Ben Bolstad
| Snapshot Date: 2026-01-23 13:40 -0500 (Fri, 23 Jan 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-24 11:34 -0500 (Sat, 24 Jan 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" | 4811 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4545 |
| 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 253/2345 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.75.0 |
| Command: /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: 2026-01-23 21:45:37 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 21:46:02 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 25.0 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
0.243 0.059 0.289
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 478920 25.6 1048721 56.1 639242 34.2
Vcells 885815 6.8 8388608 64.0 2083259 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri Jan 23 21:45:53 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 Jan 23 21:45:53 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: 0x652c40e91c10>
>
>
>
> 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 Jan 23 21:45:53 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 Jan 23 21:45:53 2026"
>
> ColMode(tmp2)
<pointer: 0x652c40e91c10>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.2864375 0.7883820 -0.1094032 -0.6199689
[2,] -0.1742292 0.6842540 -1.3617122 -0.6141546
[3,] 0.3320032 -0.4268767 0.4910896 0.4276826
[4,] -0.7142146 0.5829643 -0.3292520 -0.7593766
> 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,] 99.2864375 0.7883820 0.1094032 0.6199689
[2,] 0.1742292 0.6842540 1.3617122 0.6141546
[3,] 0.3320032 0.4268767 0.4910896 0.4276826
[4,] 0.7142146 0.5829643 0.3292520 0.7593766
> 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,] 9.9642580 0.8879088 0.3307615 0.7873810
[2,] 0.4174077 0.8271964 1.1669242 0.7836802
[3,] 0.5761972 0.6533581 0.7007778 0.6539745
[4,] 0.8451122 0.7635210 0.5738049 0.8714221
>
> 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,] 223.92902 34.66747 28.41702 33.49378
[2,] 29.34831 33.95622 38.03095 33.45096
[3,] 31.09397 31.96046 32.49887 31.96743
[4,] 34.16534 33.21817 31.06730 34.47360
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x652c41ce8ff0>
> exp(tmp5)
<pointer: 0x652c41ce8ff0>
> log(tmp5,2)
<pointer: 0x652c41ce8ff0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 466.0789
> Min(tmp5)
[1] 53.4416
> mean(tmp5)
[1] 73.84173
> Sum(tmp5)
[1] 14768.35
> Var(tmp5)
[1] 845.9071
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.34709 73.63271 70.69340 69.93145 72.17190 70.32533 71.95914 72.71766
[9] 72.93988 72.69873
> rowSums(tmp5)
[1] 1826.942 1472.654 1413.868 1398.629 1443.438 1406.507 1439.183 1454.353
[9] 1458.798 1453.975
> rowVars(tmp5)
[1] 7857.61829 67.41496 67.63754 74.85949 59.92721 73.62497
[7] 40.61514 66.60192 116.25832 62.82234
> rowSd(tmp5)
[1] 88.643208 8.210661 8.224205 8.652138 7.741267 8.580499 6.373001
[8] 8.161000 10.782315 7.926054
> rowMax(tmp5)
[1] 466.07891 87.44337 87.93732 87.88016 87.82758 88.53986 81.57020
[8] 84.60140 95.67369 87.01759
> rowMin(tmp5)
[1] 59.14630 57.76024 56.13793 55.48098 54.89986 54.88915 53.44160 54.58319
[9] 56.49711 54.77476
>
> colMeans(tmp5)
[1] 108.59828 74.59648 72.26688 69.80625 74.57764 73.96031 72.74077
[8] 72.23984 71.63307 72.04728 72.65858 72.82062 73.00005 67.76687
[15] 69.19675 69.73220 71.96209 72.42574 74.02921 70.77567
> colSums(tmp5)
[1] 1085.9828 745.9648 722.6688 698.0625 745.7764 739.6031 727.4077
[8] 722.3984 716.3307 720.4728 726.5858 728.2062 730.0005 677.6687
[15] 691.9675 697.3220 719.6209 724.2574 740.2921 707.7567
> colVars(tmp5)
[1] 15821.61102 131.00682 65.20879 37.57023 52.37294 51.29802
[7] 51.18816 81.43864 112.60798 154.68405 20.99246 120.02587
[13] 63.13429 27.09896 65.27210 44.79692 68.99203 93.31217
[19] 103.61097 56.30346
> colSd(tmp5)
[1] 125.783986 11.445821 8.075196 6.129456 7.236915 7.162263
[7] 7.154590 9.024336 10.611691 12.437204 4.581753 10.955632
[13] 7.945709 5.205666 8.079115 6.693050 8.306144 9.659822
[19] 10.178947 7.503563
> colMax(tmp5)
[1] 466.07891 91.41139 87.82758 78.99715 88.37525 87.88016 84.81997
[8] 86.88204 88.53986 92.14277 77.90322 90.01038 87.44337 75.45898
[15] 80.11875 81.57020 83.37825 83.13710 95.67369 79.02944
> colMin(tmp5)
[1] 54.77476 53.44160 59.14630 58.01266 62.71386 66.47534 62.90499 56.49711
[9] 54.58319 54.88915 65.60619 60.88544 63.30199 57.73515 55.48098 57.76024
[17] 60.16170 54.89986 61.40263 59.58361
>
>
> ### 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] 91.34709 73.63271 70.69340 69.93145 72.17190 70.32533 71.95914 72.71766
[9] NA 72.69873
> rowSums(tmp5)
[1] 1826.942 1472.654 1413.868 1398.629 1443.438 1406.507 1439.183 1454.353
[9] NA 1453.975
> rowVars(tmp5)
[1] 7857.61829 67.41496 67.63754 74.85949 59.92721 73.62497
[7] 40.61514 66.60192 92.49338 62.82234
> rowSd(tmp5)
[1] 88.643208 8.210661 8.224205 8.652138 7.741267 8.580499 6.373001
[8] 8.161000 9.617348 7.926054
> rowMax(tmp5)
[1] 466.07891 87.44337 87.93732 87.88016 87.82758 88.53986 81.57020
[8] 84.60140 NA 87.01759
> rowMin(tmp5)
[1] 59.14630 57.76024 56.13793 55.48098 54.89986 54.88915 53.44160 54.58319
[9] NA 54.77476
>
> colMeans(tmp5)
[1] 108.59828 74.59648 72.26688 69.80625 74.57764 73.96031 72.74077
[8] 72.23984 71.63307 72.04728 72.65858 72.82062 73.00005 67.76687
[15] 69.19675 69.73220 71.96209 72.42574 NA 70.77567
> colSums(tmp5)
[1] 1085.9828 745.9648 722.6688 698.0625 745.7764 739.6031 727.4077
[8] 722.3984 716.3307 720.4728 726.5858 728.2062 730.0005 677.6687
[15] 691.9675 697.3220 719.6209 724.2574 NA 707.7567
> colVars(tmp5)
[1] 15821.61102 131.00682 65.20879 37.57023 52.37294 51.29802
[7] 51.18816 81.43864 112.60798 154.68405 20.99246 120.02587
[13] 63.13429 27.09896 65.27210 44.79692 68.99203 93.31217
[19] NA 56.30346
> colSd(tmp5)
[1] 125.783986 11.445821 8.075196 6.129456 7.236915 7.162263
[7] 7.154590 9.024336 10.611691 12.437204 4.581753 10.955632
[13] 7.945709 5.205666 8.079115 6.693050 8.306144 9.659822
[19] NA 7.503563
> colMax(tmp5)
[1] 466.07891 91.41139 87.82758 78.99715 88.37525 87.88016 84.81997
[8] 86.88204 88.53986 92.14277 77.90322 90.01038 87.44337 75.45898
[15] 80.11875 81.57020 83.37825 83.13710 NA 79.02944
> colMin(tmp5)
[1] 54.77476 53.44160 59.14630 58.01266 62.71386 66.47534 62.90499 56.49711
[9] 54.58319 54.88915 65.60619 60.88544 63.30199 57.73515 55.48098 57.76024
[17] 60.16170 54.89986 NA 59.58361
>
> Max(tmp5,na.rm=TRUE)
[1] 466.0789
> Min(tmp5,na.rm=TRUE)
[1] 53.4416
> mean(tmp5,na.rm=TRUE)
[1] 73.73202
> Sum(tmp5,na.rm=TRUE)
[1] 14672.67
> Var(tmp5,na.rm=TRUE)
[1] 847.76
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.34709 73.63271 70.69340 69.93145 72.17190 70.32533 71.95914 72.71766
[9] 71.74337 72.69873
> rowSums(tmp5,na.rm=TRUE)
[1] 1826.942 1472.654 1413.868 1398.629 1443.438 1406.507 1439.183 1454.353
[9] 1363.124 1453.975
> rowVars(tmp5,na.rm=TRUE)
[1] 7857.61829 67.41496 67.63754 74.85949 59.92721 73.62497
[7] 40.61514 66.60192 92.49338 62.82234
> rowSd(tmp5,na.rm=TRUE)
[1] 88.643208 8.210661 8.224205 8.652138 7.741267 8.580499 6.373001
[8] 8.161000 9.617348 7.926054
> rowMax(tmp5,na.rm=TRUE)
[1] 466.07891 87.44337 87.93732 87.88016 87.82758 88.53986 81.57020
[8] 84.60140 91.41139 87.01759
> rowMin(tmp5,na.rm=TRUE)
[1] 59.14630 57.76024 56.13793 55.48098 54.89986 54.88915 53.44160 54.58319
[9] 56.49711 54.77476
>
> colMeans(tmp5,na.rm=TRUE)
[1] 108.59828 74.59648 72.26688 69.80625 74.57764 73.96031 72.74077
[8] 72.23984 71.63307 72.04728 72.65858 72.82062 73.00005 67.76687
[15] 69.19675 69.73220 71.96209 72.42574 71.62426 70.77567
> colSums(tmp5,na.rm=TRUE)
[1] 1085.9828 745.9648 722.6688 698.0625 745.7764 739.6031 727.4077
[8] 722.3984 716.3307 720.4728 726.5858 728.2062 730.0005 677.6687
[15] 691.9675 697.3220 719.6209 724.2574 644.6184 707.7567
> colVars(tmp5,na.rm=TRUE)
[1] 15821.61102 131.00682 65.20879 37.57023 52.37294 51.29802
[7] 51.18816 81.43864 112.60798 154.68405 20.99246 120.02587
[13] 63.13429 27.09896 65.27210 44.79692 68.99203 93.31217
[19] 51.49517 56.30346
> colSd(tmp5,na.rm=TRUE)
[1] 125.783986 11.445821 8.075196 6.129456 7.236915 7.162263
[7] 7.154590 9.024336 10.611691 12.437204 4.581753 10.955632
[13] 7.945709 5.205666 8.079115 6.693050 8.306144 9.659822
[19] 7.176014 7.503563
> colMax(tmp5,na.rm=TRUE)
[1] 466.07891 91.41139 87.82758 78.99715 88.37525 87.88016 84.81997
[8] 86.88204 88.53986 92.14277 77.90322 90.01038 87.44337 75.45898
[15] 80.11875 81.57020 83.37825 83.13710 82.61329 79.02944
> colMin(tmp5,na.rm=TRUE)
[1] 54.77476 53.44160 59.14630 58.01266 62.71386 66.47534 62.90499 56.49711
[9] 54.58319 54.88915 65.60619 60.88544 63.30199 57.73515 55.48098 57.76024
[17] 60.16170 54.89986 61.40263 59.58361
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.34709 73.63271 70.69340 69.93145 72.17190 70.32533 71.95914 72.71766
[9] NaN 72.69873
> rowSums(tmp5,na.rm=TRUE)
[1] 1826.942 1472.654 1413.868 1398.629 1443.438 1406.507 1439.183 1454.353
[9] 0.000 1453.975
> rowVars(tmp5,na.rm=TRUE)
[1] 7857.61829 67.41496 67.63754 74.85949 59.92721 73.62497
[7] 40.61514 66.60192 NA 62.82234
> rowSd(tmp5,na.rm=TRUE)
[1] 88.643208 8.210661 8.224205 8.652138 7.741267 8.580499 6.373001
[8] 8.161000 NA 7.926054
> rowMax(tmp5,na.rm=TRUE)
[1] 466.07891 87.44337 87.93732 87.88016 87.82758 88.53986 81.57020
[8] 84.60140 NA 87.01759
> rowMin(tmp5,na.rm=TRUE)
[1] 59.14630 57.76024 56.13793 55.48098 54.89986 54.88915 53.44160 54.58319
[9] NA 54.77476
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 112.21425 72.72816 72.57548 71.11665 73.04457 74.38191 73.32999
[8] 73.98903 71.94077 71.89375 72.65529 73.70181 72.20934 68.88151
[15] 69.62233 68.87962 72.54542 71.64596 NaN 69.85859
> colSums(tmp5,na.rm=TRUE)
[1] 1009.9283 654.5534 653.1794 640.0498 657.4012 669.4372 659.9699
[8] 665.9013 647.4669 647.0438 653.8976 663.3163 649.8840 619.9335
[15] 626.6010 619.9165 652.9088 644.8136 0.0000 628.7273
> colVars(tmp5,na.rm=TRUE)
[1] 17652.21568 108.11306 72.28850 22.94864 32.47873 55.71061
[7] 53.68093 57.19712 125.61886 173.75439 23.61640 126.29340
[13] 63.99229 16.50919 71.39353 42.21881 73.78792 98.13541
[19] NA 53.87964
> colSd(tmp5,na.rm=TRUE)
[1] 132.861641 10.397743 8.502264 4.790474 5.699012 7.463954
[7] 7.326727 7.562878 11.207982 13.181593 4.859671 11.238033
[13] 7.999518 4.063150 8.449469 6.497600 8.589990 9.906332
[19] NA 7.340275
> colMax(tmp5,na.rm=TRUE)
[1] 466.07891 87.01759 87.82758 78.99715 80.62032 87.88016 84.81997
[8] 86.88204 88.53986 92.14277 77.90322 90.01038 87.44337 75.45898
[15] 80.11875 81.57020 83.37825 83.13710 -Inf 78.21839
> colMin(tmp5,na.rm=TRUE)
[1] 54.77476 53.44160 59.14630 65.10154 62.71386 66.47534 62.90499 62.84534
[9] 54.58319 54.88915 65.60619 60.88544 63.30199 62.04520 55.48098 57.76024
[17] 60.16170 54.89986 Inf 59.58361
>
>
>
>
> 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] 251.6566 151.7583 259.2681 237.7480 197.2513 373.4753 125.3404 207.6722
[9] 217.0477 256.5612
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 251.6566 151.7583 259.2681 237.7480 197.2513 373.4753 125.3404 207.6722
[9] 217.0477 256.5612
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 1.421085e-14 0.000000e+00 2.842171e-14 -1.136868e-13 1.705303e-13
[6] 5.684342e-14 8.526513e-14 -1.136868e-13 0.000000e+00 -5.684342e-14
[11] -5.684342e-14 5.684342e-14 1.136868e-13 0.000000e+00 -1.705303e-13
[16] -2.842171e-14 -1.278977e-13 0.000000e+00 1.421085e-14 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
8 3
8 14
10 5
7 16
8 13
3 8
4 3
7 6
4 5
2 11
7 13
1 19
7 17
1 3
5 14
3 19
1 15
8 8
7 18
2 6
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] 2.960312
> Min(tmp)
[1] -2.550811
> mean(tmp)
[1] 0.1383207
> Sum(tmp)
[1] 13.83207
> Var(tmp)
[1] 1.124216
>
> rowMeans(tmp)
[1] 0.1383207
> rowSums(tmp)
[1] 13.83207
> rowVars(tmp)
[1] 1.124216
> rowSd(tmp)
[1] 1.060291
> rowMax(tmp)
[1] 2.960312
> rowMin(tmp)
[1] -2.550811
>
> colMeans(tmp)
[1] -0.68370431 -0.24958552 0.28952207 1.50380555 -0.21429282 -0.76680839
[7] -1.50290800 0.68705161 -0.83886490 -1.02733602 -1.49873823 -1.80914455
[13] 1.18794084 0.83594263 0.93056006 -0.25062916 -1.45524535 0.68105774
[19] -1.09769542 0.70181781 -1.78793100 2.23798240 -0.57317418 0.90007212
[25] 0.68118891 1.04532661 0.58648963 -0.93617278 -1.04363653 0.65948302
[31] -0.46433896 -0.84477550 1.56114476 -0.45576881 0.29915881 -0.48202218
[37] 0.73471062 0.28215728 0.36175172 -0.45606089 -2.55081140 -0.15691426
[43] -1.35266612 0.36613132 1.14686775 -0.39963109 2.01364012 -0.74369076
[49] 0.42578933 -0.19612281 1.44582773 -0.35095211 -1.10339158 -0.55139529
[55] 1.96241757 0.27543796 -0.29906383 1.13436379 0.81875910 0.42418260
[61] 0.97031731 2.37376734 0.40694563 0.28806723 0.29213068 2.96031175
[67] -0.09519560 -0.32349796 -1.16567367 -1.44636321 1.34361797 -0.15530375
[73] 0.86859348 0.46565977 0.46803053 -0.90791714 1.92499423 1.03862941
[79] 1.73225534 -1.19695157 0.58407780 -0.47996831 0.29337460 0.27832733
[85] 1.00815240 0.03156674 -0.33769471 0.95586633 -0.67600930 -1.48949133
[91] -1.72113037 0.55378746 0.08670226 0.23517044 2.33972557 1.23517576
[97] 0.70088801 0.15304714 -0.43192336 0.63290097
> colSums(tmp)
[1] -0.68370431 -0.24958552 0.28952207 1.50380555 -0.21429282 -0.76680839
[7] -1.50290800 0.68705161 -0.83886490 -1.02733602 -1.49873823 -1.80914455
[13] 1.18794084 0.83594263 0.93056006 -0.25062916 -1.45524535 0.68105774
[19] -1.09769542 0.70181781 -1.78793100 2.23798240 -0.57317418 0.90007212
[25] 0.68118891 1.04532661 0.58648963 -0.93617278 -1.04363653 0.65948302
[31] -0.46433896 -0.84477550 1.56114476 -0.45576881 0.29915881 -0.48202218
[37] 0.73471062 0.28215728 0.36175172 -0.45606089 -2.55081140 -0.15691426
[43] -1.35266612 0.36613132 1.14686775 -0.39963109 2.01364012 -0.74369076
[49] 0.42578933 -0.19612281 1.44582773 -0.35095211 -1.10339158 -0.55139529
[55] 1.96241757 0.27543796 -0.29906383 1.13436379 0.81875910 0.42418260
[61] 0.97031731 2.37376734 0.40694563 0.28806723 0.29213068 2.96031175
[67] -0.09519560 -0.32349796 -1.16567367 -1.44636321 1.34361797 -0.15530375
[73] 0.86859348 0.46565977 0.46803053 -0.90791714 1.92499423 1.03862941
[79] 1.73225534 -1.19695157 0.58407780 -0.47996831 0.29337460 0.27832733
[85] 1.00815240 0.03156674 -0.33769471 0.95586633 -0.67600930 -1.48949133
[91] -1.72113037 0.55378746 0.08670226 0.23517044 2.33972557 1.23517576
[97] 0.70088801 0.15304714 -0.43192336 0.63290097
> 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] -0.68370431 -0.24958552 0.28952207 1.50380555 -0.21429282 -0.76680839
[7] -1.50290800 0.68705161 -0.83886490 -1.02733602 -1.49873823 -1.80914455
[13] 1.18794084 0.83594263 0.93056006 -0.25062916 -1.45524535 0.68105774
[19] -1.09769542 0.70181781 -1.78793100 2.23798240 -0.57317418 0.90007212
[25] 0.68118891 1.04532661 0.58648963 -0.93617278 -1.04363653 0.65948302
[31] -0.46433896 -0.84477550 1.56114476 -0.45576881 0.29915881 -0.48202218
[37] 0.73471062 0.28215728 0.36175172 -0.45606089 -2.55081140 -0.15691426
[43] -1.35266612 0.36613132 1.14686775 -0.39963109 2.01364012 -0.74369076
[49] 0.42578933 -0.19612281 1.44582773 -0.35095211 -1.10339158 -0.55139529
[55] 1.96241757 0.27543796 -0.29906383 1.13436379 0.81875910 0.42418260
[61] 0.97031731 2.37376734 0.40694563 0.28806723 0.29213068 2.96031175
[67] -0.09519560 -0.32349796 -1.16567367 -1.44636321 1.34361797 -0.15530375
[73] 0.86859348 0.46565977 0.46803053 -0.90791714 1.92499423 1.03862941
[79] 1.73225534 -1.19695157 0.58407780 -0.47996831 0.29337460 0.27832733
[85] 1.00815240 0.03156674 -0.33769471 0.95586633 -0.67600930 -1.48949133
[91] -1.72113037 0.55378746 0.08670226 0.23517044 2.33972557 1.23517576
[97] 0.70088801 0.15304714 -0.43192336 0.63290097
> colMin(tmp)
[1] -0.68370431 -0.24958552 0.28952207 1.50380555 -0.21429282 -0.76680839
[7] -1.50290800 0.68705161 -0.83886490 -1.02733602 -1.49873823 -1.80914455
[13] 1.18794084 0.83594263 0.93056006 -0.25062916 -1.45524535 0.68105774
[19] -1.09769542 0.70181781 -1.78793100 2.23798240 -0.57317418 0.90007212
[25] 0.68118891 1.04532661 0.58648963 -0.93617278 -1.04363653 0.65948302
[31] -0.46433896 -0.84477550 1.56114476 -0.45576881 0.29915881 -0.48202218
[37] 0.73471062 0.28215728 0.36175172 -0.45606089 -2.55081140 -0.15691426
[43] -1.35266612 0.36613132 1.14686775 -0.39963109 2.01364012 -0.74369076
[49] 0.42578933 -0.19612281 1.44582773 -0.35095211 -1.10339158 -0.55139529
[55] 1.96241757 0.27543796 -0.29906383 1.13436379 0.81875910 0.42418260
[61] 0.97031731 2.37376734 0.40694563 0.28806723 0.29213068 2.96031175
[67] -0.09519560 -0.32349796 -1.16567367 -1.44636321 1.34361797 -0.15530375
[73] 0.86859348 0.46565977 0.46803053 -0.90791714 1.92499423 1.03862941
[79] 1.73225534 -1.19695157 0.58407780 -0.47996831 0.29337460 0.27832733
[85] 1.00815240 0.03156674 -0.33769471 0.95586633 -0.67600930 -1.48949133
[91] -1.72113037 0.55378746 0.08670226 0.23517044 2.33972557 1.23517576
[97] 0.70088801 0.15304714 -0.43192336 0.63290097
> colMedians(tmp)
[1] -0.68370431 -0.24958552 0.28952207 1.50380555 -0.21429282 -0.76680839
[7] -1.50290800 0.68705161 -0.83886490 -1.02733602 -1.49873823 -1.80914455
[13] 1.18794084 0.83594263 0.93056006 -0.25062916 -1.45524535 0.68105774
[19] -1.09769542 0.70181781 -1.78793100 2.23798240 -0.57317418 0.90007212
[25] 0.68118891 1.04532661 0.58648963 -0.93617278 -1.04363653 0.65948302
[31] -0.46433896 -0.84477550 1.56114476 -0.45576881 0.29915881 -0.48202218
[37] 0.73471062 0.28215728 0.36175172 -0.45606089 -2.55081140 -0.15691426
[43] -1.35266612 0.36613132 1.14686775 -0.39963109 2.01364012 -0.74369076
[49] 0.42578933 -0.19612281 1.44582773 -0.35095211 -1.10339158 -0.55139529
[55] 1.96241757 0.27543796 -0.29906383 1.13436379 0.81875910 0.42418260
[61] 0.97031731 2.37376734 0.40694563 0.28806723 0.29213068 2.96031175
[67] -0.09519560 -0.32349796 -1.16567367 -1.44636321 1.34361797 -0.15530375
[73] 0.86859348 0.46565977 0.46803053 -0.90791714 1.92499423 1.03862941
[79] 1.73225534 -1.19695157 0.58407780 -0.47996831 0.29337460 0.27832733
[85] 1.00815240 0.03156674 -0.33769471 0.95586633 -0.67600930 -1.48949133
[91] -1.72113037 0.55378746 0.08670226 0.23517044 2.33972557 1.23517576
[97] 0.70088801 0.15304714 -0.43192336 0.63290097
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.6837043 -0.2495855 0.2895221 1.503806 -0.2142928 -0.7668084 -1.502908
[2,] -0.6837043 -0.2495855 0.2895221 1.503806 -0.2142928 -0.7668084 -1.502908
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.6870516 -0.8388649 -1.027336 -1.498738 -1.809145 1.187941 0.8359426
[2,] 0.6870516 -0.8388649 -1.027336 -1.498738 -1.809145 1.187941 0.8359426
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.9305601 -0.2506292 -1.455245 0.6810577 -1.097695 0.7018178 -1.787931
[2,] 0.9305601 -0.2506292 -1.455245 0.6810577 -1.097695 0.7018178 -1.787931
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 2.237982 -0.5731742 0.9000721 0.6811889 1.045327 0.5864896 -0.9361728
[2,] 2.237982 -0.5731742 0.9000721 0.6811889 1.045327 0.5864896 -0.9361728
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -1.043637 0.659483 -0.464339 -0.8447755 1.561145 -0.4557688 0.2991588
[2,] -1.043637 0.659483 -0.464339 -0.8447755 1.561145 -0.4557688 0.2991588
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.4820222 0.7347106 0.2821573 0.3617517 -0.4560609 -2.550811 -0.1569143
[2,] -0.4820222 0.7347106 0.2821573 0.3617517 -0.4560609 -2.550811 -0.1569143
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -1.352666 0.3661313 1.146868 -0.3996311 2.01364 -0.7436908 0.4257893
[2,] -1.352666 0.3661313 1.146868 -0.3996311 2.01364 -0.7436908 0.4257893
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.1961228 1.445828 -0.3509521 -1.103392 -0.5513953 1.962418 0.275438
[2,] -0.1961228 1.445828 -0.3509521 -1.103392 -0.5513953 1.962418 0.275438
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.2990638 1.134364 0.8187591 0.4241826 0.9703173 2.373767 0.4069456
[2,] -0.2990638 1.134364 0.8187591 0.4241826 0.9703173 2.373767 0.4069456
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.2880672 0.2921307 2.960312 -0.0951956 -0.323498 -1.165674 -1.446363
[2,] 0.2880672 0.2921307 2.960312 -0.0951956 -0.323498 -1.165674 -1.446363
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 1.343618 -0.1553038 0.8685935 0.4656598 0.4680305 -0.9079171 1.924994
[2,] 1.343618 -0.1553038 0.8685935 0.4656598 0.4680305 -0.9079171 1.924994
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 1.038629 1.732255 -1.196952 0.5840778 -0.4799683 0.2933746 0.2783273
[2,] 1.038629 1.732255 -1.196952 0.5840778 -0.4799683 0.2933746 0.2783273
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 1.008152 0.03156674 -0.3376947 0.9558663 -0.6760093 -1.489491 -1.72113
[2,] 1.008152 0.03156674 -0.3376947 0.9558663 -0.6760093 -1.489491 -1.72113
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.5537875 0.08670226 0.2351704 2.339726 1.235176 0.700888 0.1530471
[2,] 0.5537875 0.08670226 0.2351704 2.339726 1.235176 0.700888 0.1530471
[,99] [,100]
[1,] -0.4319234 0.632901
[2,] -0.4319234 0.632901
>
>
> Max(tmp2)
[1] 2.083306
> Min(tmp2)
[1] -2.590189
> mean(tmp2)
[1] -0.06709755
> Sum(tmp2)
[1] -6.709755
> Var(tmp2)
[1] 1.01216
>
> rowMeans(tmp2)
[1] -0.040592910 0.224317768 -0.191830124 -0.641394724 0.295250672
[6] -1.292282844 -0.354345004 0.512535298 2.083305788 0.181591938
[11] -0.815462336 -1.879040628 0.664317054 -1.589382925 0.075481156
[16] -0.108598367 0.268126923 -0.333888399 -0.136317675 -1.677529590
[21] -0.965779629 0.399874194 -0.843027243 0.385697818 -0.792783083
[26] -0.010534463 -0.117583122 0.712026978 -1.720756315 1.145042255
[31] 1.283228176 -0.431629277 -0.642064217 -0.137772964 -1.292197472
[36] -0.686692531 1.579856886 0.271708641 1.479242677 -1.178951641
[41] 1.816018473 -2.358465056 -1.234307077 1.152168017 0.283069975
[46] -0.451199406 -0.755547644 0.288067062 -1.418017414 -1.386327299
[51] -0.170014790 -0.671534644 -0.072455696 1.116133273 0.785427058
[56] 0.020046246 0.680755885 -0.971082073 0.324868615 0.494157004
[61] 0.138426664 0.381438667 -2.258144557 -0.275689354 1.170637587
[66] -1.009908678 0.596703745 -1.514020123 1.445283886 -0.509385984
[71] -1.229806639 0.975267964 -1.221279408 0.043774593 0.831779301
[76] -1.124133438 -0.937587153 0.756831133 0.824837685 -0.834763884
[81] 1.731152045 0.084777931 -0.673462193 1.460943018 0.118015338
[86] 0.161153720 -0.255530736 0.521890212 1.244559526 -0.601964445
[91] -2.590189027 -1.101725216 -0.382466605 0.643430671 0.403255678
[96] 1.295658409 1.235407910 0.006396791 0.916989728 1.668763325
> rowSums(tmp2)
[1] -0.040592910 0.224317768 -0.191830124 -0.641394724 0.295250672
[6] -1.292282844 -0.354345004 0.512535298 2.083305788 0.181591938
[11] -0.815462336 -1.879040628 0.664317054 -1.589382925 0.075481156
[16] -0.108598367 0.268126923 -0.333888399 -0.136317675 -1.677529590
[21] -0.965779629 0.399874194 -0.843027243 0.385697818 -0.792783083
[26] -0.010534463 -0.117583122 0.712026978 -1.720756315 1.145042255
[31] 1.283228176 -0.431629277 -0.642064217 -0.137772964 -1.292197472
[36] -0.686692531 1.579856886 0.271708641 1.479242677 -1.178951641
[41] 1.816018473 -2.358465056 -1.234307077 1.152168017 0.283069975
[46] -0.451199406 -0.755547644 0.288067062 -1.418017414 -1.386327299
[51] -0.170014790 -0.671534644 -0.072455696 1.116133273 0.785427058
[56] 0.020046246 0.680755885 -0.971082073 0.324868615 0.494157004
[61] 0.138426664 0.381438667 -2.258144557 -0.275689354 1.170637587
[66] -1.009908678 0.596703745 -1.514020123 1.445283886 -0.509385984
[71] -1.229806639 0.975267964 -1.221279408 0.043774593 0.831779301
[76] -1.124133438 -0.937587153 0.756831133 0.824837685 -0.834763884
[81] 1.731152045 0.084777931 -0.673462193 1.460943018 0.118015338
[86] 0.161153720 -0.255530736 0.521890212 1.244559526 -0.601964445
[91] -2.590189027 -1.101725216 -0.382466605 0.643430671 0.403255678
[96] 1.295658409 1.235407910 0.006396791 0.916989728 1.668763325
> 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] -0.040592910 0.224317768 -0.191830124 -0.641394724 0.295250672
[6] -1.292282844 -0.354345004 0.512535298 2.083305788 0.181591938
[11] -0.815462336 -1.879040628 0.664317054 -1.589382925 0.075481156
[16] -0.108598367 0.268126923 -0.333888399 -0.136317675 -1.677529590
[21] -0.965779629 0.399874194 -0.843027243 0.385697818 -0.792783083
[26] -0.010534463 -0.117583122 0.712026978 -1.720756315 1.145042255
[31] 1.283228176 -0.431629277 -0.642064217 -0.137772964 -1.292197472
[36] -0.686692531 1.579856886 0.271708641 1.479242677 -1.178951641
[41] 1.816018473 -2.358465056 -1.234307077 1.152168017 0.283069975
[46] -0.451199406 -0.755547644 0.288067062 -1.418017414 -1.386327299
[51] -0.170014790 -0.671534644 -0.072455696 1.116133273 0.785427058
[56] 0.020046246 0.680755885 -0.971082073 0.324868615 0.494157004
[61] 0.138426664 0.381438667 -2.258144557 -0.275689354 1.170637587
[66] -1.009908678 0.596703745 -1.514020123 1.445283886 -0.509385984
[71] -1.229806639 0.975267964 -1.221279408 0.043774593 0.831779301
[76] -1.124133438 -0.937587153 0.756831133 0.824837685 -0.834763884
[81] 1.731152045 0.084777931 -0.673462193 1.460943018 0.118015338
[86] 0.161153720 -0.255530736 0.521890212 1.244559526 -0.601964445
[91] -2.590189027 -1.101725216 -0.382466605 0.643430671 0.403255678
[96] 1.295658409 1.235407910 0.006396791 0.916989728 1.668763325
> rowMin(tmp2)
[1] -0.040592910 0.224317768 -0.191830124 -0.641394724 0.295250672
[6] -1.292282844 -0.354345004 0.512535298 2.083305788 0.181591938
[11] -0.815462336 -1.879040628 0.664317054 -1.589382925 0.075481156
[16] -0.108598367 0.268126923 -0.333888399 -0.136317675 -1.677529590
[21] -0.965779629 0.399874194 -0.843027243 0.385697818 -0.792783083
[26] -0.010534463 -0.117583122 0.712026978 -1.720756315 1.145042255
[31] 1.283228176 -0.431629277 -0.642064217 -0.137772964 -1.292197472
[36] -0.686692531 1.579856886 0.271708641 1.479242677 -1.178951641
[41] 1.816018473 -2.358465056 -1.234307077 1.152168017 0.283069975
[46] -0.451199406 -0.755547644 0.288067062 -1.418017414 -1.386327299
[51] -0.170014790 -0.671534644 -0.072455696 1.116133273 0.785427058
[56] 0.020046246 0.680755885 -0.971082073 0.324868615 0.494157004
[61] 0.138426664 0.381438667 -2.258144557 -0.275689354 1.170637587
[66] -1.009908678 0.596703745 -1.514020123 1.445283886 -0.509385984
[71] -1.229806639 0.975267964 -1.221279408 0.043774593 0.831779301
[76] -1.124133438 -0.937587153 0.756831133 0.824837685 -0.834763884
[81] 1.731152045 0.084777931 -0.673462193 1.460943018 0.118015338
[86] 0.161153720 -0.255530736 0.521890212 1.244559526 -0.601964445
[91] -2.590189027 -1.101725216 -0.382466605 0.643430671 0.403255678
[96] 1.295658409 1.235407910 0.006396791 0.916989728 1.668763325
>
> colMeans(tmp2)
[1] -0.06709755
> colSums(tmp2)
[1] -6.709755
> colVars(tmp2)
[1] 1.01216
> colSd(tmp2)
[1] 1.006061
> colMax(tmp2)
[1] 2.083306
> colMin(tmp2)
[1] -2.590189
> colMedians(tmp2)
[1] -0.002068836
> colRanges(tmp2)
[,1]
[1,] -2.590189
[2,] 2.083306
>
> 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] -6.3549695 2.1075221 -2.8221226 0.5402177 2.9794878 -3.3201786
[7] -0.7963076 2.3233685 -6.1274242 -4.2143215
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.83751863
[2,] -0.59474548
[3,] -0.45967783
[4,] -0.29574709
[5,] -0.04951573
>
> rowApply(tmp,sum)
[1] -1.0500747 -2.0972398 -1.2865455 2.7736148 -1.8618518 0.5849697
[7] -2.9836033 -2.8971431 -2.9902297 -3.8766245
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 1 4 2 5 3 4 5 8 5
[2,] 10 5 9 3 6 2 5 10 4 10
[3,] 9 7 6 9 1 1 9 9 2 1
[4,] 2 9 3 8 7 10 3 7 5 9
[5,] 4 2 10 10 10 6 7 6 10 4
[6,] 3 3 7 5 2 7 8 1 9 3
[7,] 8 6 1 1 8 5 6 8 7 7
[8,] 5 10 5 4 9 9 10 3 3 8
[9,] 7 8 2 6 4 4 1 2 6 2
[10,] 6 4 8 7 3 8 2 4 1 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.86418302 -2.39483382 -1.48829399 0.40008901 -2.76711700 -2.24298028
[7] -4.77130176 2.79300156 0.21829615 -1.48399823 3.00096140 -1.34254488
[13] 2.04670866 0.87497784 -1.58477318 -1.28043021 -2.82333282 2.03289375
[19] 0.08513228 -2.45648276
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.0588652
[2,] -0.2041863
[3,] -0.1233030
[4,] 0.4823344
[5,] 1.7682031
>
> rowApply(tmp,sum)
[1] -0.4008875 -6.0529947 0.2999947 0.4125322 -6.5784899
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 8 19 20 11 8
[2,] 5 13 2 3 16
[3,] 13 4 8 6 14
[4,] 17 8 10 20 4
[5,] 12 2 7 10 11
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.2041863 -0.81390569 0.2729418 0.7642490 0.1360659 -0.3751442
[2,] 0.4823344 -0.07364258 -1.0325254 -0.8503891 -1.1203147 -1.0465045
[3,] 1.7682031 -1.04577116 -0.1744110 0.0485975 -0.5350048 -0.5522337
[4,] -0.1233030 -1.03655261 -0.8085169 1.6336696 -0.3790710 1.0526255
[5,] -1.0588652 0.57503823 0.2542176 -1.1960380 -0.8687924 -1.3217235
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.8556651 1.3521663 -0.8140001 -0.31150150 0.6721598 0.7845440
[2,] -0.6916369 -0.7324989 0.3532096 -0.33819099 0.4160546 0.1906520
[3,] -0.6526802 0.3513380 0.2069207 -0.55399001 1.5521391 -3.4368141
[4,] -1.2885321 1.3127569 1.5919402 0.09414528 -0.5847713 -0.7891377
[5,] -1.2827874 0.5092394 -1.1197743 -0.37446101 0.9453793 1.9082109
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.1265190 0.10566152 -1.1931786 -1.3725079 0.2811453 0.4677704
[2,] -0.9152266 -0.07149094 0.1006155 -0.5196159 -0.8556620 2.7866825
[3,] 0.5761930 0.94276145 -0.1428232 0.5848938 1.1175412 0.9759308
[4,] 1.3798686 1.03891892 0.5436651 -0.8667768 -2.1810916 -0.9757014
[5,] 1.1323926 -1.14087312 -0.8930519 0.8935765 -1.1852657 -1.2217886
[,19] [,20]
[1,] 1.0171838 -0.1881670
[2,] -1.2542070 -0.8806377
[3,] -0.9832054 0.2524095
[4,] 1.5204404 -0.7220440
[5,] -0.2150796 -0.9180436
>
>
> 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 : 652 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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-3.23-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 -0.491384 0.2487541 0.771703 -0.1191654 -0.2520603 -0.4877969 -1.322267
col8 col9 col10 col11 col12 col13 col14
row1 1.046764 0.5926951 0.9609079 -0.4887292 0.9881413 1.664143 -0.4199622
col15 col16 col17 col18 col19 col20
row1 0.8146144 0.3639426 -1.634184 -0.8063812 -1.919052 -1.471008
> tmp[,"col10"]
col10
row1 0.9609079
row2 0.6219918
row3 1.1624975
row4 -1.7290439
row5 -0.5888557
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.491384 0.2487541 0.771703 -0.1191654 -0.2520603 -0.4877969 -1.3222668
row5 -1.049628 0.3550367 1.100680 -1.4284730 -1.0827708 0.5177299 -0.5741672
col8 col9 col10 col11 col12 col13 col14
row1 1.046764 0.5926951 0.9609079 -0.4887292 0.9881413 1.6641429 -0.4199622
row5 1.228790 -0.4148064 -0.5888557 0.6712632 0.6704486 -0.3476054 0.4402577
col15 col16 col17 col18 col19 col20
row1 0.8146144 0.3639426 -1.634184 -0.8063812 -1.9190520 -1.4710082
row5 0.4520755 -0.6754959 -1.151478 0.5219970 0.2745087 -0.6120719
> tmp[,c("col6","col20")]
col6 col20
row1 -0.48779693 -1.4710082
row2 -0.69679403 0.1307797
row3 0.91760283 -0.7113237
row4 -0.09481259 -0.7592146
row5 0.51772989 -0.6120719
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.4877969 -1.4710082
row5 0.5177299 -0.6120719
>
>
>
>
> 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 50.16169 49.46811 48.83827 49.24709 50.50374 106.2381 50.16408 49.67889
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.19326 49.11588 48.69798 49.21879 49.87629 51.1256 50.91463 50.18555
col17 col18 col19 col20
row1 47.07501 49.8569 48.78883 106.1679
> tmp[,"col10"]
col10
row1 49.11588
row2 29.80776
row3 29.45048
row4 29.22406
row5 49.70989
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.16169 49.46811 48.83827 49.24709 50.50374 106.2381 50.16408 49.67889
row5 52.83625 47.33660 51.39828 50.78314 50.54523 105.0126 48.90391 52.49870
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.19326 49.11588 48.69798 49.21879 49.87629 51.12560 50.91463 50.18555
row5 49.32493 49.70989 50.27400 49.64468 49.34256 51.02661 49.27473 50.20798
col17 col18 col19 col20
row1 47.07501 49.8569 48.78883 106.1679
row5 49.16082 52.6739 48.91027 106.3433
> tmp[,c("col6","col20")]
col6 col20
row1 106.23807 106.16789
row2 75.25164 73.65166
row3 72.79441 74.98462
row4 74.65785 75.65219
row5 105.01262 106.34333
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 106.2381 106.1679
row5 105.0126 106.3433
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 106.2381 106.1679
row5 105.0126 106.3433
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.8398215
[2,] -0.1389551
[3,] -0.2709417
[4,] 1.7148703
[5,] 1.0019614
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.3517145 -0.6883192
[2,] 0.1663088 0.5617482
[3,] 1.7621956 0.8008345
[4,] -1.0946122 -1.3364975
[5,] 1.7349638 -0.7217401
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 1.0729028 1.1945488
[2,] 1.5734360 -0.8398886
[3,] -0.3853566 -0.4985761
[4,] 0.9223673 -0.4645365
[5,] -0.2996008 0.4749761
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 1.072903
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 1.072903
[2,] 1.573436
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 1.3007496 1.854830 0.209864 0.9246329 0.37513623 0.73993802 0.6307686
row1 0.3028815 2.001538 -0.614225 0.1476934 -0.08443549 -0.05833709 0.6827859
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.2039753 1.2056981 -2.0687336 1.6511979 -0.008529647 -0.4976214
row1 0.8448393 0.9548297 0.3196559 -0.1224375 -1.513957316 0.6394027
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 0.1771869 -0.2657386 0.230073 -2.075738 -0.1398332 -2.137420 1.4032149
row1 0.3417668 -0.5825140 -1.164548 -1.038030 -0.6589746 -1.003396 0.3528918
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.8252857 0.6246664 1.723123 -0.1486555 -0.5012698 0.6194912 0.2332493
[,8] [,9] [,10]
row2 -1.058397 -0.9702602 -1.624804
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.2567446 2.397114 2.828594 -0.2136263 1.697419 0.5958167 -1.850846
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.173729 0.07593449 -0.9468648 -0.6118351 -0.1528877 -0.3599739 1.748214
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.06737064 0.8391402 0.04667738 -0.05487024 -1.270096 -1.289013
>
>
> 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: 0x652c4102d3a0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a02e32f82c"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a09ad0c2b"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a0268d253"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a043e9c142"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a032229c91"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a03f13fa77"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a01c7892d3"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a046ab9e6"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a06bbd6a43"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a045886218"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a060d44ae2"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a03f0128ae"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a061ecc0b1"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a012c29af6"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3897a0512d470b"
>
>
> ### 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: 0x652c41dc5d70>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x652c41dc5d70>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x652c41dc5d70>
> rowMedians(tmp)
[1] -0.248737314 -0.306042605 -0.150641128 0.279756459 -0.101996290
[6] 0.409633416 -0.268194878 -0.276417557 -0.076798695 0.164985854
[11] -0.402719456 -0.994205632 0.117894379 -0.464797167 0.027257282
[16] 0.527588718 -0.275836773 -0.107236956 -0.408406947 0.822513777
[21] -0.280310974 0.313490057 -0.104558474 0.553793970 0.092652617
[26] 0.005421543 -0.031335277 -0.417221242 -0.172777258 -0.206073836
[31] -0.286331539 0.752004214 0.035804550 0.126028503 -0.343404248
[36] 0.026531081 -0.386255416 0.488213146 0.097455832 -0.185924626
[41] -0.149979268 -0.663903362 -0.148366622 -0.311783936 0.013514557
[46] 0.062894215 -0.237446104 0.021320005 -0.415827690 0.160610620
[51] 0.088930406 0.145050142 -0.461139422 0.053061012 0.592189205
[56] 0.057740786 0.492197314 0.189735785 0.187350494 -0.446198345
[61] -0.135914852 0.315476498 -0.056505083 0.227299905 0.018375596
[66] -0.324311865 0.487020432 -0.134306500 -0.507129695 -0.056355399
[71] 0.384833451 0.190786898 0.413891471 -0.276927763 0.474786661
[76] -0.691936610 0.292498824 0.134669416 0.441130331 0.278237441
[81] -0.676892624 0.292272304 0.144423305 0.086670160 0.424935213
[86] 0.089686354 -0.220373230 -0.139273651 0.208256398 0.298962828
[91] -0.205610705 0.120964544 -0.095285172 0.029953863 0.256272289
[96] 0.100937503 -0.384097537 -0.228534688 0.042587168 -0.149172994
[101] -0.010864736 0.388859869 -0.022072189 -0.678353479 -0.477225916
[106] 0.095966685 0.337436623 0.262427560 0.096487718 0.205487886
[111] -0.467989289 -0.267787401 0.271419535 -0.265028553 -0.069897705
[116] -0.148589831 0.199111960 0.172662336 0.431962571 0.101174397
[121] -0.565846252 -0.157984320 0.139064468 -0.110491015 0.193424428
[126] 0.234125816 0.426886998 -0.477417165 0.017933743 0.275793055
[131] -0.064299536 0.391081579 -0.107638456 0.218733769 0.196682498
[136] -0.275627429 0.428402656 -0.556975406 -0.588866191 -0.120300978
[141] -0.320894467 -0.189675744 -0.069482122 -0.300908950 -0.237718809
[146] 0.521819849 -0.323248459 -0.189133855 -0.106275020 -0.256498054
[151] -0.660403383 0.685891852 -0.034919609 0.140512515 -0.459542257
[156] 0.016654260 -0.293468346 0.037809712 -0.236535223 0.367172848
[161] -0.073482985 -0.226935739 0.310521723 0.362572597 0.423781624
[166] -0.266189514 -0.070057095 -0.180399965 -0.165742088 0.093144638
[171] 0.398793016 -0.238759039 0.196728501 0.695187120 0.015948070
[176] -0.802962891 -0.589040144 -0.595373850 -0.050375392 -0.096678710
[181] -0.168478271 -0.182554029 -0.041348187 0.308478090 0.149981796
[186] -0.036522224 -0.105934451 0.113353167 0.347614760 -0.087060070
[191] -0.066150269 -0.036104710 -0.169176114 0.330063546 0.487156999
[196] 0.397581973 0.527769023 -0.257154661 -0.332810329 0.100246983
[201] -0.204163151 0.269427261 -0.367005848 0.718642568 0.190471620
[206] -0.330517520 -0.078677483 0.335328827 0.664954858 -0.114123363
[211] 0.224448920 0.766839518 -0.517542511 -0.226198556 0.130761003
[216] -0.265829187 -0.120386773 0.224190308 0.080468214 -0.024356890
[221] -0.133114430 -0.521700766 -0.003716234 -0.751059231 0.007290106
[226] -0.423714281 -0.129137368 -0.056340903 0.587136272 -0.360466497
>
> proc.time()
user system elapsed
1.315 1.466 2.770
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: 0x6125b2c9dc10>
> .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: 0x6125b2c9dc10>
> .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: 0x6125b2c9dc10>
> .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: 0x6125b2c9dc10>
> 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: 0x6125b39602d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6125b39602d0>
> .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: 0x6125b39602d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6125b39602d0>
> .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: 0x6125b39602d0>
> 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: 0x6125b4035d70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6125b4035d70>
> .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: 0x6125b4035d70>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6125b4035d70>
> .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: 0x6125b4035d70>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x6125b4035d70>
> .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: 0x6125b4035d70>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x6125b4035d70>
> .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: 0x6125b4035d70>
> 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: 0x6125b3ba9370>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x6125b3ba9370>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6125b3ba9370>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6125b3ba9370>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile38983a2064a74d" "BufferedMatrixFile38983a5de4e4b4"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile38983a2064a74d" "BufferedMatrixFile38983a5de4e4b4"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6125b3af4ff0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6125b3af4ff0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6125b3af4ff0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6125b3af4ff0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6125b3af4ff0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6125b3af4ff0>
> .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: 0x6125b3cd73d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6125b3cd73d0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6125b3cd73d0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x6125b3cd73d0>
> 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: 0x6125b5488fb0>
> .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: 0x6125b5488fb0>
> rm(P)
>
> proc.time()
user system elapsed
0.249 0.049 0.284
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
0.258 0.045 0.290