Ben Bolstad
| Snapshot Date: 2026-05-11 13:45 -0400 (Mon, 11 May 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: 2d99771 |
| git_last_commit_date: 2026-04-28 08:32:08 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-12 11:33 -0400 (Tue, 12 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4892 |
| 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 259/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.77.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.4 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: 1.77.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BufferedMatrix_1.77.0.tar.gz |
| StartedAt: 2026-05-11 21:52:22 -0400 (Mon, 11 May 2026) |
| EndedAt: 2026-05-11 21:52:47 -0400 (Mon, 11 May 2026) |
| EllapsedTime: 25.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BufferedMatrix_1.77.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-12 01:52:22 UTC
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.77.0’
* 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 13.3.0-6ubuntu2~24.04.1) 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-3.24-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.77.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.24-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-3.24-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-3.24-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-3.24-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-3.24-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-3.24-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.24-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 version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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 0.046 0.281
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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-3.24-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 480233 25.7 1053308 56.3 637571 34.1
Vcells 887253 6.8 8388608 64.0 2083896 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] "Mon May 11 21:52:38 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] "Mon May 11 21:52:38 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: 0x5d81d1d14520>
>
>
>
> 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] "Mon May 11 21:52:38 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] "Mon May 11 21:52:38 2026"
>
> ColMode(tmp2)
<pointer: 0x5d81d1d14520>
>
>
>
> ### 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,] 100.4069153 -0.1135637 1.5463871 0.006530448
[2,] -1.6731648 -1.0120143 0.4687453 -0.788139499
[3,] -1.1489729 -0.3035485 -1.9114222 -0.884065538
[4,] -0.4930314 0.2244759 -0.8462809 -1.285411528
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-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,] 100.4069153 0.1135637 1.5463871 0.006530448
[2,] 1.6731648 1.0120143 0.4687453 0.788139499
[3,] 1.1489729 0.3035485 1.9114222 0.884065538
[4,] 0.4930314 0.2244759 0.8462809 1.285411528
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-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,] 10.020325 0.3369921 1.2435381 0.08081119
[2,] 1.293509 1.0059892 0.6846497 0.88777221
[3,] 1.071902 0.5509523 1.3825419 0.94024759
[4,] 0.702162 0.4737889 0.9199353 1.13375991
>
> 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-3.24-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,] 225.61017 28.48348 38.98177 25.81464
[2,] 39.60825 36.07191 32.31524 34.66586
[3,] 36.86799 30.81307 40.73684 35.28654
[4,] 32.51465 29.96236 35.04563 37.62301
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5d81d2aff8f0>
> exp(tmp5)
<pointer: 0x5d81d2aff8f0>
> log(tmp5,2)
<pointer: 0x5d81d2aff8f0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 469.578
> Min(tmp5)
[1] 53.63673
> mean(tmp5)
[1] 72.80211
> Sum(tmp5)
[1] 14560.42
> Var(tmp5)
[1] 863.795
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.94741 72.39226 70.23901 71.17389 70.89252 70.77664 70.55414 70.55349
[9] 71.54842 67.94331
> rowSums(tmp5)
[1] 1838.948 1447.845 1404.780 1423.478 1417.850 1415.533 1411.083 1411.070
[9] 1430.968 1358.866
> rowVars(tmp5)
[1] 7991.43730 81.68817 90.94851 59.55089 49.62955 109.09749
[7] 48.93767 44.09825 53.24438 77.46335
> rowSd(tmp5)
[1] 89.394839 9.038151 9.536693 7.716922 7.044824 10.444974 6.995547
[8] 6.640651 7.296875 8.801327
> rowMax(tmp5)
[1] 469.57800 87.82566 86.37417 82.52209 82.91594 88.45784 83.34956
[8] 80.84842 84.98416 90.28333
> rowMin(tmp5)
[1] 53.72980 54.16950 56.63783 53.63673 56.62179 56.44691 59.04265 57.30193
[9] 61.19134 55.19159
>
> colMeans(tmp5)
[1] 107.94324 68.26354 70.91157 69.68689 73.71815 70.01564 72.29865
[8] 72.11887 71.07164 73.16610 69.22035 73.84820 71.32267 69.79337
[15] 71.60844 70.66987 70.80054 66.30276 72.30605 70.97564
> colSums(tmp5)
[1] 1079.4324 682.6354 709.1157 696.8689 737.1815 700.1564 722.9865
[8] 721.1887 710.7164 731.6610 692.2035 738.4820 713.2267 697.9337
[15] 716.0844 706.6987 708.0054 663.0276 723.0605 709.7564
> colVars(tmp5)
[1] 16205.03175 45.05294 51.33449 78.83829 85.77728 81.68464
[7] 88.20615 91.04633 101.08493 84.53200 96.31192 115.84129
[13] 100.58536 46.84648 35.07172 27.70364 64.31899 65.53355
[19] 98.48476 22.63362
> colSd(tmp5)
[1] 127.298986 6.712149 7.164809 8.879093 9.261602 9.037956
[7] 9.391813 9.541820 10.054100 9.194129 9.813864 10.762959
[13] 10.029225 6.844449 5.922138 5.263424 8.019912 8.095279
[19] 9.923949 4.757480
> colMax(tmp5)
[1] 469.57800 76.55843 84.78840 80.78522 88.45784 82.22152 85.98387
[8] 83.75871 87.82566 87.62746 83.67418 90.28333 92.02253 81.67371
[15] 81.78485 79.18336 80.56712 81.00825 86.37417 74.54043
> colMin(tmp5)
[1] 56.62179 59.22313 63.17645 53.72980 56.90451 56.63783 61.19134 53.63673
[9] 57.04308 59.02096 57.30193 54.16950 60.59602 59.32319 61.73928 63.33402
[17] 55.19159 57.42536 57.03415 61.07226
>
>
> ### 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] 91.94741 72.39226 70.23901 71.17389 70.89252 70.77664 NA 70.55349
[9] 71.54842 67.94331
> rowSums(tmp5)
[1] 1838.948 1447.845 1404.780 1423.478 1417.850 1415.533 NA 1411.070
[9] 1430.968 1358.866
> rowVars(tmp5)
[1] 7991.43730 81.68817 90.94851 59.55089 49.62955 109.09749
[7] 42.08201 44.09825 53.24438 77.46335
> rowSd(tmp5)
[1] 89.394839 9.038151 9.536693 7.716922 7.044824 10.444974 6.487064
[8] 6.640651 7.296875 8.801327
> rowMax(tmp5)
[1] 469.57800 87.82566 86.37417 82.52209 82.91594 88.45784 NA
[8] 80.84842 84.98416 90.28333
> rowMin(tmp5)
[1] 53.72980 54.16950 56.63783 53.63673 56.62179 56.44691 NA 57.30193
[9] 61.19134 55.19159
>
> colMeans(tmp5)
[1] 107.94324 68.26354 70.91157 69.68689 73.71815 70.01564 72.29865
[8] 72.11887 NA 73.16610 69.22035 73.84820 71.32267 69.79337
[15] 71.60844 70.66987 70.80054 66.30276 72.30605 70.97564
> colSums(tmp5)
[1] 1079.4324 682.6354 709.1157 696.8689 737.1815 700.1564 722.9865
[8] 721.1887 NA 731.6610 692.2035 738.4820 713.2267 697.9337
[15] 716.0844 706.6987 708.0054 663.0276 723.0605 709.7564
> colVars(tmp5)
[1] 16205.03175 45.05294 51.33449 78.83829 85.77728 81.68464
[7] 88.20615 91.04633 NA 84.53200 96.31192 115.84129
[13] 100.58536 46.84648 35.07172 27.70364 64.31899 65.53355
[19] 98.48476 22.63362
> colSd(tmp5)
[1] 127.298986 6.712149 7.164809 8.879093 9.261602 9.037956
[7] 9.391813 9.541820 NA 9.194129 9.813864 10.762959
[13] 10.029225 6.844449 5.922138 5.263424 8.019912 8.095279
[19] 9.923949 4.757480
> colMax(tmp5)
[1] 469.57800 76.55843 84.78840 80.78522 88.45784 82.22152 85.98387
[8] 83.75871 NA 87.62746 83.67418 90.28333 92.02253 81.67371
[15] 81.78485 79.18336 80.56712 81.00825 86.37417 74.54043
> colMin(tmp5)
[1] 56.62179 59.22313 63.17645 53.72980 56.90451 56.63783 61.19134 53.63673
[9] NA 59.02096 57.30193 54.16950 60.59602 59.32319 61.73928 63.33402
[17] 55.19159 57.42536 57.03415 61.07226
>
> Max(tmp5,na.rm=TRUE)
[1] 469.578
> Min(tmp5,na.rm=TRUE)
[1] 53.63673
> mean(tmp5,na.rm=TRUE)
[1] 72.74911
> Sum(tmp5,na.rm=TRUE)
[1] 14477.07
> Var(tmp5,na.rm=TRUE)
[1] 867.5929
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.94741 72.39226 70.23901 71.17389 70.89252 70.77664 69.88070 70.55349
[9] 71.54842 67.94331
> rowSums(tmp5,na.rm=TRUE)
[1] 1838.948 1447.845 1404.780 1423.478 1417.850 1415.533 1327.733 1411.070
[9] 1430.968 1358.866
> rowVars(tmp5,na.rm=TRUE)
[1] 7991.43730 81.68817 90.94851 59.55089 49.62955 109.09749
[7] 42.08201 44.09825 53.24438 77.46335
> rowSd(tmp5,na.rm=TRUE)
[1] 89.394839 9.038151 9.536693 7.716922 7.044824 10.444974 6.487064
[8] 6.640651 7.296875 8.801327
> rowMax(tmp5,na.rm=TRUE)
[1] 469.57800 87.82566 86.37417 82.52209 82.91594 88.45784 81.78485
[8] 80.84842 84.98416 90.28333
> rowMin(tmp5,na.rm=TRUE)
[1] 53.72980 54.16950 56.63783 53.63673 56.62179 56.44691 59.04265 57.30193
[9] 61.19134 55.19159
>
> colMeans(tmp5,na.rm=TRUE)
[1] 107.94324 68.26354 70.91157 69.68689 73.71815 70.01564 72.29865
[8] 72.11887 69.70742 73.16610 69.22035 73.84820 71.32267 69.79337
[15] 71.60844 70.66987 70.80054 66.30276 72.30605 70.97564
> colSums(tmp5,na.rm=TRUE)
[1] 1079.4324 682.6354 709.1157 696.8689 737.1815 700.1564 722.9865
[8] 721.1887 627.3668 731.6610 692.2035 738.4820 713.2267 697.9337
[15] 716.0844 706.6987 708.0054 663.0276 723.0605 709.7564
> colVars(tmp5,na.rm=TRUE)
[1] 16205.03175 45.05294 51.33449 78.83829 85.77728 81.68464
[7] 88.20615 91.04633 92.78341 84.53200 96.31192 115.84129
[13] 100.58536 46.84648 35.07172 27.70364 64.31899 65.53355
[19] 98.48476 22.63362
> colSd(tmp5,na.rm=TRUE)
[1] 127.298986 6.712149 7.164809 8.879093 9.261602 9.037956
[7] 9.391813 9.541820 9.632414 9.194129 9.813864 10.762959
[13] 10.029225 6.844449 5.922138 5.263424 8.019912 8.095279
[19] 9.923949 4.757480
> colMax(tmp5,na.rm=TRUE)
[1] 469.57800 76.55843 84.78840 80.78522 88.45784 82.22152 85.98387
[8] 83.75871 87.82566 87.62746 83.67418 90.28333 92.02253 81.67371
[15] 81.78485 79.18336 80.56712 81.00825 86.37417 74.54043
> colMin(tmp5,na.rm=TRUE)
[1] 56.62179 59.22313 63.17645 53.72980 56.90451 56.63783 61.19134 53.63673
[9] 57.04308 59.02096 57.30193 54.16950 60.59602 59.32319 61.73928 63.33402
[17] 55.19159 57.42536 57.03415 61.07226
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.94741 72.39226 70.23901 71.17389 70.89252 70.77664 NaN 70.55349
[9] 71.54842 67.94331
> rowSums(tmp5,na.rm=TRUE)
[1] 1838.948 1447.845 1404.780 1423.478 1417.850 1415.533 0.000 1411.070
[9] 1430.968 1358.866
> rowVars(tmp5,na.rm=TRUE)
[1] 7991.43730 81.68817 90.94851 59.55089 49.62955 109.09749
[7] NA 44.09825 53.24438 77.46335
> rowSd(tmp5,na.rm=TRUE)
[1] 89.394839 9.038151 9.536693 7.716922 7.044824 10.444974 NA
[8] 6.640651 7.296875 8.801327
> rowMax(tmp5,na.rm=TRUE)
[1] 469.57800 87.82566 86.37417 82.52209 82.91594 88.45784 NA
[8] 80.84842 84.98416 90.28333
> rowMin(tmp5,na.rm=TRUE)
[1] 53.72980 54.16950 56.63783 53.63673 56.62179 56.44691 NA 57.30193
[9] 61.19134 55.19159
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 113.08230 67.37926 71.55379 69.83234 74.13601 70.15653 73.25076
[8] 73.25299 NaN 73.07199 70.35121 73.21192 70.85499 69.75013
[15] 70.47773 70.22190 71.40471 65.65222 71.91871 71.77074
> colSums(tmp5,na.rm=TRUE)
[1] 1017.7407 606.4134 643.9841 628.4910 667.2241 631.4088 659.2568
[8] 659.2769 0.0000 657.6479 633.1609 658.9073 637.6949 627.7512
[15] 634.2996 631.9971 642.6424 590.8700 647.2684 645.9367
> colVars(tmp5,na.rm=TRUE)
[1] 17933.54802 41.88765 53.11122 88.45508 94.53513 91.67192
[7] 89.03379 87.95709 NA 94.99885 93.96402 125.76685
[13] 110.69787 52.68125 25.07246 28.90905 68.25243 68.96431
[19] 109.10757 18.35076
> colSd(tmp5,na.rm=TRUE)
[1] 133.916198 6.472067 7.287745 9.405056 9.722918 9.574545
[7] 9.435772 9.378544 NA 9.746735 9.693504 11.214582
[13] 10.521306 7.258185 5.007241 5.376714 8.261503 8.304475
[19] 10.445457 4.283778
> colMax(tmp5,na.rm=TRUE)
[1] 469.57800 76.55843 84.78840 80.78522 88.45784 82.22152 85.98387
[8] 83.75871 -Inf 87.62746 83.67418 90.28333 92.02253 81.67371
[15] 76.20246 79.18336 80.56712 81.00825 86.37417 74.54043
> colMin(tmp5,na.rm=TRUE)
[1] 56.62179 59.22313 63.17645 53.72980 56.90451 56.63783 61.19134 53.63673
[9] Inf 59.02096 57.30193 54.16950 60.59602 59.32319 61.73928 63.33402
[17] 55.19159 57.42536 57.03415 61.07226
>
>
>
>
> 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] 170.1898 218.7582 270.9490 253.8147 159.8183 173.6181 235.0807 261.2088
[9] 248.8481 210.1361
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 170.1898 218.7582 270.9490 253.8147 159.8183 173.6181 235.0807 261.2088
[9] 248.8481 210.1361
>
>
>
> 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] 1.136868e-13 0.000000e+00 -3.552714e-14 4.263256e-14 -5.684342e-14
[6] 5.684342e-14 -4.263256e-14 0.000000e+00 1.847411e-13 1.421085e-13
[11] -1.136868e-13 5.684342e-14 0.000000e+00 0.000000e+00 -1.136868e-13
[16] -2.842171e-14 5.684342e-14 -5.684342e-14 2.842171e-14 2.842171e-13
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
7 7
1 13
8 16
8 3
9 14
6 12
10 12
4 1
2 20
7 9
2 12
9 12
6 11
3 18
5 20
8 5
2 20
4 11
6 15
4 14
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] 2.270706
> Min(tmp)
[1] -2.597547
> mean(tmp)
[1] 0.0009744189
> Sum(tmp)
[1] 0.09744189
> Var(tmp)
[1] 1.259551
>
> rowMeans(tmp)
[1] 0.0009744189
> rowSums(tmp)
[1] 0.09744189
> rowVars(tmp)
[1] 1.259551
> rowSd(tmp)
[1] 1.122297
> rowMax(tmp)
[1] 2.270706
> rowMin(tmp)
[1] -2.597547
>
> colMeans(tmp)
[1] -0.17913029 0.65885809 -0.53369404 -0.45904651 -1.23235925 0.72302756
[7] 1.51197171 -0.97814874 -1.49906167 1.78887163 0.62658924 -0.40186984
[13] -1.23019400 -1.31834686 0.38015897 0.54718447 1.95517573 -0.48035954
[19] 0.57707154 -0.64405769 -1.32496136 0.96095710 -2.51996993 -1.84070013
[25] 1.50144188 -0.51366059 0.65458830 -0.97309233 -0.59686345 -0.04739436
[31] -0.86622362 0.56606649 0.08128688 1.80848808 -1.40045187 -0.60098368
[37] 1.12563736 0.17197510 -0.29662298 -2.59754746 1.39653348 0.81321568
[43] 0.18871536 -0.92502935 -0.64254280 1.65744993 1.97259252 0.58661336
[49] -0.39258001 0.65862643 1.41316227 -0.76551376 0.50446039 -0.21221513
[55] 0.42926184 0.18369927 -2.14729646 2.06200869 -0.42159544 0.89161370
[61] 0.12948989 1.66554390 0.43428688 -1.24428562 1.07751734 -1.04302969
[67] -1.17981402 1.50650856 0.53981802 0.58566260 -1.86998668 -0.65951885
[73] -1.30901810 0.84759173 0.09264923 0.16741164 1.14858364 -1.05938782
[79] 1.26239208 0.54281986 -0.08309549 -1.09160543 -0.30360574 0.90530081
[85] 1.31972215 2.02077159 0.99016623 -1.69386097 -0.31124920 -1.96310380
[91] -0.23829587 -0.63527642 0.93391882 -0.35037317 -0.73111386 -1.40560905
[97] -1.04377703 -0.55097103 0.06776898 2.27070591
> colSums(tmp)
[1] -0.17913029 0.65885809 -0.53369404 -0.45904651 -1.23235925 0.72302756
[7] 1.51197171 -0.97814874 -1.49906167 1.78887163 0.62658924 -0.40186984
[13] -1.23019400 -1.31834686 0.38015897 0.54718447 1.95517573 -0.48035954
[19] 0.57707154 -0.64405769 -1.32496136 0.96095710 -2.51996993 -1.84070013
[25] 1.50144188 -0.51366059 0.65458830 -0.97309233 -0.59686345 -0.04739436
[31] -0.86622362 0.56606649 0.08128688 1.80848808 -1.40045187 -0.60098368
[37] 1.12563736 0.17197510 -0.29662298 -2.59754746 1.39653348 0.81321568
[43] 0.18871536 -0.92502935 -0.64254280 1.65744993 1.97259252 0.58661336
[49] -0.39258001 0.65862643 1.41316227 -0.76551376 0.50446039 -0.21221513
[55] 0.42926184 0.18369927 -2.14729646 2.06200869 -0.42159544 0.89161370
[61] 0.12948989 1.66554390 0.43428688 -1.24428562 1.07751734 -1.04302969
[67] -1.17981402 1.50650856 0.53981802 0.58566260 -1.86998668 -0.65951885
[73] -1.30901810 0.84759173 0.09264923 0.16741164 1.14858364 -1.05938782
[79] 1.26239208 0.54281986 -0.08309549 -1.09160543 -0.30360574 0.90530081
[85] 1.31972215 2.02077159 0.99016623 -1.69386097 -0.31124920 -1.96310380
[91] -0.23829587 -0.63527642 0.93391882 -0.35037317 -0.73111386 -1.40560905
[97] -1.04377703 -0.55097103 0.06776898 2.27070591
> 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] -0.17913029 0.65885809 -0.53369404 -0.45904651 -1.23235925 0.72302756
[7] 1.51197171 -0.97814874 -1.49906167 1.78887163 0.62658924 -0.40186984
[13] -1.23019400 -1.31834686 0.38015897 0.54718447 1.95517573 -0.48035954
[19] 0.57707154 -0.64405769 -1.32496136 0.96095710 -2.51996993 -1.84070013
[25] 1.50144188 -0.51366059 0.65458830 -0.97309233 -0.59686345 -0.04739436
[31] -0.86622362 0.56606649 0.08128688 1.80848808 -1.40045187 -0.60098368
[37] 1.12563736 0.17197510 -0.29662298 -2.59754746 1.39653348 0.81321568
[43] 0.18871536 -0.92502935 -0.64254280 1.65744993 1.97259252 0.58661336
[49] -0.39258001 0.65862643 1.41316227 -0.76551376 0.50446039 -0.21221513
[55] 0.42926184 0.18369927 -2.14729646 2.06200869 -0.42159544 0.89161370
[61] 0.12948989 1.66554390 0.43428688 -1.24428562 1.07751734 -1.04302969
[67] -1.17981402 1.50650856 0.53981802 0.58566260 -1.86998668 -0.65951885
[73] -1.30901810 0.84759173 0.09264923 0.16741164 1.14858364 -1.05938782
[79] 1.26239208 0.54281986 -0.08309549 -1.09160543 -0.30360574 0.90530081
[85] 1.31972215 2.02077159 0.99016623 -1.69386097 -0.31124920 -1.96310380
[91] -0.23829587 -0.63527642 0.93391882 -0.35037317 -0.73111386 -1.40560905
[97] -1.04377703 -0.55097103 0.06776898 2.27070591
> colMin(tmp)
[1] -0.17913029 0.65885809 -0.53369404 -0.45904651 -1.23235925 0.72302756
[7] 1.51197171 -0.97814874 -1.49906167 1.78887163 0.62658924 -0.40186984
[13] -1.23019400 -1.31834686 0.38015897 0.54718447 1.95517573 -0.48035954
[19] 0.57707154 -0.64405769 -1.32496136 0.96095710 -2.51996993 -1.84070013
[25] 1.50144188 -0.51366059 0.65458830 -0.97309233 -0.59686345 -0.04739436
[31] -0.86622362 0.56606649 0.08128688 1.80848808 -1.40045187 -0.60098368
[37] 1.12563736 0.17197510 -0.29662298 -2.59754746 1.39653348 0.81321568
[43] 0.18871536 -0.92502935 -0.64254280 1.65744993 1.97259252 0.58661336
[49] -0.39258001 0.65862643 1.41316227 -0.76551376 0.50446039 -0.21221513
[55] 0.42926184 0.18369927 -2.14729646 2.06200869 -0.42159544 0.89161370
[61] 0.12948989 1.66554390 0.43428688 -1.24428562 1.07751734 -1.04302969
[67] -1.17981402 1.50650856 0.53981802 0.58566260 -1.86998668 -0.65951885
[73] -1.30901810 0.84759173 0.09264923 0.16741164 1.14858364 -1.05938782
[79] 1.26239208 0.54281986 -0.08309549 -1.09160543 -0.30360574 0.90530081
[85] 1.31972215 2.02077159 0.99016623 -1.69386097 -0.31124920 -1.96310380
[91] -0.23829587 -0.63527642 0.93391882 -0.35037317 -0.73111386 -1.40560905
[97] -1.04377703 -0.55097103 0.06776898 2.27070591
> colMedians(tmp)
[1] -0.17913029 0.65885809 -0.53369404 -0.45904651 -1.23235925 0.72302756
[7] 1.51197171 -0.97814874 -1.49906167 1.78887163 0.62658924 -0.40186984
[13] -1.23019400 -1.31834686 0.38015897 0.54718447 1.95517573 -0.48035954
[19] 0.57707154 -0.64405769 -1.32496136 0.96095710 -2.51996993 -1.84070013
[25] 1.50144188 -0.51366059 0.65458830 -0.97309233 -0.59686345 -0.04739436
[31] -0.86622362 0.56606649 0.08128688 1.80848808 -1.40045187 -0.60098368
[37] 1.12563736 0.17197510 -0.29662298 -2.59754746 1.39653348 0.81321568
[43] 0.18871536 -0.92502935 -0.64254280 1.65744993 1.97259252 0.58661336
[49] -0.39258001 0.65862643 1.41316227 -0.76551376 0.50446039 -0.21221513
[55] 0.42926184 0.18369927 -2.14729646 2.06200869 -0.42159544 0.89161370
[61] 0.12948989 1.66554390 0.43428688 -1.24428562 1.07751734 -1.04302969
[67] -1.17981402 1.50650856 0.53981802 0.58566260 -1.86998668 -0.65951885
[73] -1.30901810 0.84759173 0.09264923 0.16741164 1.14858364 -1.05938782
[79] 1.26239208 0.54281986 -0.08309549 -1.09160543 -0.30360574 0.90530081
[85] 1.31972215 2.02077159 0.99016623 -1.69386097 -0.31124920 -1.96310380
[91] -0.23829587 -0.63527642 0.93391882 -0.35037317 -0.73111386 -1.40560905
[97] -1.04377703 -0.55097103 0.06776898 2.27070591
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.1791303 0.6588581 -0.533694 -0.4590465 -1.232359 0.7230276 1.511972
[2,] -0.1791303 0.6588581 -0.533694 -0.4590465 -1.232359 0.7230276 1.511972
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.9781487 -1.499062 1.788872 0.6265892 -0.4018698 -1.230194 -1.318347
[2,] -0.9781487 -1.499062 1.788872 0.6265892 -0.4018698 -1.230194 -1.318347
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.380159 0.5471845 1.955176 -0.4803595 0.5770715 -0.6440577 -1.324961
[2,] 0.380159 0.5471845 1.955176 -0.4803595 0.5770715 -0.6440577 -1.324961
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.9609571 -2.51997 -1.8407 1.501442 -0.5136606 0.6545883 -0.9730923
[2,] 0.9609571 -2.51997 -1.8407 1.501442 -0.5136606 0.6545883 -0.9730923
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.5968634 -0.04739436 -0.8662236 0.5660665 0.08128688 1.808488 -1.400452
[2,] -0.5968634 -0.04739436 -0.8662236 0.5660665 0.08128688 1.808488 -1.400452
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.6009837 1.125637 0.1719751 -0.296623 -2.597547 1.396533 0.8132157
[2,] -0.6009837 1.125637 0.1719751 -0.296623 -2.597547 1.396533 0.8132157
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.1887154 -0.9250293 -0.6425428 1.65745 1.972593 0.5866134 -0.39258
[2,] 0.1887154 -0.9250293 -0.6425428 1.65745 1.972593 0.5866134 -0.39258
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.6586264 1.413162 -0.7655138 0.5044604 -0.2122151 0.4292618 0.1836993
[2,] 0.6586264 1.413162 -0.7655138 0.5044604 -0.2122151 0.4292618 0.1836993
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -2.147296 2.062009 -0.4215954 0.8916137 0.1294899 1.665544 0.4342869
[2,] -2.147296 2.062009 -0.4215954 0.8916137 0.1294899 1.665544 0.4342869
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -1.244286 1.077517 -1.04303 -1.179814 1.506509 0.539818 0.5856626
[2,] -1.244286 1.077517 -1.04303 -1.179814 1.506509 0.539818 0.5856626
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.869987 -0.6595189 -1.309018 0.8475917 0.09264923 0.1674116 1.148584
[2,] -1.869987 -0.6595189 -1.309018 0.8475917 0.09264923 0.1674116 1.148584
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.059388 1.262392 0.5428199 -0.08309549 -1.091605 -0.3036057 0.9053008
[2,] -1.059388 1.262392 0.5428199 -0.08309549 -1.091605 -0.3036057 0.9053008
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 1.319722 2.020772 0.9901662 -1.693861 -0.3112492 -1.963104 -0.2382959
[2,] 1.319722 2.020772 0.9901662 -1.693861 -0.3112492 -1.963104 -0.2382959
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.6352764 0.9339188 -0.3503732 -0.7311139 -1.405609 -1.043777 -0.550971
[2,] -0.6352764 0.9339188 -0.3503732 -0.7311139 -1.405609 -1.043777 -0.550971
[,99] [,100]
[1,] 0.06776898 2.270706
[2,] 0.06776898 2.270706
>
>
> Max(tmp2)
[1] 1.746526
> Min(tmp2)
[1] -2.673062
> mean(tmp2)
[1] -0.1308301
> Sum(tmp2)
[1] -13.08301
> Var(tmp2)
[1] 0.8931725
>
> rowMeans(tmp2)
[1] 3.858641e-01 1.619721e+00 1.746526e+00 -1.417940e+00 -2.370330e+00
[6] 5.944804e-01 -2.013676e+00 -6.149356e-01 4.144252e-01 7.464354e-02
[11] -9.705934e-01 -1.909176e+00 -5.568803e-01 -7.167668e-01 -5.292290e-01
[16] 8.557351e-01 -4.582693e-01 5.582048e-01 6.629538e-01 -9.340223e-01
[21] 7.972077e-01 -2.058545e+00 1.828682e-01 8.418722e-01 -1.352056e+00
[26] -4.299695e-01 -2.673062e+00 4.767215e-03 4.652389e-01 -1.997644e-01
[31] 7.793827e-01 5.410987e-01 7.936509e-01 6.560559e-01 -7.651179e-01
[36] 4.653154e-01 -9.030531e-01 1.856543e-01 8.196208e-05 -1.559462e-01
[41] 4.294476e-01 -1.235964e+00 1.040592e+00 -3.234893e-01 -2.048398e+00
[46] 6.196489e-01 4.256485e-01 -3.791503e-02 6.978660e-01 5.405540e-02
[51] -1.298972e+00 -5.283295e-01 1.183029e+00 1.148859e-01 -2.347056e+00
[56] -3.232798e-01 -9.319883e-01 -3.810943e-01 4.148422e-01 -3.681987e-01
[61] -5.399368e-01 2.709758e-01 2.462084e-01 8.062316e-01 -4.519421e-01
[66] -4.534202e-01 1.601833e+00 -3.684354e-01 -1.944407e-01 -1.234179e+00
[71] 1.156988e+00 3.587568e-01 -2.349249e-01 -3.760873e-01 -6.120112e-01
[76] -1.322644e+00 -1.236821e+00 2.585833e-01 7.139903e-02 8.677318e-01
[81] -1.268125e-01 -6.847910e-01 6.649586e-01 -1.272895e+00 1.244573e+00
[86] -1.302930e-01 -5.171878e-02 9.254684e-01 6.910573e-01 -6.572820e-01
[91] -1.726795e-01 -6.249220e-01 5.392100e-01 1.020831e+00 -8.903763e-01
[96] 1.282430e+00 1.437504e+00 5.091749e-02 -1.504226e+00 -1.895779e-01
> rowSums(tmp2)
[1] 3.858641e-01 1.619721e+00 1.746526e+00 -1.417940e+00 -2.370330e+00
[6] 5.944804e-01 -2.013676e+00 -6.149356e-01 4.144252e-01 7.464354e-02
[11] -9.705934e-01 -1.909176e+00 -5.568803e-01 -7.167668e-01 -5.292290e-01
[16] 8.557351e-01 -4.582693e-01 5.582048e-01 6.629538e-01 -9.340223e-01
[21] 7.972077e-01 -2.058545e+00 1.828682e-01 8.418722e-01 -1.352056e+00
[26] -4.299695e-01 -2.673062e+00 4.767215e-03 4.652389e-01 -1.997644e-01
[31] 7.793827e-01 5.410987e-01 7.936509e-01 6.560559e-01 -7.651179e-01
[36] 4.653154e-01 -9.030531e-01 1.856543e-01 8.196208e-05 -1.559462e-01
[41] 4.294476e-01 -1.235964e+00 1.040592e+00 -3.234893e-01 -2.048398e+00
[46] 6.196489e-01 4.256485e-01 -3.791503e-02 6.978660e-01 5.405540e-02
[51] -1.298972e+00 -5.283295e-01 1.183029e+00 1.148859e-01 -2.347056e+00
[56] -3.232798e-01 -9.319883e-01 -3.810943e-01 4.148422e-01 -3.681987e-01
[61] -5.399368e-01 2.709758e-01 2.462084e-01 8.062316e-01 -4.519421e-01
[66] -4.534202e-01 1.601833e+00 -3.684354e-01 -1.944407e-01 -1.234179e+00
[71] 1.156988e+00 3.587568e-01 -2.349249e-01 -3.760873e-01 -6.120112e-01
[76] -1.322644e+00 -1.236821e+00 2.585833e-01 7.139903e-02 8.677318e-01
[81] -1.268125e-01 -6.847910e-01 6.649586e-01 -1.272895e+00 1.244573e+00
[86] -1.302930e-01 -5.171878e-02 9.254684e-01 6.910573e-01 -6.572820e-01
[91] -1.726795e-01 -6.249220e-01 5.392100e-01 1.020831e+00 -8.903763e-01
[96] 1.282430e+00 1.437504e+00 5.091749e-02 -1.504226e+00 -1.895779e-01
> 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] 3.858641e-01 1.619721e+00 1.746526e+00 -1.417940e+00 -2.370330e+00
[6] 5.944804e-01 -2.013676e+00 -6.149356e-01 4.144252e-01 7.464354e-02
[11] -9.705934e-01 -1.909176e+00 -5.568803e-01 -7.167668e-01 -5.292290e-01
[16] 8.557351e-01 -4.582693e-01 5.582048e-01 6.629538e-01 -9.340223e-01
[21] 7.972077e-01 -2.058545e+00 1.828682e-01 8.418722e-01 -1.352056e+00
[26] -4.299695e-01 -2.673062e+00 4.767215e-03 4.652389e-01 -1.997644e-01
[31] 7.793827e-01 5.410987e-01 7.936509e-01 6.560559e-01 -7.651179e-01
[36] 4.653154e-01 -9.030531e-01 1.856543e-01 8.196208e-05 -1.559462e-01
[41] 4.294476e-01 -1.235964e+00 1.040592e+00 -3.234893e-01 -2.048398e+00
[46] 6.196489e-01 4.256485e-01 -3.791503e-02 6.978660e-01 5.405540e-02
[51] -1.298972e+00 -5.283295e-01 1.183029e+00 1.148859e-01 -2.347056e+00
[56] -3.232798e-01 -9.319883e-01 -3.810943e-01 4.148422e-01 -3.681987e-01
[61] -5.399368e-01 2.709758e-01 2.462084e-01 8.062316e-01 -4.519421e-01
[66] -4.534202e-01 1.601833e+00 -3.684354e-01 -1.944407e-01 -1.234179e+00
[71] 1.156988e+00 3.587568e-01 -2.349249e-01 -3.760873e-01 -6.120112e-01
[76] -1.322644e+00 -1.236821e+00 2.585833e-01 7.139903e-02 8.677318e-01
[81] -1.268125e-01 -6.847910e-01 6.649586e-01 -1.272895e+00 1.244573e+00
[86] -1.302930e-01 -5.171878e-02 9.254684e-01 6.910573e-01 -6.572820e-01
[91] -1.726795e-01 -6.249220e-01 5.392100e-01 1.020831e+00 -8.903763e-01
[96] 1.282430e+00 1.437504e+00 5.091749e-02 -1.504226e+00 -1.895779e-01
> rowMin(tmp2)
[1] 3.858641e-01 1.619721e+00 1.746526e+00 -1.417940e+00 -2.370330e+00
[6] 5.944804e-01 -2.013676e+00 -6.149356e-01 4.144252e-01 7.464354e-02
[11] -9.705934e-01 -1.909176e+00 -5.568803e-01 -7.167668e-01 -5.292290e-01
[16] 8.557351e-01 -4.582693e-01 5.582048e-01 6.629538e-01 -9.340223e-01
[21] 7.972077e-01 -2.058545e+00 1.828682e-01 8.418722e-01 -1.352056e+00
[26] -4.299695e-01 -2.673062e+00 4.767215e-03 4.652389e-01 -1.997644e-01
[31] 7.793827e-01 5.410987e-01 7.936509e-01 6.560559e-01 -7.651179e-01
[36] 4.653154e-01 -9.030531e-01 1.856543e-01 8.196208e-05 -1.559462e-01
[41] 4.294476e-01 -1.235964e+00 1.040592e+00 -3.234893e-01 -2.048398e+00
[46] 6.196489e-01 4.256485e-01 -3.791503e-02 6.978660e-01 5.405540e-02
[51] -1.298972e+00 -5.283295e-01 1.183029e+00 1.148859e-01 -2.347056e+00
[56] -3.232798e-01 -9.319883e-01 -3.810943e-01 4.148422e-01 -3.681987e-01
[61] -5.399368e-01 2.709758e-01 2.462084e-01 8.062316e-01 -4.519421e-01
[66] -4.534202e-01 1.601833e+00 -3.684354e-01 -1.944407e-01 -1.234179e+00
[71] 1.156988e+00 3.587568e-01 -2.349249e-01 -3.760873e-01 -6.120112e-01
[76] -1.322644e+00 -1.236821e+00 2.585833e-01 7.139903e-02 8.677318e-01
[81] -1.268125e-01 -6.847910e-01 6.649586e-01 -1.272895e+00 1.244573e+00
[86] -1.302930e-01 -5.171878e-02 9.254684e-01 6.910573e-01 -6.572820e-01
[91] -1.726795e-01 -6.249220e-01 5.392100e-01 1.020831e+00 -8.903763e-01
[96] 1.282430e+00 1.437504e+00 5.091749e-02 -1.504226e+00 -1.895779e-01
>
> colMeans(tmp2)
[1] -0.1308301
> colSums(tmp2)
[1] -13.08301
> colVars(tmp2)
[1] 0.8931725
> colSd(tmp2)
[1] 0.9450781
> colMax(tmp2)
[1] 1.746526
> colMin(tmp2)
[1] -2.673062
> colMedians(tmp2)
[1] -0.08926566
> colRanges(tmp2)
[,1]
[1,] -2.673062
[2,] 1.746526
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.00156797 1.80993888 2.67077127 -10.69021644 1.68514255
[6] 0.04959628 -0.29200559 -5.20698967 5.34718044 -0.39572558
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.1827843
[2,] -0.6624793
[3,] -0.1484910
[4,] 0.1133019
[5,] 0.9481356
>
> rowApply(tmp,sum)
[1] -4.1979724 -0.3522029 -3.3223195 4.2121780 -2.5301568 0.4902081
[7] -0.3940919 -1.4552461 -4.3467831 4.8725106
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 5 8 3 3 6 2 6 5 9 1
[2,] 2 2 10 10 2 7 3 9 10 7
[3,] 3 10 7 2 8 8 10 7 3 6
[4,] 1 1 4 1 1 6 4 2 6 9
[5,] 9 3 9 8 3 4 7 8 5 2
[6,] 6 5 8 7 5 10 5 6 1 4
[7,] 4 6 6 9 9 3 1 1 8 8
[8,] 7 4 2 4 4 1 9 3 4 5
[9,] 10 7 5 5 10 5 8 10 7 3
[10,] 8 9 1 6 7 9 2 4 2 10
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.26103993 1.22629817 2.09406050 -0.22959782 -1.58446985 -0.66658633
[7] 0.47909407 -2.07026370 0.65197412 2.72275277 3.70606687 -2.11866603
[13] -0.83508019 0.50233007 2.38300342 -0.09115523 -1.30302357 -2.82619922
[19] -3.90189077 3.66734138
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.2615561
[2,] -0.6784983
[3,] -0.6404975
[4,] -0.2446615
[5,] 1.5641735
>
> rowApply(tmp,sum)
[1] -6.608518 1.484624 -3.342145 5.873714 3.137274
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 10 19 5 6 5
[2,] 15 15 8 8 15
[3,] 12 20 6 5 20
[4,] 19 9 4 19 3
[5,] 7 2 13 12 10
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.6784983 0.23327274 -0.2226886 1.0389990 -0.85285273 -1.1478244
[2,] 1.5641735 1.00950076 1.7076713 -0.4754941 -1.27794059 1.1970888
[3,] -1.2615561 -0.71145027 -0.8414850 -1.2772557 -0.01583927 -1.5414024
[4,] -0.2446615 0.02695701 -0.2805738 1.6576339 0.37673889 0.3949809
[5,] -0.6404975 0.66801793 1.7311366 -1.1734809 0.18542385 0.4305707
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.05490519 -0.8537526 0.1498426 1.2983367 0.7525778 -1.7147034
[2,] -0.79642955 -0.4805707 -0.8713207 -0.7827037 -0.1876567 1.4416776
[3,] -0.76304719 -0.2891381 1.1010779 1.3298972 -0.3708715 -1.4286698
[4,] 1.32589937 0.8063590 -0.3503557 1.0798703 2.1453040 -0.7541734
[5,] 0.76757663 -1.2531612 0.6227301 -0.2026478 1.3667132 0.3372030
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.8334487 -0.4054984 1.0172664 -0.70245264 -0.86096727 -2.08652614
[2,] -0.4808546 -0.2794579 1.3343058 -0.76304590 -1.34722999 0.56695886
[3,] -0.5963183 1.0294396 1.1382524 0.40099633 1.69305103 -0.04135345
[4,] 0.8221100 0.3845336 -0.2402108 0.02873357 -0.85633332 0.26557076
[5,] 0.2534315 -0.2266868 -0.8666103 0.94461341 0.06845597 -1.53084925
[,19] [,20]
[1,] -1.48105206 0.7963568
[2,] -0.14472252 0.5506741
[3,] -1.32574797 0.4292757
[4,] -0.99027493 0.2756066
[5,] 0.03990672 1.6154283
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-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-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 652 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-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 -0.5645488 -1.220748 -0.4537028 -2.961407 -0.4214979 1.101894 -1.918756
col8 col9 col10 col11 col12 col13 col14 col15
row1 1.719162 1.738465 1.173142 0.1064714 1.398459 0.1071391 0.7656237 1.661827
col16 col17 col18 col19 col20
row1 -0.155351 0.8961089 -0.4084821 -0.02562199 -1.636817
> tmp[,"col10"]
col10
row1 1.173141992
row2 -1.066663426
row3 0.285632152
row4 0.002733051
row5 -0.960884164
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -0.5645488 -1.220748 -0.453702786 -2.9614068 -0.4214979 1.1018941
row5 0.7725137 -1.541792 -0.005883233 -0.5357445 -0.1786832 -0.5189345
col7 col8 col9 col10 col11 col12 col13
row1 -1.91875616 1.719162 1.7384647 1.1731420 0.1064714 1.398459 0.1071391
row5 0.07787817 -1.005118 -0.2264344 -0.9608842 -0.1130470 -1.007701 0.7994430
col14 col15 col16 col17 col18 col19
row1 0.7656237 1.6618266 -0.1553510 0.8961089 -0.4084821379 -0.02562199
row5 0.6441422 0.3807968 0.4980107 -0.8445696 -0.0007572463 -0.85394328
col20
row1 -1.6368166
row5 0.9737929
> tmp[,c("col6","col20")]
col6 col20
row1 1.10189406 -1.6368166
row2 -0.37913551 -0.3925038
row3 0.05958938 0.7642195
row4 -0.12022385 -1.5341709
row5 -0.51893447 0.9737929
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 1.1018941 -1.6368166
row5 -0.5189345 0.9737929
>
>
>
>
> 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 49.56799 49.2134 48.92857 50.67056 48.32524 105.3726 49.33985 49.98765
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.92564 50.56615 50.93977 51.41769 48.52127 49.14028 49.69006 48.56717
col17 col18 col19 col20
row1 50.78182 49.60974 49.92146 105.0127
> tmp[,"col10"]
col10
row1 50.56615
row2 28.40475
row3 30.82845
row4 29.55063
row5 50.99999
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.56799 49.21340 48.92857 50.67056 48.32524 105.3726 49.33985 49.98765
row5 49.93904 48.50246 51.19993 50.36403 49.83399 104.4019 52.24712 49.80817
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.92564 50.56615 50.93977 51.41769 48.52127 49.14028 49.69006 48.56717
row5 49.43924 50.99999 50.70652 50.43036 48.91645 50.63135 50.17556 49.20719
col17 col18 col19 col20
row1 50.78182 49.60974 49.92146 105.0127
row5 50.45185 51.98883 49.85115 105.0944
> tmp[,c("col6","col20")]
col6 col20
row1 105.37262 105.01267
row2 76.92105 74.81752
row3 73.45719 75.27659
row4 74.59306 75.81961
row5 104.40194 105.09438
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.3726 105.0127
row5 104.4019 105.0944
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.3726 105.0127
row5 104.4019 105.0944
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.1962776
[2,] 0.3914357
[3,] -0.1511086
[4,] 0.6844817
[5,] -0.2433633
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.2833688 -2.0432718
[2,] -0.0175350 0.6413176
[3,] 0.1508105 0.2359237
[4,] 0.7214196 -0.8416849
[5,] -0.1691560 0.9951240
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.6963820 0.3594457
[2,] 2.1605043 1.8912647
[3,] 1.0990996 -1.2560568
[4,] 0.3661544 0.1967333
[5,] 0.1830968 0.2385324
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.696382
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.696382
[2,] 2.160504
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 0.357462418 -0.03779598 -0.5811724 -1.188493 -0.1649985 -0.002053512
row1 0.001175732 0.90482873 0.3838776 1.115308 -0.5491493 -0.834067533
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.8297631 -0.5063651 -1.7668171 -0.6411599 -0.4640322 0.4347643 -2.246021
row1 -0.3902969 -1.6775313 0.6961772 1.0513656 0.3695795 1.4223950 0.353592
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 1.1678786 1.823644 0.1383263 1.105327 0.9787646 -0.5326735 0.3496535
row1 0.2137679 1.881822 0.5394174 -0.572164 1.3566367 -0.8621308 -0.2711682
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.650404 -0.4855045 -0.9101826 -0.05203287 -0.3023268 -1.435308 -0.5885178
[,8] [,9] [,10]
row2 -1.215372 0.9208791 -0.7610822
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.8606067 0.5098366 0.8795061 -0.4672874 -0.3822962 1.792888 0.3585347
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.353983 1.658272 -0.971786 -0.2791835 -0.4314227 -1.574451 0.4295808
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.623429 -1.08981 -0.1710165 -1.13607 -1.087032 -0.2635294
>
>
> 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: 0x5d81d3704290>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a124633d490"
[2] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a12327589fc"
[3] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a12388a0825"
[4] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a1245fecd2f"
[5] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a1212514037"
[6] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a129374684"
[7] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a122ff6a6f4"
[8] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a127f73cca0"
[9] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a121b640c8f"
[10] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a1246f5d281"
[11] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a126534d2e0"
[12] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a126c5acbc"
[13] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a12f50ea04"
[14] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a126a048cff"
[15] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c2a125c97a9f9"
>
>
> ### 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: 0x5d81d3afdcd0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5d81d3afdcd0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5d81d3afdcd0>
> rowMedians(tmp)
[1] 0.2160891674 -0.0670095762 -0.0081076590 0.1024692133 -0.0446868006
[6] -0.2191216715 -0.0564542444 0.2252997059 0.0173193834 -0.3508659707
[11] -0.0781161743 -0.0692039121 0.4102201855 0.0405840522 -0.3764197037
[16] -0.0514613730 -0.0016056658 0.5426806264 -0.1461302517 -0.0206732893
[21] -0.2804453059 -0.0101897707 0.2116087729 0.3678064149 -0.2701410690
[26] -0.2953857418 0.6938900781 -0.3927696611 -0.0921491742 -0.5913131688
[31] -0.0338324642 -0.1796601280 0.4025458074 0.0453955878 -0.2140990725
[36] 0.1662296530 0.4290664658 0.6409376837 0.3441876484 0.0672884074
[41] 0.2288339199 -0.0969824533 -0.6851242521 -0.0752300498 -0.2487788672
[46] 0.0580056924 0.4956461796 0.2722490612 -0.5399919413 -0.1810749447
[51] -0.1094179633 -0.3780823418 -0.4326907401 -0.3656406464 0.1350078827
[56] 0.0664000148 0.7870821304 0.0432434005 0.2125980342 0.1553809551
[61] 0.1030665924 -0.1878184076 0.5350291942 -0.2708712360 -0.4594914431
[66] 0.2388121191 -0.2981714829 0.2571951026 0.4376324891 -0.3745662043
[71] -0.2711344527 0.2484158794 -0.2519367801 -0.1646335867 0.8263057215
[76] -0.1062928487 -0.1204962168 -0.0682893515 0.2623884280 0.0955411539
[81] 0.6342637818 0.6052288353 0.4840036043 -0.2220683259 -0.2443223484
[86] -0.1498513544 0.3836467956 0.5109058150 -0.2615059045 -0.4857548527
[91] 0.2123379880 -0.1009831088 0.1957380122 -0.0429666966 0.0410819571
[96] 0.2378732168 -0.0226237559 0.0856499735 -0.3014037800 0.0246709160
[101] 0.4120798052 0.1984968911 0.0348956396 0.2636174929 -0.5040929387
[106] -0.5728667061 -0.1605734122 -0.1816006976 -0.1337897321 -0.3061513848
[111] 0.1617472219 -0.2296597726 -0.4182932250 0.1571289816 0.1558685963
[116] 0.0710199968 -0.6151533832 -0.1769368832 -0.4319160479 -0.2981838942
[121] 0.2284223174 -0.7929441440 0.1820142672 -0.4846848130 0.1154495047
[126] 0.3480156550 0.1186521218 -0.3559901680 -0.3932360501 0.1702110106
[131] -0.1631685785 -0.0700829210 -0.0318673200 -0.5261051449 -0.4985599181
[136] 0.1797339230 -0.1992798356 -0.3732467896 -0.2985247653 -0.4736348062
[141] 0.3169871577 -0.1163551649 -0.2716699510 -0.3465150423 -0.7635521090
[146] -0.0434152761 -0.2706434196 -0.0135726457 0.1057336147 -0.0104693172
[151] -0.6722707648 -0.5249571341 0.8388212632 -0.2776630393 0.0591540111
[156] -0.2425488462 0.0044285118 0.2276371779 0.1614059005 -0.7267595574
[161] -0.0577626162 0.1930372594 -0.1131761263 -0.5667548433 0.1218522156
[166] 0.1980784795 0.3533915069 -0.1593678626 -0.1862025526 -0.0080864305
[171] -0.3325075579 -0.0133209916 0.4094862172 0.2301169478 0.2268172030
[176] 0.0440982462 -0.0625470406 -0.1362874077 -0.7451278065 0.1133183081
[181] 0.5387783693 -0.3006692643 -0.1051884738 -0.2099458758 -0.1484834142
[186] -0.0222867267 -0.1052116098 -0.5257304184 -0.9177748046 0.3530404874
[191] 0.9658105535 -0.2593494869 -0.3126556068 -0.6687765958 -0.2709364672
[196] -0.4427834105 -0.0478847004 -0.5177682198 -0.2486567320 0.5063377415
[201] -0.0836715004 0.0883528373 -0.4712185167 0.5917496685 0.1995524697
[206] 0.4768429672 -0.2111314065 -0.4640041255 0.0354334318 -0.2411238379
[211] 0.6533141979 0.2521292325 -0.4668414974 -0.6171892588 -0.0569392805
[216] 0.1446938106 0.0463270933 0.0008338704 -0.1335492711 -0.3788424287
[221] 0.3996934770 0.2606597882 -0.3279831821 0.1444640344 0.0768539412
[226] 0.3862374058 0.0257812804 0.2009502847 -0.2413977778 0.0529790289
>
> proc.time()
user system elapsed
1.305 0.690 1.982
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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: 0x64e47cff6520>
> .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: 0x64e47cff6520>
> .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: 0x64e47cff6520>
> .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: 0x64e47cff6520>
> 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: 0x64e47cb9ff60>
> .Call("R_bm_AddColumn",P)
<pointer: 0x64e47cb9ff60>
> .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: 0x64e47cb9ff60>
> .Call("R_bm_AddColumn",P)
<pointer: 0x64e47cb9ff60>
> .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: 0x64e47cb9ff60>
> 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: 0x64e47d749b40>
> .Call("R_bm_AddColumn",P)
<pointer: 0x64e47d749b40>
> .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: 0x64e47d749b40>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x64e47d749b40>
> .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: 0x64e47d749b40>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x64e47d749b40>
> .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: 0x64e47d749b40>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x64e47d749b40>
> .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: 0x64e47d749b40>
> 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: 0x64e47d786bc0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x64e47d786bc0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x64e47d786bc0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x64e47d786bc0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1c2aa217e8b370" "BufferedMatrixFile1c2aa21df90517"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1c2aa217e8b370" "BufferedMatrixFile1c2aa21df90517"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x64e47d720000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x64e47d720000>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x64e47d720000>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x64e47d720000>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x64e47d720000>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x64e47d720000>
> .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: 0x64e47c853e30>
> .Call("R_bm_AddColumn",P)
<pointer: 0x64e47c853e30>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x64e47c853e30>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x64e47c853e30>
> 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: 0x64e47ce7da50>
> .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: 0x64e47ce7da50>
> rm(P)
>
> proc.time()
user system elapsed
0.259 0.054 0.302
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.260 0.042 0.290