47572 68.50813 69.05162 72.18380 NaN
> colSums(tmp5,na.rm=TRUE)
[1] 1010.9293 644.1173 657.4215 633.8574 617.4976 615.6972 655.5925
[8] 617.8297 607.7362 624.2499 605.4469 638.5909 655.4082 630.9634
[15] 658.5885 598.2815 616.5731 621.4646 649.6542 0.0000
> colVars(tmp5,na.rm=TRUE)
[1] 18060.46258 54.66378 119.02147 26.45714 25.63035 34.54357
[7] 96.31610 137.91791 85.89080 113.59563 57.99402 64.46973
[13] 132.73517 63.74596 52.89863 111.43971 61.25858 38.57309
[19] 30.68616 NA
> colSd(tmp5,na.rm=TRUE)
[1] 134.389220 7.393496 10.909696 5.143650 5.062643 5.877378
[7] 9.814076 11.743846 9.267729 10.658125 7.615381 8.029305
[13] 11.521075 7.984106 7.273144 10.556501 7.826786 6.210724
[19] 5.539509 NA
> colMax(tmp5,na.rm=TRUE)
[1] 470.25655 79.74835 87.50226 77.11305 73.63355 75.67339 91.56124
[8] 81.63416 87.52432 84.55285 81.16837 83.50245 91.87853 83.59874
[15] 89.05374 82.81489 77.64380 81.40889 79.89241 -Inf
> colMin(tmp5,na.rm=TRUE)
[1] 62.09059 59.05844 52.23979 60.00638 57.28468 57.15740 61.32334 54.96348
[9] 56.68621 55.90811 56.04922 56.88274 55.20710 55.36624 64.35140 53.93235
[17] 54.33715 59.85700 64.56728 Inf
>
>
>
>
> 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] 198.8071 247.6235 206.7018 227.2167 308.8392 181.5160 179.1209 278.1300
[9] 218.2303 238.8384
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 198.8071 247.6235 206.7018 227.2167 308.8392 181.5160 179.1209 278.1300
[9] 218.2303 238.8384
>
>
>
> 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 -5.684342e-14 -8.526513e-14 0.000000e+00 -5.684342e-14
[6] 8.526513e-14 1.136868e-13 0.000000e+00 -5.684342e-14 -5.684342e-14
[11] 1.136868e-13 -1.136868e-13 8.526513e-14 5.684342e-14 -5.684342e-14
[16] 8.526513e-14 5.684342e-14 -1.421085e-13 8.526513e-14 -2.842171e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
1 4
2 11
2 20
7 3
5 17
10 7
2 12
8 16
2 16
2 3
9 3
10 3
3 15
3 12
2 7
10 19
4 17
4 16
8 7
6 11
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] 2.51284
> Min(tmp)
[1] -1.965364
> mean(tmp)
[1] 0.140833
> Sum(tmp)
[1] 14.0833
> Var(tmp)
[1] 0.8186949
>
> rowMeans(tmp)
[1] 0.140833
> rowSums(tmp)
[1] 14.0833
> rowVars(tmp)
[1] 0.8186949
> rowSd(tmp)
[1] 0.9048176
> rowMax(tmp)
[1] 2.51284
> rowMin(tmp)
[1] -1.965364
>
> colMeans(tmp)
[1] -0.98312271 0.75037505 1.05115201 -0.16156065 -0.78909400 0.59532143
[7] -0.42207813 1.97794037 0.15459647 0.37696560 -1.71638771 1.84709092
[13] 0.29873393 -0.29515468 0.96802047 2.12391937 0.26801104 0.77792937
[19] -1.82487728 0.10090862 1.80903245 0.06901741 -0.43389552 -0.89095969
[25] 1.11967544 -0.44404801 0.10052919 0.95685048 -0.07959527 -0.14875148
[31] -0.39554282 -0.64815256 1.42198527 0.57804458 -0.66382733 -1.15453939
[37] -0.98125986 0.11997616 0.78695277 0.93786658 -0.92009134 0.47180918
[43] -0.45443982 0.45965562 0.21824088 0.85041307 -0.22508046 2.51283993
[49] 0.65938835 0.73026975 0.72277362 -1.10514251 0.32498120 1.30643324
[55] -0.47351456 0.29256488 -0.95574558 1.13880714 1.15063964 -0.03189602
[61] 0.56526911 0.63903608 0.83430529 1.03844425 -0.62438721 -0.63643076
[67] -0.48157702 0.99826203 -0.97165655 0.27663681 1.16284459 -0.35761870
[73] -1.03491592 -1.53129216 0.22839810 -0.01073758 0.43854067 -0.22501992
[79] -0.44557381 -0.01699379 0.73998206 1.53835182 1.38930263 0.49475941
[85] 0.17476931 -1.09614303 0.42012231 0.75315482 1.24488590 -1.33433123
[91] 0.50415275 0.53531744 -0.56100424 -0.68656282 -0.71338280 -0.73955463
[97] -1.96536354 -0.18535497 -0.63823842 0.53194637
> colSums(tmp)
[1] -0.98312271 0.75037505 1.05115201 -0.16156065 -0.78909400 0.59532143
[7] -0.42207813 1.97794037 0.15459647 0.37696560 -1.71638771 1.84709092
[13] 0.29873393 -0.29515468 0.96802047 2.12391937 0.26801104 0.77792937
[19] -1.82487728 0.10090862 1.80903245 0.06901741 -0.43389552 -0.89095969
[25] 1.11967544 -0.44404801 0.10052919 0.95685048 -0.07959527 -0.14875148
[31] -0.39554282 -0.64815256 1.42198527 0.57804458 -0.66382733 -1.15453939
[37] -0.98125986 0.11997616 0.78695277 0.93786658 -0.92009134 0.47180918
[43] -0.45443982 0.45965562 0.21824088 0.85041307 -0.22508046 2.51283993
[49] 0.65938835 0.73026975 0.72277362 -1.10514251 0.32498120 1.30643324
[55] -0.47351456 0.29256488 -0.95574558 1.13880714 1.15063964 -0.03189602
[61] 0.56526911 0.63903608 0.83430529 1.03844425 -0.62438721 -0.63643076
[67] -0.48157702 0.99826203 -0.97165655 0.27663681 1.16284459 -0.35761870
[73] -1.03491592 -1.53129216 0.22839810 -0.01073758 0.43854067 -0.22501992
[79] -0.44557381 -0.01699379 0.73998206 1.53835182 1.38930263 0.49475941
[85] 0.17476931 -1.09614303 0.42012231 0.75315482 1.24488590 -1.33433123
[91] 0.50415275 0.53531744 -0.56100424 -0.68656282 -0.71338280 -0.73955463
[97] -1.96536354 -0.18535497 -0.63823842 0.53194637
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.98312271 0.75037505 1.05115201 -0.16156065 -0.78909400 0.59532143
[7] -0.42207813 1.97794037 0.15459647 0.37696560 -1.71638771 1.84709092
[13] 0.29873393 -0.29515468 0.96802047 2.12391937 0.26801104 0.77792937
[19] -1.82487728 0.10090862 1.80903245 0.06901741 -0.43389552 -0.89095969
[25] 1.11967544 -0.44404801 0.10052919 0.95685048 -0.07959527 -0.14875148
[31] -0.39554282 -0.64815256 1.42198527 0.57804458 -0.66382733 -1.15453939
[37] -0.98125986 0.11997616 0.78695277 0.93786658 -0.92009134 0.47180918
[43] -0.45443982 0.45965562 0.21824088 0.85041307 -0.22508046 2.51283993
[49] 0.65938835 0.73026975 0.72277362 -1.10514251 0.32498120 1.30643324
[55] -0.47351456 0.29256488 -0.95574558 1.13880714 1.15063964 -0.03189602
[61] 0.56526911 0.63903608 0.83430529 1.03844425 -0.62438721 -0.63643076
[67] -0.48157702 0.99826203 -0.97165655 0.27663681 1.16284459 -0.35761870
[73] -1.03491592 -1.53129216 0.22839810 -0.01073758 0.43854067 -0.22501992
[79] -0.44557381 -0.01699379 0.73998206 1.53835182 1.38930263 0.49475941
[85] 0.17476931 -1.09614303 0.42012231 0.75315482 1.24488590 -1.33433123
[91] 0.50415275 0.53531744 -0.56100424 -0.68656282 -0.71338280 -0.73955463
[97] -1.96536354 -0.18535497 -0.63823842 0.53194637
> colMin(tmp)
[1] -0.98312271 0.75037505 1.05115201 -0.16156065 -0.78909400 0.59532143
[7] -0.42207813 1.97794037 0.15459647 0.37696560 -1.71638771 1.84709092
[13] 0.29873393 -0.29515468 0.96802047 2.12391937 0.26801104 0.77792937
[19] -1.82487728 0.10090862 1.80903245 0.06901741 -0.43389552 -0.89095969
[25] 1.11967544 -0.44404801 0.10052919 0.95685048 -0.07959527 -0.14875148
[31] -0.39554282 -0.64815256 1.42198527 0.57804458 -0.66382733 -1.15453939
[37] -0.98125986 0.11997616 0.78695277 0.93786658 -0.92009134 0.47180918
[43] -0.45443982 0.45965562 0.21824088 0.85041307 -0.22508046 2.51283993
[49] 0.65938835 0.73026975 0.72277362 -1.10514251 0.32498120 1.30643324
[55] -0.47351456 0.29256488 -0.95574558 1.13880714 1.15063964 -0.03189602
[61] 0.56526911 0.63903608 0.83430529 1.03844425 -0.62438721 -0.63643076
[67] -0.48157702 0.99826203 -0.97165655 0.27663681 1.16284459 -0.35761870
[73] -1.03491592 -1.53129216 0.22839810 -0.01073758 0.43854067 -0.22501992
[79] -0.44557381 -0.01699379 0.73998206 1.53835182 1.38930263 0.49475941
[85] 0.17476931 -1.09614303 0.42012231 0.75315482 1.24488590 -1.33433123
[91] 0.50415275 0.53531744 -0.56100424 -0.68656282 -0.71338280 -0.73955463
[97] -1.96536354 -0.18535497 -0.63823842 0.53194637
> colMedians(tmp)
[1] -0.98312271 0.75037505 1.05115201 -0.16156065 -0.78909400 0.59532143
[7] -0.42207813 1.97794037 0.15459647 0.37696560 -1.71638771 1.84709092
[13] 0.29873393 -0.29515468 0.96802047 2.12391937 0.26801104 0.77792937
[19] -1.82487728 0.10090862 1.80903245 0.06901741 -0.43389552 -0.89095969
[25] 1.11967544 -0.44404801 0.10052919 0.95685048 -0.07959527 -0.14875148
[31] -0.39554282 -0.64815256 1.42198527 0.57804458 -0.66382733 -1.15453939
[37] -0.98125986 0.11997616 0.78695277 0.93786658 -0.92009134 0.47180918
[43] -0.45443982 0.45965562 0.21824088 0.85041307 -0.22508046 2.51283993
[49] 0.65938835 0.73026975 0.72277362 -1.10514251 0.32498120 1.30643324
[55] -0.47351456 0.29256488 -0.95574558 1.13880714 1.15063964 -0.03189602
[61] 0.56526911 0.63903608 0.83430529 1.03844425 -0.62438721 -0.63643076
[67] -0.48157702 0.99826203 -0.97165655 0.27663681 1.16284459 -0.35761870
[73] -1.03491592 -1.53129216 0.22839810 -0.01073758 0.43854067 -0.22501992
[79] -0.44557381 -0.01699379 0.73998206 1.53835182 1.38930263 0.49475941
[85] 0.17476931 -1.09614303 0.42012231 0.75315482 1.24488590 -1.33433123
[91] 0.50415275 0.53531744 -0.56100424 -0.68656282 -0.71338280 -0.73955463
[97] -1.96536354 -0.18535497 -0.63823842 0.53194637
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.9831227 0.750375 1.051152 -0.1615606 -0.789094 0.5953214 -0.4220781
[2,] -0.9831227 0.750375 1.051152 -0.1615606 -0.789094 0.5953214 -0.4220781
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1.97794 0.1545965 0.3769656 -1.716388 1.847091 0.2987339 -0.2951547
[2,] 1.97794 0.1545965 0.3769656 -1.716388 1.847091 0.2987339 -0.2951547
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.9680205 2.123919 0.268011 0.7779294 -1.824877 0.1009086 1.809032
[2,] 0.9680205 2.123919 0.268011 0.7779294 -1.824877 0.1009086 1.809032
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.06901741 -0.4338955 -0.8909597 1.119675 -0.444048 0.1005292 0.9568505
[2,] 0.06901741 -0.4338955 -0.8909597 1.119675 -0.444048 0.1005292 0.9568505
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.07959527 -0.1487515 -0.3955428 -0.6481526 1.421985 0.5780446 -0.6638273
[2,] -0.07959527 -0.1487515 -0.3955428 -0.6481526 1.421985 0.5780446 -0.6638273
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.154539 -0.9812599 0.1199762 0.7869528 0.9378666 -0.9200913 0.4718092
[2,] -1.154539 -0.9812599 0.1199762 0.7869528 0.9378666 -0.9200913 0.4718092
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.4544398 0.4596556 0.2182409 0.8504131 -0.2250805 2.51284 0.6593883
[2,] -0.4544398 0.4596556 0.2182409 0.8504131 -0.2250805 2.51284 0.6593883
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.7302698 0.7227736 -1.105143 0.3249812 1.306433 -0.4735146 0.2925649
[2,] 0.7302698 0.7227736 -1.105143 0.3249812 1.306433 -0.4735146 0.2925649
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.9557456 1.138807 1.15064 -0.03189602 0.5652691 0.6390361 0.8343053
[2,] -0.9557456 1.138807 1.15064 -0.03189602 0.5652691 0.6390361 0.8343053
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 1.038444 -0.6243872 -0.6364308 -0.481577 0.998262 -0.9716566 0.2766368
[2,] 1.038444 -0.6243872 -0.6364308 -0.481577 0.998262 -0.9716566 0.2766368
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 1.162845 -0.3576187 -1.034916 -1.531292 0.2283981 -0.01073758 0.4385407
[2,] 1.162845 -0.3576187 -1.034916 -1.531292 0.2283981 -0.01073758 0.4385407
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.2250199 -0.4455738 -0.01699379 0.7399821 1.538352 1.389303 0.4947594
[2,] -0.2250199 -0.4455738 -0.01699379 0.7399821 1.538352 1.389303 0.4947594
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.1747693 -1.096143 0.4201223 0.7531548 1.244886 -1.334331 0.5041527
[2,] 0.1747693 -1.096143 0.4201223 0.7531548 1.244886 -1.334331 0.5041527
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.5353174 -0.5610042 -0.6865628 -0.7133828 -0.7395546 -1.965364 -0.185355
[2,] 0.5353174 -0.5610042 -0.6865628 -0.7133828 -0.7395546 -1.965364 -0.185355
[,99] [,100]
[1,] -0.6382384 0.5319464
[2,] -0.6382384 0.5319464
>
>
> Max(tmp2)
[1] 2.617388
> Min(tmp2)
[1] -2.682912
> mean(tmp2)
[1] 0.09216595
> Sum(tmp2)
[1] 9.216595
> Var(tmp2)
[1] 1.167519
>
> rowMeans(tmp2)
[1] -0.581094090 1.736909326 0.563638730 0.797768045 -1.257376206
[6] -0.008763108 -0.908454951 1.545397117 -1.307836421 1.768806557
[11] 1.499040196 0.269155456 -1.079832193 -2.184541002 0.123956391
[16] -0.131369048 0.492216826 0.818399860 1.916497949 0.027629151
[21] 0.851023298 -0.761527835 0.201048977 2.617388165 -0.034466821
[26] 0.179717631 -0.062488619 -0.478065020 -1.504431209 0.932497607
[31] -0.690091442 0.089336696 -0.730768793 -1.086336853 1.526926268
[36] 1.799044983 -0.174563944 0.036286859 -1.152891628 0.751565816
[41] -0.454182917 -2.058257336 1.617618200 -1.893440713 0.129610234
[46] -0.180407826 -0.071349269 0.646234212 -1.362335240 0.128396567
[51] -1.100528656 -0.587892193 0.599566707 1.631304341 1.249896209
[56] 1.430514481 -0.440920816 0.797874020 0.873551990 -0.587610868
[61] 0.947229491 -1.576239410 0.335719094 1.305475709 0.425714120
[66] -0.220909419 0.196525651 -0.260548231 0.765207618 0.808942549
[71] -0.067245600 0.155893652 1.489346650 -0.964946124 -0.256480864
[76] -0.426201930 -1.150047496 0.539032863 1.921269168 -0.263669720
[81] -0.972324893 0.823698117 2.182397342 1.076142916 0.754185302
[86] -2.682912345 1.194537176 0.093069902 0.718652950 1.325876698
[91] 1.154099937 -1.295985104 -0.460559852 -0.809635568 -2.333570053
[96] -0.713267390 -0.347904628 -0.614441531 -0.511812976 0.155287025
> rowSums(tmp2)
[1] -0.581094090 1.736909326 0.563638730 0.797768045 -1.257376206
[6] -0.008763108 -0.908454951 1.545397117 -1.307836421 1.768806557
[11] 1.499040196 0.269155456 -1.079832193 -2.184541002 0.123956391
[16] -0.131369048 0.492216826 0.818399860 1.916497949 0.027629151
[21] 0.851023298 -0.761527835 0.201048977 2.617388165 -0.034466821
[26] 0.179717631 -0.062488619 -0.478065020 -1.504431209 0.932497607
[31] -0.690091442 0.089336696 -0.730768793 -1.086336853 1.526926268
[36] 1.799044983 -0.174563944 0.036286859 -1.152891628 0.751565816
[41] -0.454182917 -2.058257336 1.617618200 -1.893440713 0.129610234
[46] -0.180407826 -0.071349269 0.646234212 -1.362335240 0.128396567
[51] -1.100528656 -0.587892193 0.599566707 1.631304341 1.249896209
[56] 1.430514481 -0.440920816 0.797874020 0.873551990 -0.587610868
[61] 0.947229491 -1.576239410 0.335719094 1.305475709 0.425714120
[66] -0.220909419 0.196525651 -0.260548231 0.765207618 0.808942549
[71] -0.067245600 0.155893652 1.489346650 -0.964946124 -0.256480864
[76] -0.426201930 -1.150047496 0.539032863 1.921269168 -0.263669720
[81] -0.972324893 0.823698117 2.182397342 1.076142916 0.754185302
[86] -2.682912345 1.194537176 0.093069902 0.718652950 1.325876698
[91] 1.154099937 -1.295985104 -0.460559852 -0.809635568 -2.333570053
[96] -0.713267390 -0.347904628 -0.614441531 -0.511812976 0.155287025
> 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] -0.581094090 1.736909326 0.563638730 0.797768045 -1.257376206
[6] -0.008763108 -0.908454951 1.545397117 -1.307836421 1.768806557
[11] 1.499040196 0.269155456 -1.079832193 -2.184541002 0.123956391
[16] -0.131369048 0.492216826 0.818399860 1.916497949 0.027629151
[21] 0.851023298 -0.761527835 0.201048977 2.617388165 -0.034466821
[26] 0.179717631 -0.062488619 -0.478065020 -1.504431209 0.932497607
[31] -0.690091442 0.089336696 -0.730768793 -1.086336853 1.526926268
[36] 1.799044983 -0.174563944 0.036286859 -1.152891628 0.751565816
[41] -0.454182917 -2.058257336 1.617618200 -1.893440713 0.129610234
[46] -0.180407826 -0.071349269 0.646234212 -1.362335240 0.128396567
[51] -1.100528656 -0.587892193 0.599566707 1.631304341 1.249896209
[56] 1.430514481 -0.440920816 0.797874020 0.873551990 -0.587610868
[61] 0.947229491 -1.576239410 0.335719094 1.305475709 0.425714120
[66] -0.220909419 0.196525651 -0.260548231 0.765207618 0.808942549
[71] -0.067245600 0.155893652 1.489346650 -0.964946124 -0.256480864
[76] -0.426201930 -1.150047496 0.539032863 1.921269168 -0.263669720
[81] -0.972324893 0.823698117 2.182397342 1.076142916 0.754185302
[86] -2.682912345 1.194537176 0.093069902 0.718652950 1.325876698
[91] 1.154099937 -1.295985104 -0.460559852 -0.809635568 -2.333570053
[96] -0.713267390 -0.347904628 -0.614441531 -0.511812976 0.155287025
> rowMin(tmp2)
[1] -0.581094090 1.736909326 0.563638730 0.797768045 -1.257376206
[6] -0.008763108 -0.908454951 1.545397117 -1.307836421 1.768806557
[11] 1.499040196 0.269155456 -1.079832193 -2.184541002 0.123956391
[16] -0.131369048 0.492216826 0.818399860 1.916497949 0.027629151
[21] 0.851023298 -0.761527835 0.201048977 2.617388165 -0.034466821
[26] 0.179717631 -0.062488619 -0.478065020 -1.504431209 0.932497607
[31] -0.690091442 0.089336696 -0.730768793 -1.086336853 1.526926268
[36] 1.799044983 -0.174563944 0.036286859 -1.152891628 0.751565816
[41] -0.454182917 -2.058257336 1.617618200 -1.893440713 0.129610234
[46] -0.180407826 -0.071349269 0.646234212 -1.362335240 0.128396567
[51] -1.100528656 -0.587892193 0.599566707 1.631304341 1.249896209
[56] 1.430514481 -0.440920816 0.797874020 0.873551990 -0.587610868
[61] 0.947229491 -1.576239410 0.335719094 1.305475709 0.425714120
[66] -0.220909419 0.196525651 -0.260548231 0.765207618 0.808942549
[71] -0.067245600 0.155893652 1.489346650 -0.964946124 -0.256480864
[76] -0.426201930 -1.150047496 0.539032863 1.921269168 -0.263669720
[81] -0.972324893 0.823698117 2.182397342 1.076142916 0.754185302
[86] -2.682912345 1.194537176 0.093069902 0.718652950 1.325876698
[91] 1.154099937 -1.295985104 -0.460559852 -0.809635568 -2.333570053
[96] -0.713267390 -0.347904628 -0.614441531 -0.511812976 0.155287025
>
> colMeans(tmp2)
[1] 0.09216595
> colSums(tmp2)
[1] 9.216595
> colVars(tmp2)
[1] 1.167519
> colSd(tmp2)
[1] 1.080518
> colMax(tmp2)
[1] 2.617388
> colMin(tmp2)
[1] -2.682912
> colMedians(tmp2)
[1] 0.0912033
> colRanges(tmp2)
[,1]
[1,] -2.682912
[2,] 2.617388
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.7246207 -2.6735970 -3.9511100 -2.1581667 0.4395994 -2.3279036
[7] 2.1327043 1.8046514 -4.6853340 1.0988692
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.6052365
[2,] -0.4785906
[3,] 0.1066260
[4,] 0.5591105
[5,] 0.7630342
>
> rowApply(tmp,sum)
[1] -1.3430352 -6.6486796 1.2976878 -4.4587768 1.4037419 -0.1612978
[7] -4.4442022 3.9256341 2.7530995 -3.3690796
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 8 10 8 1 2 9 4 7 2 6
[2,] 1 1 7 5 5 10 3 8 10 2
[3,] 4 6 4 8 7 7 8 2 1 3
[4,] 6 9 2 7 4 3 2 4 5 9
[5,] 7 4 1 10 3 1 9 9 4 7
[6,] 9 8 6 4 8 4 5 1 6 1
[7,] 2 7 10 2 10 6 7 6 8 8
[8,] 5 2 9 9 9 8 10 3 3 4
[9,] 3 3 3 3 1 5 6 5 9 5
[10,] 10 5 5 6 6 2 1 10 7 10
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.202612729 1.533137479 3.743468575 4.184588708 -0.508346925
[6] 1.224083227 -0.900427513 -4.088637046 2.820922283 0.009632494
[11] -2.420776259 -1.051888472 -0.065270893 -0.778801411 1.010725235
[16] 2.266574285 2.357086159 3.246183521 2.669042628 1.848802731
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.87071988
[2,] -0.03323857
[3,] 0.47038130
[4,] 0.53012607
[5,] 1.10606381
>
> rowApply(tmp,sum)
[1] 6.6062272 4.5796569 0.8847801 2.9005222 3.3315251
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 8 16 16 5 13
[2,] 3 10 9 16 17
[3,] 18 6 13 19 10
[4,] 20 11 15 13 12
[5,] 12 1 20 17 9
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.03323857 -0.507677468 1.65576921 2.4851217 0.39576186 0.2545469
[2,] 1.10606381 0.126971781 -0.17434482 0.2739342 -3.63728421 2.4772064
[3,] 0.47038130 -0.003359701 0.42694161 0.4304889 1.50306346 -0.3305431
[4,] -0.87071988 1.188247579 1.74519683 0.6214647 1.24593171 -1.7962501
[5,] 0.53012607 0.728955287 0.08990575 0.3735792 -0.01581975 0.6191231
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.50642484 -2.54831137 1.2267376 -0.11773497 0.93132768 -0.2993504
[2,] 0.35007311 -0.05213998 1.5418208 -0.62014861 0.08667219 -0.1265750
[3,] -1.07680706 -0.59682038 0.1523771 -0.05479038 -1.68157966 0.4297035
[4,] 0.03475497 -0.72412395 0.3790216 1.12165221 -0.90416671 0.2477687
[5,] 0.29797632 -0.16724136 -0.4790348 -0.31934575 -0.85302976 -1.3034352
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.0831735 0.2911938 1.3802037 1.9888485 0.9041148 -0.3459481
[2,] 0.7732595 1.7674583 -0.4009520 -1.3323003 0.5376432 1.3706089
[3,] 0.1269786 -0.6697703 -0.2661879 0.4897391 1.0086657 0.3112586
[4,] -0.4887038 -1.3893363 -0.5331141 1.4046994 -0.7406627 0.8430490
[5,] 0.6063683 -0.7783469 0.8307755 -0.2844124 0.6473252 1.0672151
[,19] [,20]
[1,] 0.0967536 0.43770713
[2,] 1.0993235 -0.58763393
[3,] 0.5804046 -0.36536381
[4,] -0.8955585 2.41137155
[5,] 1.7881195 -0.04727821
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/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: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 653 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 566 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/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 -0.9715206 -1.514058 1.977765 0.7195547 -1.141487 -1.388944 0.8590328
col8 col9 col10 col11 col12 col13 col14
row1 -0.07621482 -0.9996331 1.242544 0.3259438 -0.7944957 0.4539644 -1.028593
col15 col16 col17 col18 col19 col20
row1 0.6994725 -0.2399663 -0.7774928 0.2681259 0.4837175 1.206935
> tmp[,"col10"]
col10
row1 1.24254367
row2 0.09757527
row3 -1.18319692
row4 0.16447512
row5 -1.09674227
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.9715206 -1.5140577 1.977765 0.7195547 -1.14148700 -1.3889436 0.8590328
row5 0.1491772 -0.5709224 -1.915986 0.2395354 0.01195018 -0.2235577 0.9772704
col8 col9 col10 col11 col12 col13 col14
row1 -0.07621482 -0.9996331 1.242544 0.3259438 -0.7944957 0.4539644 -1.0285934
row5 -1.21832130 1.6762409 -1.096742 0.8317442 1.8841502 0.8064723 -0.4380622
col15 col16 col17 col18 col19 col20
row1 0.6994725 -0.2399663 -0.7774928 0.2681259 0.4837175 1.206935
row5 -0.3458975 -0.5537049 -0.8360182 -0.4477752 -0.6210836 1.032836
> tmp[,c("col6","col20")]
col6 col20
row1 -1.38894361 1.20693497
row2 -0.43491634 -0.05419904
row3 0.37846852 1.43396786
row4 -0.02576803 1.34833781
row5 -0.22355766 1.03283553
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.3889436 1.206935
row5 -0.2235577 1.032836
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.08441 49.23696 51.92308 50.06741 51.67601 105.8506 51.14073 50.9087
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.70361 49.1663 49.74931 52.67608 51.83906 50.34887 50.47196 50.09701
col17 col18 col19 col20
row1 49.96509 53.0701 49.54128 104.7624
> tmp[,"col10"]
col10
row1 49.16630
row2 31.24383
row3 29.40722
row4 31.72273
row5 48.62618
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.08441 49.23696 51.92308 50.06741 51.67601 105.8506 51.14073 50.90870
row5 50.27255 50.89541 50.10837 49.07768 48.79891 105.9835 48.86350 51.23797
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.70361 49.16630 49.74931 52.67608 51.83906 50.34887 50.47196 50.09701
row5 51.03295 48.62618 49.03670 49.81684 49.39025 50.47650 49.84349 49.21432
col17 col18 col19 col20
row1 49.96509 53.07010 49.54128 104.7624
row5 48.38117 48.89342 49.58489 104.9459
> tmp[,c("col6","col20")]
col6 col20
row1 105.85062 104.76242
row2 75.16979 75.77060
row3 75.85536 74.90982
row4 76.36982 75.84267
row5 105.98352 104.94591
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.8506 104.7624
row5 105.9835 104.9459
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.8506 104.7624
row5 105.9835 104.9459
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 2.6087428
[2,] 2.0095475
[3,] 1.3455392
[4,] -0.3087211
[5,] -0.2392201
> tmp[,c("col17","col7")]
col17 col7
[1,] -1.5122162 0.04472613
[2,] 0.7393850 -0.52607087
[3,] -1.8005657 -0.97439869
[4,] 1.0637697 0.45021973
[5,] -0.4451424 1.51130044
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 2.0877814 0.3030119
[2,] -1.4722230 1.0173884
[3,] -0.3784547 0.2230977
[4,] 1.7988910 -1.1136781
[5,] -1.3901148 0.7697173
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 2.087781
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 2.087781
[2,] -1.472223
>
>
>
> 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 -2.110679 -1.350948 -0.7848737 -0.4367119 -0.6514033 -0.2972172 0.1875521
row1 -1.162929 -1.302859 -0.2072968 1.4152241 -2.5421730 -0.9537091 0.1820834
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.1753349 1.259741 -0.5385107 0.5394737 -0.06715386 0.09759491
row1 -0.5669146 -0.164611 -0.6537155 0.9953414 -0.70778408 -0.42742040
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 1.7676101 -2.129823 0.9150942 0.6533831 0.3726901 0.05480014 0.1221550
row1 0.2072263 1.290307 -0.6833244 0.3235595 -1.2625895 1.57632118 -0.3007326
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.3323998 1.083693 0.7432595 -1.615244 -0.1119924 0.1721664 0.2702911
[,8] [,9] [,10]
row2 -0.6047675 1.12037 0.5635139
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 1.444648 1.269458 -0.7641299 -0.149165 0.110691 -0.8673138 1.978109
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.140827 -0.6018398 0.1306967 1.671494 0.7495539 0.6519787 -0.3282126
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.5883399 -0.95159 -1.804267 0.3842758 0.08944929 -0.2452242
>
>
> 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: 0x5dd04887fdf0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c1dd5708"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c68f22ec0"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c456c2470"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c58dddb0d"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c647e7bf"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c4830513d"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c44fab9ec"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c2a14cd06"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c3124b54e"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c151245c1"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c2d57f430"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c58091207"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c42cbe517"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c385846f3"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM36d29c57a21aba"
>
>
> ### 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: 0x5dd049f6f2b0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5dd049f6f2b0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5dd049f6f2b0>
> rowMedians(tmp)
[1] -0.252959922 0.659713690 -0.414291131 0.146531047 -0.516495677
[6] 0.410890080 0.215049295 -0.003652565 0.396466156 -0.099120050
[11] -0.438858396 -0.450554765 0.276269141 0.141963566 -0.053619935
[16] -0.002179471 0.320548669 0.109015691 0.492832377 0.183722271
[21] -0.048940090 0.229044299 0.107431019 -0.185520619 -0.229561327
[26] 0.444474733 -0.001692696 -0.079614517 0.275700080 -0.580158189
[31] 0.087622081 -0.017746374 -0.550694291 0.467182196 -0.320326569
[36] -0.243633242 0.262909046 -0.040187501 -0.093932254 0.375671392
[41] 0.557554988 0.186122009 0.321435896 -0.026355458 -0.265414554
[46] -0.400314031 0.227086969 -0.036627535 0.461382841 0.019635097
[51] -0.076565903 -0.234886330 0.095794062 -0.484697872 0.354567982
[56] 0.269762537 -0.356023395 -0.218938407 0.389070491 0.199890157
[61] 0.553910130 -0.155825208 0.088406283 -0.244143026 0.052154258
[66] -0.286090224 0.360125231 0.113703686 -0.590643468 0.073254592
[71] 0.012649393 0.003068444 -0.027847656 -0.073833008 -0.121198649
[76] 0.187962731 0.244784937 -0.296263294 -0.410599736 -0.095439106
[81] -0.097280406 -0.723126514 0.271628280 0.525803442 0.284348321
[86] -0.061796002 0.726499483 -0.040250713 -0.054899755 -0.065173446
[91] 0.540494564 -0.203494460 -0.097087559 0.451183828 -0.476655019
[96] -0.057846913 -0.061017717 -0.584962029 -0.336885183 -0.139474521
[101] -0.133646754 0.241236164 0.100272681 -0.178925681 0.172333791
[106] -0.688171350 0.528222472 -0.092756229 0.122785373 0.036630802
[111] -0.556988707 0.102269264 -0.043175572 0.035184333 -0.155398389
[116] -0.041282054 0.397255423 -0.401793226 0.534865063 -0.523854836
[121] 0.501550265 -0.337234212 -0.548017330 0.030481074 0.436274421
[126] 1.239346755 -0.221121202 0.328730743 0.083599948 0.337012888
[131] 0.004816672 -0.432845695 -0.068056482 -0.014577860 0.054354133
[136] 0.077395289 -0.093241849 0.151026684 -0.320481362 0.085780044
[141] -0.563697400 -0.136762949 0.382413270 -0.167075996 -0.138162365
[146] -0.028561962 0.397352749 0.065470367 -0.103928103 -0.114482917
[151] 0.127248151 -0.349330040 0.087689919 -0.298663767 -0.426719153
[156] -0.183215398 0.273065878 -0.123592902 -0.266378000 -0.579855113
[161] 0.158557126 -0.509660309 -0.420604485 0.085462639 0.066104842
[166] 0.198835569 0.095880964 0.226424951 0.345791646 0.586684160
[171] -0.229883468 -0.332988553 0.126339131 0.485087044 0.106881623
[176] -0.404445729 0.198800497 -0.163886961 -0.151128874 0.609798308
[181] -0.180700339 0.655205430 -0.346270378 -0.128419896 -0.041980085
[186] 0.390040379 0.726722233 0.146354479 0.330486170 -0.256237614
[191] -0.504942637 0.571446869 -0.322320854 -0.422489867 0.030074012
[196] 0.072107412 -0.317096824 -0.572905437 -0.039035565 0.467086141
[201] 0.008285080 0.205784920 0.476830004 0.357287745 0.440711714
[206] -0.053404964 0.011929897 -0.787418922 -0.730777527 -0.473899093
[211] 0.059708520 -0.222601235 -0.274667361 -0.141032364 -0.131615687
[216] -0.561245536 0.066447485 -0.322182901 0.032752261 0.011168339
[221] -0.316313936 -0.250035576 -0.075751237 -0.681409971 0.140501390
[226] 0.126969329 -0.002206597 0.122957603 -0.017628667 -0.302648143
>
> proc.time()
user system elapsed
1.383 1.452 2.825
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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: 0x60b7afe25c10>
> .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: 0x60b7afe25c10>
> .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: 0x60b7afe25c10>
> .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: 0x60b7afe25c10>
> 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: 0x60b7b0ae82d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b7b0ae82d0>
> .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: 0x60b7b0ae82d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b7b0ae82d0>
> .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: 0x60b7b0ae82d0>
> 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: 0x60b7b11bdd70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b7b11bdd70>
> .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: 0x60b7b11bdd70>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x60b7b11bdd70>
> .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: 0x60b7b11bdd70>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x60b7b11bdd70>
> .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: 0x60b7b11bdd70>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x60b7b11bdd70>
> .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: 0x60b7b11bdd70>
> 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: 0x60b7b0d31370>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x60b7b0d31370>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b7b0d31370>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b7b0d31370>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile36d32a2ea45be0" "BufferedMatrixFile36d32a655ab9e7"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile36d32a2ea45be0" "BufferedMatrixFile36d32a655ab9e7"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b7b0c7cff0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b7b0c7cff0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x60b7b0c7cff0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x60b7b0c7cff0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x60b7b0c7cff0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x60b7b0c7cff0>
> .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: 0x60b7b0e5f3d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b7b0e5f3d0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x60b7b0e5f3d0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x60b7b0e5f3d0>
> 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: 0x60b7b2610fb0>
> .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: 0x60b7b2610fb0>
> rm(P)
>
> proc.time()
user system elapsed
0.284 0.068 0.331
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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Type 'license()' or 'licence()' for distribution details.
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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
0.258 0.056 0.296