Ben Bolstad
| Snapshot Date: 2026-02-20 13:40 -0500 (Fri, 20 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 2026-02-21 11:32 -0500 (Sat, 21 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: 2026-02-20 21:46:22 -0500 (Fri, 20 Feb 2026) |
| EndedAt: 2026-02-20 21:46:47 -0500 (Fri, 20 Feb 2026) |
| EllapsedTime: 25.1 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
0.242 0.047 0.279
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] "Fri Feb 20 21:46:37 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] "Fri Feb 20 21:46:37 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: 0x62c20c5b9c10>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri Feb 20 21:46:37 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] "Fri Feb 20 21:46:38 2026"
>
> ColMode(tmp2)
<pointer: 0x62c20c5b9c10>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 101.2912943 0.8172907 -2.2525284 -0.8946943
[2,] -1.1195739 -0.8965155 1.1208748 -0.2611970
[3,] 0.3915493 -1.5382065 -0.8864368 0.7788925
[4,] 0.1211340 -0.1521028 0.4889909 1.3887567
> 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,] 101.2912943 0.8172907 2.2525284 0.8946943
[2,] 1.1195739 0.8965155 1.1208748 0.2611970
[3,] 0.3915493 1.5382065 0.8864368 0.7788925
[4,] 0.1211340 0.1521028 0.4889909 1.3887567
> 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,] 10.064358 0.9040413 1.5008426 0.9458828
[2,] 1.058099 0.9468450 1.0587138 0.5110743
[3,] 0.625739 1.2402445 0.9415077 0.8825489
[4,] 0.348043 0.3900036 0.6992788 1.1784552
>
> 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,] 226.93487 34.85770 42.26095 35.35352
[2,] 36.70057 35.36497 36.70801 30.37194
[3,] 31.64894 38.94065 35.30151 34.60438
[4,] 28.60156 29.05214 32.48178 38.17331
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x62c20d0a4820>
> exp(tmp5)
<pointer: 0x62c20d0a4820>
> log(tmp5,2)
<pointer: 0x62c20d0a4820>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 472.3352
> Min(tmp5)
[1] 53.37656
> mean(tmp5)
[1] 72.10558
> Sum(tmp5)
[1] 14421.12
> Var(tmp5)
[1] 878.7599
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.01082 70.16462 71.38558 69.49321 67.16601 74.27930 68.31527 69.33122
[9] 69.85662 71.05318
> rowSums(tmp5)
[1] 1800.216 1403.292 1427.712 1389.864 1343.320 1485.586 1366.305 1386.624
[9] 1397.132 1421.064
> rowVars(tmp5)
[1] 8153.81309 52.58068 62.19987 87.84649 41.75433 92.06149
[7] 86.62507 80.37261 31.87205 105.18943
> rowSd(tmp5)
[1] 90.298467 7.251253 7.886689 9.372646 6.461759 9.594868 9.307259
[8] 8.965077 5.645534 10.256190
> rowMax(tmp5)
[1] 472.33520 80.16707 85.60661 84.17648 81.59565 90.33347 85.12766
[8] 85.52273 78.17520 88.25703
> rowMin(tmp5)
[1] 58.54860 56.96598 56.45025 55.70874 58.25840 62.27197 54.94860 53.37656
[9] 62.06999 54.96602
>
> colMeans(tmp5)
[1] 108.53431 70.89765 70.35522 69.72687 65.72513 72.14357 72.33990
[8] 67.27420 69.11321 67.50052 72.58019 70.96326 72.53302 69.77898
[15] 72.35466 75.43436 68.07572 70.90248 66.78001 69.09843
> colSums(tmp5)
[1] 1085.3431 708.9765 703.5522 697.2687 657.2513 721.4357 723.3990
[8] 672.7420 691.1321 675.0052 725.8019 709.6326 725.3302 697.7898
[15] 723.5466 754.3436 680.7572 709.0248 667.8001 690.9843
> colVars(tmp5)
[1] 16426.12643 63.77959 73.09417 52.88808 60.11686 49.39908
[7] 72.50046 65.02792 77.15656 33.71007 104.84730 93.51408
[13] 69.51652 41.55126 56.77500 92.63065 81.06283 73.85336
[19] 61.01613 109.72001
> colSd(tmp5)
[1] 128.164451 7.986213 8.549513 7.272419 7.753506 7.028448
[7] 8.514720 8.063989 8.783881 5.806037 10.239497 9.670268
[13] 8.337657 6.446027 7.534919 9.624482 9.003490 8.593798
[19] 7.811282 10.474732
> colMax(tmp5)
[1] 472.33520 81.04987 87.96064 79.45274 80.78816 85.12766 82.41139
[8] 78.17520 88.27609 75.65409 85.52273 83.02239 82.15389 82.11343
[15] 80.91631 90.33347 85.60661 83.72226 85.43168 85.90904
> colMin(tmp5)
[1] 56.18580 60.46822 57.17331 55.13307 55.70874 61.43151 58.20148 54.94860
[9] 59.23048 58.72535 55.40210 53.37656 57.49313 61.66821 58.54860 60.76739
[17] 58.85947 56.45025 56.96598 54.96602
>
>
> ### 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] 90.01082 70.16462 71.38558 69.49321 67.16601 74.27930 68.31527 69.33122
[9] 69.85662 NA
> rowSums(tmp5)
[1] 1800.216 1403.292 1427.712 1389.864 1343.320 1485.586 1366.305 1386.624
[9] 1397.132 NA
> rowVars(tmp5)
[1] 8153.81309 52.58068 62.19987 87.84649 41.75433 92.06149
[7] 86.62507 80.37261 31.87205 95.89899
> rowSd(tmp5)
[1] 90.298467 7.251253 7.886689 9.372646 6.461759 9.594868 9.307259
[8] 8.965077 5.645534 9.792803
> rowMax(tmp5)
[1] 472.33520 80.16707 85.60661 84.17648 81.59565 90.33347 85.12766
[8] 85.52273 78.17520 NA
> rowMin(tmp5)
[1] 58.54860 56.96598 56.45025 55.70874 58.25840 62.27197 54.94860 53.37656
[9] 62.06999 NA
>
> colMeans(tmp5)
[1] 108.53431 70.89765 70.35522 69.72687 65.72513 72.14357 72.33990
[8] 67.27420 69.11321 67.50052 72.58019 70.96326 72.53302 69.77898
[15] 72.35466 75.43436 68.07572 70.90248 66.78001 NA
> colSums(tmp5)
[1] 1085.3431 708.9765 703.5522 697.2687 657.2513 721.4357 723.3990
[8] 672.7420 691.1321 675.0052 725.8019 709.6326 725.3302 697.7898
[15] 723.5466 754.3436 680.7572 709.0248 667.8001 NA
> colVars(tmp5)
[1] 16426.12643 63.77959 73.09417 52.88808 60.11686 49.39908
[7] 72.50046 65.02792 77.15656 33.71007 104.84730 93.51408
[13] 69.51652 41.55126 56.77500 92.63065 81.06283 73.85336
[19] 61.01613 NA
> colSd(tmp5)
[1] 128.164451 7.986213 8.549513 7.272419 7.753506 7.028448
[7] 8.514720 8.063989 8.783881 5.806037 10.239497 9.670268
[13] 8.337657 6.446027 7.534919 9.624482 9.003490 8.593798
[19] 7.811282 NA
> colMax(tmp5)
[1] 472.33520 81.04987 87.96064 79.45274 80.78816 85.12766 82.41139
[8] 78.17520 88.27609 75.65409 85.52273 83.02239 82.15389 82.11343
[15] 80.91631 90.33347 85.60661 83.72226 85.43168 NA
> colMin(tmp5)
[1] 56.18580 60.46822 57.17331 55.13307 55.70874 61.43151 58.20148 54.94860
[9] 59.23048 58.72535 55.40210 53.37656 57.49313 61.66821 58.54860 60.76739
[17] 58.85947 56.45025 56.96598 NA
>
> Max(tmp5,na.rm=TRUE)
[1] 472.3352
> Min(tmp5,na.rm=TRUE)
[1] 53.37656
> mean(tmp5,na.rm=TRUE)
[1] 72.19171
> Sum(tmp5,na.rm=TRUE)
[1] 14366.15
> Var(tmp5,na.rm=TRUE)
[1] 881.7069
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.01082 70.16462 71.38558 69.49321 67.16601 74.27930 68.31527 69.33122
[9] 69.85662 71.89987
> rowSums(tmp5,na.rm=TRUE)
[1] 1800.216 1403.292 1427.712 1389.864 1343.320 1485.586 1366.305 1386.624
[9] 1397.132 1366.098
> rowVars(tmp5,na.rm=TRUE)
[1] 8153.81309 52.58068 62.19987 87.84649 41.75433 92.06149
[7] 86.62507 80.37261 31.87205 95.89899
> rowSd(tmp5,na.rm=TRUE)
[1] 90.298467 7.251253 7.886689 9.372646 6.461759 9.594868 9.307259
[8] 8.965077 5.645534 9.792803
> rowMax(tmp5,na.rm=TRUE)
[1] 472.33520 80.16707 85.60661 84.17648 81.59565 90.33347 85.12766
[8] 85.52273 78.17520 88.25703
> rowMin(tmp5,na.rm=TRUE)
[1] 58.54860 56.96598 56.45025 55.70874 58.25840 62.27197 54.94860 53.37656
[9] 62.06999 55.13307
>
> colMeans(tmp5,na.rm=TRUE)
[1] 108.53431 70.89765 70.35522 69.72687 65.72513 72.14357 72.33990
[8] 67.27420 69.11321 67.50052 72.58019 70.96326 72.53302 69.77898
[15] 72.35466 75.43436 68.07572 70.90248 66.78001 70.66870
> colSums(tmp5,na.rm=TRUE)
[1] 1085.3431 708.9765 703.5522 697.2687 657.2513 721.4357 723.3990
[8] 672.7420 691.1321 675.0052 725.8019 709.6326 725.3302 697.7898
[15] 723.5466 754.3436 680.7572 709.0248 667.8001 636.0183
> colVars(tmp5,na.rm=TRUE)
[1] 16426.12643 63.77959 73.09417 52.88808 60.11686 49.39908
[7] 72.50046 65.02792 77.15656 33.71007 104.84730 93.51408
[13] 69.51652 41.55126 56.77500 92.63065 81.06283 73.85336
[19] 61.01613 95.69543
> colSd(tmp5,na.rm=TRUE)
[1] 128.164451 7.986213 8.549513 7.272419 7.753506 7.028448
[7] 8.514720 8.063989 8.783881 5.806037 10.239497 9.670268
[13] 8.337657 6.446027 7.534919 9.624482 9.003490 8.593798
[19] 7.811282 9.782404
> colMax(tmp5,na.rm=TRUE)
[1] 472.33520 81.04987 87.96064 79.45274 80.78816 85.12766 82.41139
[8] 78.17520 88.27609 75.65409 85.52273 83.02239 82.15389 82.11343
[15] 80.91631 90.33347 85.60661 83.72226 85.43168 85.90904
> colMin(tmp5,na.rm=TRUE)
[1] 56.18580 60.46822 57.17331 55.13307 55.70874 61.43151 58.20148 54.94860
[9] 59.23048 58.72535 55.40210 53.37656 57.49313 61.66821 58.54860 60.76739
[17] 58.85947 56.45025 56.96598 58.25840
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.01082 70.16462 71.38558 69.49321 67.16601 74.27930 68.31527 69.33122
[9] 69.85662 NaN
> rowSums(tmp5,na.rm=TRUE)
[1] 1800.216 1403.292 1427.712 1389.864 1343.320 1485.586 1366.305 1386.624
[9] 1397.132 0.000
> rowVars(tmp5,na.rm=TRUE)
[1] 8153.81309 52.58068 62.19987 87.84649 41.75433 92.06149
[7] 86.62507 80.37261 31.87205 NA
> rowSd(tmp5,na.rm=TRUE)
[1] 90.298467 7.251253 7.886689 9.372646 6.461759 9.594868 9.307259
[8] 8.965077 5.645534 NA
> rowMax(tmp5,na.rm=TRUE)
[1] 472.33520 80.16707 85.60661 84.17648 81.59565 90.33347 85.12766
[8] 85.52273 78.17520 NA
> rowMin(tmp5,na.rm=TRUE)
[1] 58.54860 56.96598 56.45025 55.70874 58.25840 62.27197 54.94860 53.37656
[9] 62.06999 NA
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 111.40023 71.92196 70.34110 71.34841 66.36780 72.15621 73.61466
[8] 66.11377 69.75188 67.97728 72.87651 69.83121 71.52042 68.40848
[15] 72.50984 74.00961 67.50492 71.41973 64.70760 NaN
> colSums(tmp5,na.rm=TRUE)
[1] 1002.6021 647.2976 633.0699 642.1357 597.3102 649.4059 662.5319
[8] 595.0240 627.7669 611.7955 655.8886 628.4809 643.6838 615.6763
[15] 652.5886 666.0865 607.5443 642.7776 582.3684 0.0000
> colVars(tmp5,na.rm=TRUE)
[1] 18386.98992 59.94843 82.22870 29.91867 62.98494 55.57217
[7] 63.28147 58.00719 82.21216 35.36676 116.96541 90.78616
[13] 66.67097 25.61479 63.60097 81.37323 87.53035 80.07509
[19] 20.32581 NA
> colSd(tmp5,na.rm=TRUE)
[1] 135.598635 7.742637 9.068004 5.469796 7.936305 7.454674
[7] 7.954965 7.616245 9.067092 5.946996 10.815055 9.528177
[13] 8.165229 5.061106 7.975021 9.020711 9.355766 8.948468
[19] 4.508415 NA
> colMax(tmp5,na.rm=TRUE)
[1] 472.33520 81.04987 87.96064 79.45274 80.78816 85.12766 82.41139
[8] 78.17520 88.27609 75.65409 85.52273 83.02239 82.15389 77.40282
[15] 80.91631 90.33347 85.60661 83.72226 73.35240 -Inf
> colMin(tmp5,na.rm=TRUE)
[1] 56.18580 60.46822 57.17331 62.62884 55.70874 61.43151 58.20148 54.94860
[9] 59.23048 58.72535 55.40210 53.37656 57.49313 61.66821 58.54860 60.76739
[17] 58.85947 56.45025 56.96598 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] 131.7087 230.5205 197.5363 131.7429 271.1533 250.3245 161.6458 232.7157
[9] 208.5598 147.4148
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 131.7087 230.5205 197.5363 131.7429 271.1533 250.3245 161.6458 232.7157
[9] 208.5598 147.4148
>
>
>
> 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] -5.684342e-14 -5.684342e-14 5.684342e-14 -5.684342e-14 5.684342e-14
[6] 5.684342e-14 -2.273737e-13 -8.526513e-14 -8.526513e-14 1.421085e-14
[11] 2.842171e-14 1.136868e-13 -5.684342e-14 0.000000e+00 -8.526513e-14
[16] 0.000000e+00 5.684342e-14 8.526513e-14 2.842171e-14 5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
8 5
4 3
6 11
2 18
10 20
9 12
9 16
10 7
4 19
2 12
10 7
1 14
7 20
3 17
4 5
9 11
5 7
5 11
6 19
10 1
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.482067
> Min(tmp)
[1] -2.008854
> mean(tmp)
[1] -0.04154184
> Sum(tmp)
[1] -4.154184
> Var(tmp)
[1] 0.8627189
>
> rowMeans(tmp)
[1] -0.04154184
> rowSums(tmp)
[1] -4.154184
> rowVars(tmp)
[1] 0.8627189
> rowSd(tmp)
[1] 0.9288266
> rowMax(tmp)
[1] 2.482067
> rowMin(tmp)
[1] -2.008854
>
> colMeans(tmp)
[1] -1.36180070 0.09514735 -1.36118057 -1.27275037 2.48206705 0.62091670
[7] 0.36400486 0.77364690 0.72314748 0.51335073 -0.59646698 -0.17141448
[13] 0.57621196 0.39892313 0.66113181 2.17228098 -1.02744840 -0.82883306
[19] 2.07794981 -0.09560953 1.41111114 0.90945776 0.11008120 -0.99802380
[25] 0.41077178 -1.05917905 0.80248782 0.69544828 -1.26029601 -0.26228078
[31] 0.05620947 1.01553326 -1.00870675 0.54159798 -2.00260186 0.44897935
[37] -0.72546105 -0.45585745 0.86638050 0.02356577 -0.14726881 0.79168718
[43] -0.29178456 0.51183330 0.28660440 -0.23304339 -1.38955371 1.40551146
[49] -0.72196813 0.16762698 -0.11230204 -0.06127855 0.76501932 -0.79265612
[55] 0.30623061 -0.88480764 -1.62842162 0.45575359 0.26248061 1.29270551
[61] -1.42024549 0.22387912 0.17519206 -0.58318134 0.76292315 0.06421571
[67] -0.58081299 -0.46228605 0.38679445 1.31259883 -1.34916250 1.26127973
[73] -1.56152702 -0.02741234 -0.56419271 0.63731861 0.35928611 -0.45494347
[79] -1.36730545 -0.56074809 -0.16809086 -0.33146622 0.47425909 -0.96734510
[85] 0.50844004 -1.15111150 -0.90226105 -2.00885368 0.55560542 0.60322607
[91] 0.01018771 -1.38786587 -1.32919295 0.45887807 0.47614619 1.41287075
[97] -0.64250073 0.32206904 0.72829221 -1.31200200
> colSums(tmp)
[1] -1.36180070 0.09514735 -1.36118057 -1.27275037 2.48206705 0.62091670
[7] 0.36400486 0.77364690 0.72314748 0.51335073 -0.59646698 -0.17141448
[13] 0.57621196 0.39892313 0.66113181 2.17228098 -1.02744840 -0.82883306
[19] 2.07794981 -0.09560953 1.41111114 0.90945776 0.11008120 -0.99802380
[25] 0.41077178 -1.05917905 0.80248782 0.69544828 -1.26029601 -0.26228078
[31] 0.05620947 1.01553326 -1.00870675 0.54159798 -2.00260186 0.44897935
[37] -0.72546105 -0.45585745 0.86638050 0.02356577 -0.14726881 0.79168718
[43] -0.29178456 0.51183330 0.28660440 -0.23304339 -1.38955371 1.40551146
[49] -0.72196813 0.16762698 -0.11230204 -0.06127855 0.76501932 -0.79265612
[55] 0.30623061 -0.88480764 -1.62842162 0.45575359 0.26248061 1.29270551
[61] -1.42024549 0.22387912 0.17519206 -0.58318134 0.76292315 0.06421571
[67] -0.58081299 -0.46228605 0.38679445 1.31259883 -1.34916250 1.26127973
[73] -1.56152702 -0.02741234 -0.56419271 0.63731861 0.35928611 -0.45494347
[79] -1.36730545 -0.56074809 -0.16809086 -0.33146622 0.47425909 -0.96734510
[85] 0.50844004 -1.15111150 -0.90226105 -2.00885368 0.55560542 0.60322607
[91] 0.01018771 -1.38786587 -1.32919295 0.45887807 0.47614619 1.41287075
[97] -0.64250073 0.32206904 0.72829221 -1.31200200
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -1.36180070 0.09514735 -1.36118057 -1.27275037 2.48206705 0.62091670
[7] 0.36400486 0.77364690 0.72314748 0.51335073 -0.59646698 -0.17141448
[13] 0.57621196 0.39892313 0.66113181 2.17228098 -1.02744840 -0.82883306
[19] 2.07794981 -0.09560953 1.41111114 0.90945776 0.11008120 -0.99802380
[25] 0.41077178 -1.05917905 0.80248782 0.69544828 -1.26029601 -0.26228078
[31] 0.05620947 1.01553326 -1.00870675 0.54159798 -2.00260186 0.44897935
[37] -0.72546105 -0.45585745 0.86638050 0.02356577 -0.14726881 0.79168718
[43] -0.29178456 0.51183330 0.28660440 -0.23304339 -1.38955371 1.40551146
[49] -0.72196813 0.16762698 -0.11230204 -0.06127855 0.76501932 -0.79265612
[55] 0.30623061 -0.88480764 -1.62842162 0.45575359 0.26248061 1.29270551
[61] -1.42024549 0.22387912 0.17519206 -0.58318134 0.76292315 0.06421571
[67] -0.58081299 -0.46228605 0.38679445 1.31259883 -1.34916250 1.26127973
[73] -1.56152702 -0.02741234 -0.56419271 0.63731861 0.35928611 -0.45494347
[79] -1.36730545 -0.56074809 -0.16809086 -0.33146622 0.47425909 -0.96734510
[85] 0.50844004 -1.15111150 -0.90226105 -2.00885368 0.55560542 0.60322607
[91] 0.01018771 -1.38786587 -1.32919295 0.45887807 0.47614619 1.41287075
[97] -0.64250073 0.32206904 0.72829221 -1.31200200
> colMin(tmp)
[1] -1.36180070 0.09514735 -1.36118057 -1.27275037 2.48206705 0.62091670
[7] 0.36400486 0.77364690 0.72314748 0.51335073 -0.59646698 -0.17141448
[13] 0.57621196 0.39892313 0.66113181 2.17228098 -1.02744840 -0.82883306
[19] 2.07794981 -0.09560953 1.41111114 0.90945776 0.11008120 -0.99802380
[25] 0.41077178 -1.05917905 0.80248782 0.69544828 -1.26029601 -0.26228078
[31] 0.05620947 1.01553326 -1.00870675 0.54159798 -2.00260186 0.44897935
[37] -0.72546105 -0.45585745 0.86638050 0.02356577 -0.14726881 0.79168718
[43] -0.29178456 0.51183330 0.28660440 -0.23304339 -1.38955371 1.40551146
[49] -0.72196813 0.16762698 -0.11230204 -0.06127855 0.76501932 -0.79265612
[55] 0.30623061 -0.88480764 -1.62842162 0.45575359 0.26248061 1.29270551
[61] -1.42024549 0.22387912 0.17519206 -0.58318134 0.76292315 0.06421571
[67] -0.58081299 -0.46228605 0.38679445 1.31259883 -1.34916250 1.26127973
[73] -1.56152702 -0.02741234 -0.56419271 0.63731861 0.35928611 -0.45494347
[79] -1.36730545 -0.56074809 -0.16809086 -0.33146622 0.47425909 -0.96734510
[85] 0.50844004 -1.15111150 -0.90226105 -2.00885368 0.55560542 0.60322607
[91] 0.01018771 -1.38786587 -1.32919295 0.45887807 0.47614619 1.41287075
[97] -0.64250073 0.32206904 0.72829221 -1.31200200
> colMedians(tmp)
[1] -1.36180070 0.09514735 -1.36118057 -1.27275037 2.48206705 0.62091670
[7] 0.36400486 0.77364690 0.72314748 0.51335073 -0.59646698 -0.17141448
[13] 0.57621196 0.39892313 0.66113181 2.17228098 -1.02744840 -0.82883306
[19] 2.07794981 -0.09560953 1.41111114 0.90945776 0.11008120 -0.99802380
[25] 0.41077178 -1.05917905 0.80248782 0.69544828 -1.26029601 -0.26228078
[31] 0.05620947 1.01553326 -1.00870675 0.54159798 -2.00260186 0.44897935
[37] -0.72546105 -0.45585745 0.86638050 0.02356577 -0.14726881 0.79168718
[43] -0.29178456 0.51183330 0.28660440 -0.23304339 -1.38955371 1.40551146
[49] -0.72196813 0.16762698 -0.11230204 -0.06127855 0.76501932 -0.79265612
[55] 0.30623061 -0.88480764 -1.62842162 0.45575359 0.26248061 1.29270551
[61] -1.42024549 0.22387912 0.17519206 -0.58318134 0.76292315 0.06421571
[67] -0.58081299 -0.46228605 0.38679445 1.31259883 -1.34916250 1.26127973
[73] -1.56152702 -0.02741234 -0.56419271 0.63731861 0.35928611 -0.45494347
[79] -1.36730545 -0.56074809 -0.16809086 -0.33146622 0.47425909 -0.96734510
[85] 0.50844004 -1.15111150 -0.90226105 -2.00885368 0.55560542 0.60322607
[91] 0.01018771 -1.38786587 -1.32919295 0.45887807 0.47614619 1.41287075
[97] -0.64250073 0.32206904 0.72829221 -1.31200200
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.361801 0.09514735 -1.361181 -1.27275 2.482067 0.6209167 0.3640049
[2,] -1.361801 0.09514735 -1.361181 -1.27275 2.482067 0.6209167 0.3640049
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.7736469 0.7231475 0.5133507 -0.596467 -0.1714145 0.576212 0.3989231
[2,] 0.7736469 0.7231475 0.5133507 -0.596467 -0.1714145 0.576212 0.3989231
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.6611318 2.172281 -1.027448 -0.8288331 2.07795 -0.09560953 1.411111
[2,] 0.6611318 2.172281 -1.027448 -0.8288331 2.07795 -0.09560953 1.411111
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.9094578 0.1100812 -0.9980238 0.4107718 -1.059179 0.8024878 0.6954483
[2,] 0.9094578 0.1100812 -0.9980238 0.4107718 -1.059179 0.8024878 0.6954483
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -1.260296 -0.2622808 0.05620947 1.015533 -1.008707 0.541598 -2.002602
[2,] -1.260296 -0.2622808 0.05620947 1.015533 -1.008707 0.541598 -2.002602
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.4489794 -0.7254611 -0.4558574 0.8663805 0.02356577 -0.1472688 0.7916872
[2,] 0.4489794 -0.7254611 -0.4558574 0.8663805 0.02356577 -0.1472688 0.7916872
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.2917846 0.5118333 0.2866044 -0.2330434 -1.389554 1.405511 -0.7219681
[2,] -0.2917846 0.5118333 0.2866044 -0.2330434 -1.389554 1.405511 -0.7219681
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.167627 -0.112302 -0.06127855 0.7650193 -0.7926561 0.3062306 -0.8848076
[2,] 0.167627 -0.112302 -0.06127855 0.7650193 -0.7926561 0.3062306 -0.8848076
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.628422 0.4557536 0.2624806 1.292706 -1.420245 0.2238791 0.1751921
[2,] -1.628422 0.4557536 0.2624806 1.292706 -1.420245 0.2238791 0.1751921
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.5831813 0.7629231 0.06421571 -0.580813 -0.4622861 0.3867945 1.312599
[2,] -0.5831813 0.7629231 0.06421571 -0.580813 -0.4622861 0.3867945 1.312599
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.349162 1.26128 -1.561527 -0.02741234 -0.5641927 0.6373186 0.3592861
[2,] -1.349162 1.26128 -1.561527 -0.02741234 -0.5641927 0.6373186 0.3592861
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.4549435 -1.367305 -0.5607481 -0.1680909 -0.3314662 0.4742591 -0.9673451
[2,] -0.4549435 -1.367305 -0.5607481 -0.1680909 -0.3314662 0.4742591 -0.9673451
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.50844 -1.151111 -0.9022611 -2.008854 0.5556054 0.6032261 0.01018771
[2,] 0.50844 -1.151111 -0.9022611 -2.008854 0.5556054 0.6032261 0.01018771
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -1.387866 -1.329193 0.4588781 0.4761462 1.412871 -0.6425007 0.322069
[2,] -1.387866 -1.329193 0.4588781 0.4761462 1.412871 -0.6425007 0.322069
[,99] [,100]
[1,] 0.7282922 -1.312002
[2,] 0.7282922 -1.312002
>
>
> Max(tmp2)
[1] 1.878539
> Min(tmp2)
[1] -1.772814
> mean(tmp2)
[1] 0.0004180027
> Sum(tmp2)
[1] 0.04180027
> Var(tmp2)
[1] 0.7185687
>
> rowMeans(tmp2)
[1] 0.312477909 0.678077063 -0.419183813 -0.691079633 -1.699013299
[6] -0.454719542 -0.272628096 0.468700277 0.908150902 0.022573760
[11] -0.008489850 -1.099853948 -0.259889889 -1.260317653 -1.227777345
[16] -0.449628721 0.917545212 -1.045073291 -0.521030760 -0.620586381
[21] 0.480323670 0.114300641 -0.880705877 -0.727642836 1.878538598
[26] 0.263359256 0.005720574 -0.356816078 1.033660483 0.337459295
[31] 0.311497661 1.351266174 1.250233105 -1.027248640 -0.352506996
[36] 0.765855299 1.300560756 -0.526223661 -0.313658373 0.362459952
[41] -0.223053892 0.384746172 -1.103476512 0.681037861 1.529024869
[46] -0.800282859 -0.035137300 -0.393095034 0.020062587 0.827832371
[51] 0.238222258 0.477644068 0.077294178 -0.112623610 -0.698779244
[56] -0.514201921 -0.358467276 1.606302862 -0.193850276 -1.576928204
[61] -0.263504130 -0.954528751 -1.661254026 0.050683186 0.176914974
[66] 0.786638876 0.334989205 -1.068225712 1.498916383 0.035646766
[71] -0.259728194 0.882241515 -0.146113469 -1.772813973 1.144546284
[76] -0.818201957 0.076383801 -0.528559517 -0.796632013 -1.644600816
[81] 0.931361541 0.365923613 1.817472959 0.643009975 0.999523330
[86] 0.432691947 0.717235269 -0.713734825 -0.077942606 1.854477775
[91] 0.721619003 -1.741712582 0.946480276 0.128057276 -0.390326790
[96] 0.008749312 0.053018471 0.193881713 0.032276502 -0.334017318
> rowSums(tmp2)
[1] 0.312477909 0.678077063 -0.419183813 -0.691079633 -1.699013299
[6] -0.454719542 -0.272628096 0.468700277 0.908150902 0.022573760
[11] -0.008489850 -1.099853948 -0.259889889 -1.260317653 -1.227777345
[16] -0.449628721 0.917545212 -1.045073291 -0.521030760 -0.620586381
[21] 0.480323670 0.114300641 -0.880705877 -0.727642836 1.878538598
[26] 0.263359256 0.005720574 -0.356816078 1.033660483 0.337459295
[31] 0.311497661 1.351266174 1.250233105 -1.027248640 -0.352506996
[36] 0.765855299 1.300560756 -0.526223661 -0.313658373 0.362459952
[41] -0.223053892 0.384746172 -1.103476512 0.681037861 1.529024869
[46] -0.800282859 -0.035137300 -0.393095034 0.020062587 0.827832371
[51] 0.238222258 0.477644068 0.077294178 -0.112623610 -0.698779244
[56] -0.514201921 -0.358467276 1.606302862 -0.193850276 -1.576928204
[61] -0.263504130 -0.954528751 -1.661254026 0.050683186 0.176914974
[66] 0.786638876 0.334989205 -1.068225712 1.498916383 0.035646766
[71] -0.259728194 0.882241515 -0.146113469 -1.772813973 1.144546284
[76] -0.818201957 0.076383801 -0.528559517 -0.796632013 -1.644600816
[81] 0.931361541 0.365923613 1.817472959 0.643009975 0.999523330
[86] 0.432691947 0.717235269 -0.713734825 -0.077942606 1.854477775
[91] 0.721619003 -1.741712582 0.946480276 0.128057276 -0.390326790
[96] 0.008749312 0.053018471 0.193881713 0.032276502 -0.334017318
> 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] 0.312477909 0.678077063 -0.419183813 -0.691079633 -1.699013299
[6] -0.454719542 -0.272628096 0.468700277 0.908150902 0.022573760
[11] -0.008489850 -1.099853948 -0.259889889 -1.260317653 -1.227777345
[16] -0.449628721 0.917545212 -1.045073291 -0.521030760 -0.620586381
[21] 0.480323670 0.114300641 -0.880705877 -0.727642836 1.878538598
[26] 0.263359256 0.005720574 -0.356816078 1.033660483 0.337459295
[31] 0.311497661 1.351266174 1.250233105 -1.027248640 -0.352506996
[36] 0.765855299 1.300560756 -0.526223661 -0.313658373 0.362459952
[41] -0.223053892 0.384746172 -1.103476512 0.681037861 1.529024869
[46] -0.800282859 -0.035137300 -0.393095034 0.020062587 0.827832371
[51] 0.238222258 0.477644068 0.077294178 -0.112623610 -0.698779244
[56] -0.514201921 -0.358467276 1.606302862 -0.193850276 -1.576928204
[61] -0.263504130 -0.954528751 -1.661254026 0.050683186 0.176914974
[66] 0.786638876 0.334989205 -1.068225712 1.498916383 0.035646766
[71] -0.259728194 0.882241515 -0.146113469 -1.772813973 1.144546284
[76] -0.818201957 0.076383801 -0.528559517 -0.796632013 -1.644600816
[81] 0.931361541 0.365923613 1.817472959 0.643009975 0.999523330
[86] 0.432691947 0.717235269 -0.713734825 -0.077942606 1.854477775
[91] 0.721619003 -1.741712582 0.946480276 0.128057276 -0.390326790
[96] 0.008749312 0.053018471 0.193881713 0.032276502 -0.334017318
> rowMin(tmp2)
[1] 0.312477909 0.678077063 -0.419183813 -0.691079633 -1.699013299
[6] -0.454719542 -0.272628096 0.468700277 0.908150902 0.022573760
[11] -0.008489850 -1.099853948 -0.259889889 -1.260317653 -1.227777345
[16] -0.449628721 0.917545212 -1.045073291 -0.521030760 -0.620586381
[21] 0.480323670 0.114300641 -0.880705877 -0.727642836 1.878538598
[26] 0.263359256 0.005720574 -0.356816078 1.033660483 0.337459295
[31] 0.311497661 1.351266174 1.250233105 -1.027248640 -0.352506996
[36] 0.765855299 1.300560756 -0.526223661 -0.313658373 0.362459952
[41] -0.223053892 0.384746172 -1.103476512 0.681037861 1.529024869
[46] -0.800282859 -0.035137300 -0.393095034 0.020062587 0.827832371
[51] 0.238222258 0.477644068 0.077294178 -0.112623610 -0.698779244
[56] -0.514201921 -0.358467276 1.606302862 -0.193850276 -1.576928204
[61] -0.263504130 -0.954528751 -1.661254026 0.050683186 0.176914974
[66] 0.786638876 0.334989205 -1.068225712 1.498916383 0.035646766
[71] -0.259728194 0.882241515 -0.146113469 -1.772813973 1.144546284
[76] -0.818201957 0.076383801 -0.528559517 -0.796632013 -1.644600816
[81] 0.931361541 0.365923613 1.817472959 0.643009975 0.999523330
[86] 0.432691947 0.717235269 -0.713734825 -0.077942606 1.854477775
[91] 0.721619003 -1.741712582 0.946480276 0.128057276 -0.390326790
[96] 0.008749312 0.053018471 0.193881713 0.032276502 -0.334017318
>
> colMeans(tmp2)
[1] 0.0004180027
> colSums(tmp2)
[1] 0.04180027
> colVars(tmp2)
[1] 0.7185687
> colSd(tmp2)
[1] 0.8476843
> colMax(tmp2)
[1] 1.878539
> colMin(tmp2)
[1] -1.772814
> colMedians(tmp2)
[1] 0.01440595
> colRanges(tmp2)
[,1]
[1,] -1.772814
[2,] 1.878539
>
> 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] -3.1165897 3.0792696 -1.3270506 1.3057154 -1.5299123 1.8043811
[7] -2.5495316 -6.7752980 0.5631645 5.3209709
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.3573891
[2,] -0.9788420
[3,] -0.1405355
[4,] 0.3419901
[5,] 0.6195439
>
> rowApply(tmp,sum)
[1] 4.164309 1.593533 -1.225327 -7.084628 4.094687 3.841492 -6.132309
[8] -2.553800 3.989449 -3.912287
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 5 3 5 3 5 3 8 7 2
[2,] 9 6 10 4 1 1 10 9 2 10
[3,] 10 10 1 1 4 6 4 2 4 8
[4,] 7 8 7 10 5 2 8 3 5 4
[5,] 3 7 8 3 2 9 6 6 1 7
[6,] 4 3 4 8 9 10 5 1 8 3
[7,] 5 1 6 6 10 7 7 7 9 1
[8,] 1 2 2 2 8 3 1 5 3 9
[9,] 8 9 9 9 6 4 2 4 6 5
[10,] 2 4 5 7 7 8 9 10 10 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.91242147 2.44777575 1.82018969 -1.89576972 -5.65272808 1.51169656
[7] -0.44549991 2.85677347 3.07093261 2.71989911 0.72777807 -0.73056218
[13] -3.93751141 2.51486368 2.34766852 0.61608268 -0.34017852 -1.16213249
[19] 0.09384072 -5.12702520
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.1169818
[2,] -0.2577573
[3,] 0.6146764
[4,] 1.0240245
[5,] 1.6484597
>
> rowApply(tmp,sum)
[1] 0.7605382 -2.2460859 7.8565471 -7.6522128 3.6297282
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 16 8 17 2 18
[2,] 13 7 14 15 19
[3,] 17 20 7 11 9
[4,] 4 6 4 13 11
[5,] 6 2 8 3 1
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.6146764 0.1335678 0.8120163 -0.95183495 -0.3590615 2.2007371
[2,] -0.2577573 -0.3584916 1.6141191 -0.46086524 -1.8062872 -0.5601421
[3,] 1.6484597 0.9899599 -0.3725190 -0.84849101 -0.3086674 1.4855211
[4,] -2.1169818 0.4463994 -0.1085777 0.00414522 -1.8844038 -1.4374437
[5,] 1.0240245 1.2363403 -0.1248490 0.36127625 -1.2943081 -0.1769759
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.13686439 -0.2755699 -1.3458124 -0.19718973 0.2645985 -1.1431766
[2,] 0.04109649 0.5213693 0.6896324 -0.09332220 0.6131709 -0.9073898
[3,] -0.39250069 2.0600111 3.7412973 2.22943803 -0.3968893 1.0335635
[4,] -0.96570636 0.7761297 0.4813004 0.83414217 -0.6067642 1.0538921
[5,] 1.00847504 -0.2251666 -0.4954851 -0.05316916 0.8536622 -0.7674515
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.09455108 -0.06371712 1.6839385 -1.05011645 0.03967794 0.8720139
[2,] 0.16529726 0.90609421 0.6107609 -0.06777887 -1.10126205 -2.0264219
[3,] -1.91903330 0.54267161 0.4022497 0.36349880 0.02474778 0.4784909
[4,] -1.12410019 -0.11146232 0.4250335 1.53794199 -0.10110019 -1.0346088
[5,] -0.96512411 1.24127730 -0.7743141 -0.16746279 0.79775800 0.5483934
[,19] [,20]
[1,] 0.6021271 -0.8449213
[2,] 0.3901457 -0.1580539
[3,] -1.0236459 -1.8816156
[4,] -0.4742701 -3.2457780
[5,] 0.5994839 1.0033436
>
>
> 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 -0.7359815 2.231589 -0.371051 0.1457049 1.044323 -0.08507539 -1.319739
col8 col9 col10 col11 col12 col13 col14
row1 -1.062844 -0.2651069 0.9475659 0.958864 1.337945 1.176805 -0.9627458
col15 col16 col17 col18 col19 col20
row1 -0.4534147 -0.7854596 0.3173063 -0.7982663 -1.636199 -0.6570418
> tmp[,"col10"]
col10
row1 0.9475659
row2 0.6270214
row3 1.3660481
row4 0.4696531
row5 -0.5321008
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.7359815 2.231589 -0.371051 0.1457049 1.044323 -0.08507539 -1.319739
row5 1.0412233 -1.000908 1.921045 1.2484624 -1.052515 -0.51787933 1.194816
col8 col9 col10 col11 col12 col13 col14
row1 -1.062844 -0.2651069 0.9475659 0.958864 1.3379448 1.17680531 -0.9627458
row5 -0.879919 0.5294170 -0.5321008 1.661109 0.0360449 0.01707204 1.2251730
col15 col16 col17 col18 col19 col20
row1 -0.4534147 -0.7854596 0.3173063 -0.7982663 -1.6361989 -0.6570418
row5 -1.7989258 2.1099130 1.1392635 -1.1407877 -0.4250433 -0.3743346
> tmp[,c("col6","col20")]
col6 col20
row1 -0.08507539 -0.6570418
row2 -0.88806153 -0.3306463
row3 0.72976579 -0.8906417
row4 0.46576450 -0.9259899
row5 -0.51787933 -0.3743346
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.08507539 -0.6570418
row5 -0.51787933 -0.3743346
>
>
>
>
> 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 51.14692 50.94484 51.76616 48.43646 50.27795 105.986 50.36201 50.73786
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.72029 49.03659 46.37596 50.99115 50.11421 48.23543 49.31342 50.51623
col17 col18 col19 col20
row1 49.29057 49.06695 50.80317 105.6769
> tmp[,"col10"]
col10
row1 49.03659
row2 29.16207
row3 29.95428
row4 29.48120
row5 50.37987
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.14692 50.94484 51.76616 48.43646 50.27795 105.9860 50.36201 50.73786
row5 48.70571 48.58098 49.61431 51.44448 50.68982 104.8554 49.13331 48.47248
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.72029 49.03659 46.37596 50.99115 50.11421 48.23543 49.31342 50.51623
row5 49.48537 50.37987 50.15097 51.03303 46.78149 49.22041 51.30513 49.54059
col17 col18 col19 col20
row1 49.29057 49.06695 50.80317 105.6769
row5 50.17741 49.51484 49.92213 105.8078
> tmp[,c("col6","col20")]
col6 col20
row1 105.98595 105.67687
row2 75.65316 73.49527
row3 74.21151 74.21244
row4 74.86235 74.98624
row5 104.85545 105.80778
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.9860 105.6769
row5 104.8554 105.8078
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.9860 105.6769
row5 104.8554 105.8078
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.8805358
[2,] 0.1024771
[3,] -0.4982455
[4,] 0.3378072
[5,] 0.2052541
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.2004497 2.5115522
[2,] 0.3728304 -0.7122783
[3,] -0.3358940 0.1975197
[4,] -0.3125386 -0.5064677
[5,] -0.6962462 0.5543422
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.3766048 1.0975711
[2,] 0.4555540 -0.1146734
[3,] -1.7824779 1.2350895
[4,] 0.1675255 0.2421701
[5,] 0.8288168 -0.5775974
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.3766048
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.3766048
[2,] 0.4555540
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 -0.852004 1.1199916 -0.03710114 0.883737 0.9926314 0.8403083 0.5477020
row1 -1.176594 -0.2060382 -1.36063877 1.785207 -0.8310527 1.1548930 0.2180298
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.4022758 -0.1669008 -2.0238322 -1.1633544 -1.619820 1.4998613 -0.2408823
row1 1.3178152 -0.9971308 0.2553238 0.4240245 -1.600111 0.1663673 -0.6866473
[,15] [,16] [,17] [,18] [,19] [,20]
row3 0.7297460 1.1400040 0.5607072 -0.1554735 -0.8688880 0.5535749
row1 0.5889962 -0.8133136 0.7225785 0.5093655 -0.5480827 -0.6240817
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.5009077 -0.4393268 -1.03463 0.2287907 0.2907669 0.1598307 1.337679
[,8] [,9] [,10]
row2 1.374543 0.1559891 0.2710608
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.9826015 -1.141679 1.227584 1.791763 0.3522671 0.1879598 -1.205738
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.4740662 -1.252244 0.8092781 0.8348699 -0.4221279 0.9943824 -1.419032
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.396247 1.070515 0.4885272 -0.09986944 1.220364 -0.3037834
>
>
> 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: 0x62c20d6d9810>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e65412bb2"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e31d7548d"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e77ffdbf1"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e606cc645"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e1b022f2c"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e888760c"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e8ea831"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e6c33338f"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e2c79c43c"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e67884571"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e2df84da3"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e280db485"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e55ec8900"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e30bdf0e8"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM39083e5bbb50a"
>
>
> ### 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: 0x62c20d4488f0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x62c20d4488f0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x62c20d4488f0>
> rowMedians(tmp)
[1] -0.3989775439 0.1170841623 0.0585374293 -0.2752885468 -0.1872481708
[6] -0.1548239864 -0.0153285656 0.3188172723 -0.2578300009 -0.0332923171
[11] -0.6737185817 -0.0316666224 0.0294289744 -0.2713870184 0.3297357944
[16] -0.5500776860 0.5154080457 -0.2399845278 0.0297304972 0.1972476648
[21] -0.0211247556 0.3837999675 0.1441428552 -0.0516604281 0.2029974247
[26] -0.1110390816 0.7913090391 0.0813929685 0.0006801251 0.0668816471
[31] -0.2354270795 0.2832129783 -0.8101674509 0.0757827437 0.6422990635
[36] -0.0009679877 0.3118154446 0.8661464165 0.1212010841 0.0474062742
[41] -0.0132525254 -0.2566345058 0.3392856843 0.2375159249 0.2876628306
[46] 0.3450965720 0.4056782632 -0.3538715800 0.0559977287 0.2964345511
[51] -0.2301235123 -0.0929227905 0.2296110645 0.1031727628 -0.0296109905
[56] -0.0869794837 0.4762533559 0.3415446099 -0.6359056861 -0.0961000241
[61] 0.0406774732 -0.0045575704 0.1659361752 0.0516632148 -0.0286410476
[66] -0.1015167158 0.1667481851 -0.3995820294 -0.1776510485 -0.0770303600
[71] -0.0700009846 0.0781493024 -0.3221173533 0.0087995441 0.5043572852
[76] 0.2653142702 -0.5421258243 -0.2628340867 -0.1407255292 -0.4236356691
[81] -0.0171211787 0.1418290839 0.0099003650 0.1035054184 0.6520842994
[86] -0.2264414327 -0.2813633277 -0.3120891894 0.3046380731 -0.0269178723
[91] -0.0360062621 0.2685645539 -0.0374556112 -0.3432890434 0.2483092706
[96] -0.3221453585 0.1208860449 0.3589372785 0.0886035434 0.0254783466
[101] -0.2611851166 -0.0010461161 0.0761568656 -0.2349793568 0.6292797496
[106] 0.2765708377 0.1079381332 -0.0662514309 -0.2036286686 -0.1948713464
[111] 0.1533381755 0.2123995293 -0.1679793324 0.2486895880 0.4460815286
[116] -0.2052135192 0.2046923895 -0.0843451083 -0.4221119180 -0.1268901874
[121] -0.1588299599 0.1504949845 0.1629271880 0.4522049996 -0.2712663242
[126] 0.0689221445 0.7837405323 0.0572403555 0.5500273905 -0.2059837677
[131] 0.0697466006 0.3525361959 -0.0421157140 -0.1289633301 0.3729757669
[136] 0.0914067977 0.1798468592 -0.3421594759 -0.5807739260 0.0485329863
[141] -0.1275706459 -0.2621958400 -0.3565629168 0.5739622809 0.4073639782
[146] -0.4300400435 0.1497966430 -0.3840981805 0.2145364340 -0.1465829670
[151] -0.0168336776 -0.2367704989 0.8087540305 0.1916504107 -0.6167269452
[156] 0.0818548558 -0.0678408236 0.1697923296 -0.4043764189 0.0287710702
[161] -0.1825003163 -0.2475247197 0.2366195499 0.0076522677 -0.3316532815
[166] 0.4330463005 -0.5513917927 0.3266380817 0.4146084796 -0.2578382880
[171] 0.5764687413 0.0963583519 0.1481157512 0.6540471393 -0.0475411979
[176] 0.1920312641 0.2046027205 0.3190574633 -0.0538967123 -0.4578419094
[181] 0.0401535438 0.0159866120 -0.2678542420 -0.2748311751 0.0046592525
[186] -0.0798403891 -0.0993999460 0.3219406493 0.0704317961 -0.0090497343
[191] -0.0859179711 -0.1507145366 0.7000989351 0.0583088600 -0.0597025504
[196] -0.1469128851 0.0560245961 -0.0430360203 -0.0396597500 0.0153421867
[201] 0.0921772675 -0.1314338090 -0.2418382064 0.0858081441 0.4503363949
[206] -0.1636136040 -0.0295332522 -0.0470909516 -0.0767193446 -0.2739509160
[211] 0.6079717987 -0.2324708371 -0.1204445764 -0.1511190898 0.2032490278
[216] 0.3652489205 0.0622111800 -0.0155958780 0.3547240673 -0.6754449952
[221] -0.4754898630 0.2160110806 -0.8005735152 -0.2850949838 -0.1500405039
[226] -0.3327685635 0.4074235999 -0.3941168215 0.6442323879 0.3234605725
>
> proc.time()
user system elapsed
1.313 1.471 2.773
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: 0x626df4dcac10>
> .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: 0x626df4dcac10>
> .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: 0x626df4dcac10>
> .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: 0x626df4dcac10>
> 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: 0x626df5a8d2d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x626df5a8d2d0>
> .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: 0x626df5a8d2d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x626df5a8d2d0>
> .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: 0x626df5a8d2d0>
> 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: 0x626df6162d70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x626df6162d70>
> .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: 0x626df6162d70>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x626df6162d70>
> .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: 0x626df6162d70>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x626df6162d70>
> .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: 0x626df6162d70>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x626df6162d70>
> .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: 0x626df6162d70>
> 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: 0x626df5cd6370>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x626df5cd6370>
> .Call("R_bm_AddColumn",P)
<pointer: 0x626df5cd6370>
> .Call("R_bm_AddColumn",P)
<pointer: 0x626df5cd6370>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile390a3f1a221" "BufferedMatrixFile390a3f535d8fe7"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile390a3f1a221" "BufferedMatrixFile390a3f535d8fe7"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x626df5c21ff0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x626df5c21ff0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x626df5c21ff0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x626df5c21ff0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x626df5c21ff0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x626df5c21ff0>
> .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: 0x626df5e043d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x626df5e043d0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x626df5e043d0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x626df5e043d0>
> 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: 0x626df75b5fb0>
> .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: 0x626df75b5fb0>
> rm(P)
>
> proc.time()
user system elapsed
0.265 0.045 0.298
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
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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
0.232 0.053 0.272