Ben Bolstad
| Snapshot Date: 2026-01-05 13:40 -0500 (Mon, 05 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 2026-01-06 11:34 -0500 (Tue, 06 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 253/2332 | 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: 2026-01-05 21:36:19 -0500 (Mon, 05 Jan 2026) |
| EndedAt: 2026-01-05 21:36:44 -0500 (Mon, 05 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) (2025-12-22 r89219)
* 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) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 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 0.057 0.290
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 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 478851 25.6 1048487 56 639317 34.2
Vcells 885659 6.8 8388608 64 2082734 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Jan 5 21:36:34 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Jan 5 21:36:34 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: 0x631b6e4752b0>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Jan 5 21:36:35 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Jan 5 21:36:35 2026"
>
> ColMode(tmp2)
<pointer: 0x631b6e4752b0>
>
>
>
> ### 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,] 99.42485278 -0.1405023 -0.2099804 -0.003625289
[2,] 0.01294009 -1.0553945 1.3870331 -0.135250770
[3,] -1.82648372 -0.6341987 -0.3457582 0.488088037
[4,] 0.78773572 -1.0920990 0.0312176 -2.088494226
> 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,] 99.42485278 0.1405023 0.2099804 0.003625289
[2,] 0.01294009 1.0553945 1.3870331 0.135250770
[3,] 1.82648372 0.6341987 0.3457582 0.488088037
[4,] 0.78773572 1.0920990 0.0312176 2.088494226
> 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,] 9.9712012 0.3748364 0.4582362 0.06021038
[2,] 0.1137545 1.0273239 1.1777237 0.36776456
[3,] 1.3514746 0.7963660 0.5880120 0.69863298
[4,] 0.8875448 1.0450354 0.1766850 1.44516235
>
> 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,] 224.13686 28.88887 29.79234 25.60573
[2,] 26.15049 36.32863 38.16427 28.81290
[3,] 40.34123 33.59786 31.22588 32.47442
[4,] 34.66318 36.54245 26.79807 41.54012
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x631b6eb7c500>
> exp(tmp5)
<pointer: 0x631b6eb7c500>
> log(tmp5,2)
<pointer: 0x631b6eb7c500>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 466.5115
> Min(tmp5)
[1] 53.29497
> mean(tmp5)
[1] 72.85802
> Sum(tmp5)
[1] 14571.6
> Var(tmp5)
[1] 845.3805
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 86.73421 70.55359 69.42108 72.29646 71.72442 69.57015 73.53940 70.50963
[9] 72.65773 71.57357
> rowSums(tmp5)
[1] 1734.684 1411.072 1388.422 1445.929 1434.488 1391.403 1470.788 1410.193
[9] 1453.155 1431.471
> rowVars(tmp5)
[1] 8046.86839 63.25989 91.52616 75.42886 73.81251 46.95843
[7] 95.22455 35.75970 55.89994 27.66618
> rowSd(tmp5)
[1] 89.704339 7.953609 9.566931 8.684979 8.591421 6.852622 9.758307
[8] 5.979941 7.476626 5.259865
> rowMax(tmp5)
[1] 466.51152 79.92837 87.75122 86.46031 94.31463 79.90706 85.66349
[8] 79.49754 84.62832 81.17865
> rowMin(tmp5)
[1] 53.29497 54.42881 55.03333 55.77667 60.13616 57.97670 53.60277 59.32015
[9] 58.42323 61.62094
>
> colMeans(tmp5)
[1] 109.35491 68.95872 70.39429 73.52338 73.87168 76.01263 68.91092
[8] 66.25119 69.23011 67.70594 74.97256 69.88472 67.20245 71.72825
[15] 68.25288 71.48707 74.82424 71.75392 72.13980 70.70077
> colSums(tmp5)
[1] 1093.5491 689.5872 703.9429 735.2338 738.7168 760.1263 689.1092
[8] 662.5119 692.3011 677.0594 749.7256 698.8472 672.0245 717.2825
[15] 682.5288 714.8707 748.2424 717.5392 721.3980 707.0077
> colVars(tmp5)
[1] 15831.43630 37.80149 59.33329 121.33051 42.04310 11.65195
[7] 46.99166 60.00770 117.76671 57.49752 105.39663 40.34994
[13] 71.64969 50.66724 80.52496 40.22668 58.56281 5.23104
[19] 57.69682 81.05776
> colSd(tmp5)
[1] 125.823036 6.148291 7.702810 11.015013 6.484065 3.413495
[7] 6.855046 7.746464 10.852037 7.582712 10.266286 6.352160
[13] 8.464614 7.118093 8.973570 6.342451 7.652634 2.287147
[19] 7.595842 9.003209
> colMax(tmp5)
[1] 466.51152 76.48952 79.43393 86.46031 82.32837 82.55369 79.99301
[8] 82.57699 87.75122 79.26516 94.31463 79.90706 79.63290 82.84886
[15] 83.63603 79.95145 84.62832 76.68629 82.76951 82.89955
> colMin(tmp5)
[1] 54.42881 60.12839 55.77667 53.29497 64.16486 71.63969 58.11500 57.37290
[9] 55.00788 57.98628 55.40658 58.34224 53.60277 60.95623 57.23199 61.96344
[17] 61.25360 68.61313 58.42323 55.03333
>
>
> ### 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] 86.73421 70.55359 69.42108 NA 71.72442 69.57015 73.53940 70.50963
[9] 72.65773 71.57357
> rowSums(tmp5)
[1] 1734.684 1411.072 1388.422 NA 1434.488 1391.403 1470.788 1410.193
[9] 1453.155 1431.471
> rowVars(tmp5)
[1] 8046.86839 63.25989 91.52616 79.59634 73.81251 46.95843
[7] 95.22455 35.75970 55.89994 27.66618
> rowSd(tmp5)
[1] 89.704339 7.953609 9.566931 8.921678 8.591421 6.852622 9.758307
[8] 5.979941 7.476626 5.259865
> rowMax(tmp5)
[1] 466.51152 79.92837 87.75122 NA 94.31463 79.90706 85.66349
[8] 79.49754 84.62832 81.17865
> rowMin(tmp5)
[1] 53.29497 54.42881 55.03333 NA 60.13616 57.97670 53.60277 59.32015
[9] 58.42323 61.62094
>
> colMeans(tmp5)
[1] 109.35491 68.95872 70.39429 73.52338 73.87168 76.01263 68.91092
[8] 66.25119 69.23011 67.70594 74.97256 69.88472 67.20245 71.72825
[15] 68.25288 71.48707 74.82424 NA 72.13980 70.70077
> colSums(tmp5)
[1] 1093.5491 689.5872 703.9429 735.2338 738.7168 760.1263 689.1092
[8] 662.5119 692.3011 677.0594 749.7256 698.8472 672.0245 717.2825
[15] 682.5288 714.8707 748.2424 NA 721.3980 707.0077
> colVars(tmp5)
[1] 15831.43630 37.80149 59.33329 121.33051 42.04310 11.65195
[7] 46.99166 60.00770 117.76671 57.49752 105.39663 40.34994
[13] 71.64969 50.66724 80.52496 40.22668 58.56281 NA
[19] 57.69682 81.05776
> colSd(tmp5)
[1] 125.823036 6.148291 7.702810 11.015013 6.484065 3.413495
[7] 6.855046 7.746464 10.852037 7.582712 10.266286 6.352160
[13] 8.464614 7.118093 8.973570 6.342451 7.652634 NA
[19] 7.595842 9.003209
> colMax(tmp5)
[1] 466.51152 76.48952 79.43393 86.46031 82.32837 82.55369 79.99301
[8] 82.57699 87.75122 79.26516 94.31463 79.90706 79.63290 82.84886
[15] 83.63603 79.95145 84.62832 NA 82.76951 82.89955
> colMin(tmp5)
[1] 54.42881 60.12839 55.77667 53.29497 64.16486 71.63969 58.11500 57.37290
[9] 55.00788 57.98628 55.40658 58.34224 53.60277 60.95623 57.23199 61.96344
[17] 61.25360 NA 58.42323 55.03333
>
> Max(tmp5,na.rm=TRUE)
[1] 466.5115
> Min(tmp5,na.rm=TRUE)
[1] 53.29497
> mean(tmp5,na.rm=TRUE)
[1] 72.85769
> Sum(tmp5,na.rm=TRUE)
[1] 14498.68
> Var(tmp5,na.rm=TRUE)
[1] 849.65
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 86.73421 70.55359 69.42108 72.26345 71.72442 69.57015 73.53940 70.50963
[9] 72.65773 71.57357
> rowSums(tmp5,na.rm=TRUE)
[1] 1734.684 1411.072 1388.422 1373.006 1434.488 1391.403 1470.788 1410.193
[9] 1453.155 1431.471
> rowVars(tmp5,na.rm=TRUE)
[1] 8046.86839 63.25989 91.52616 79.59634 73.81251 46.95843
[7] 95.22455 35.75970 55.89994 27.66618
> rowSd(tmp5,na.rm=TRUE)
[1] 89.704339 7.953609 9.566931 8.921678 8.591421 6.852622 9.758307
[8] 5.979941 7.476626 5.259865
> rowMax(tmp5,na.rm=TRUE)
[1] 466.51152 79.92837 87.75122 86.46031 94.31463 79.90706 85.66349
[8] 79.49754 84.62832 81.17865
> rowMin(tmp5,na.rm=TRUE)
[1] 53.29497 54.42881 55.03333 55.77667 60.13616 57.97670 53.60277 59.32015
[9] 58.42323 61.62094
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.35491 68.95872 70.39429 73.52338 73.87168 76.01263 68.91092
[8] 66.25119 69.23011 67.70594 74.97256 69.88472 67.20245 71.72825
[15] 68.25288 71.48707 74.82424 71.62394 72.13980 70.70077
> colSums(tmp5,na.rm=TRUE)
[1] 1093.5491 689.5872 703.9429 735.2338 738.7168 760.1263 689.1092
[8] 662.5119 692.3011 677.0594 749.7256 698.8472 672.0245 717.2825
[15] 682.5288 714.8707 748.2424 644.6155 721.3980 707.0077
> colVars(tmp5,na.rm=TRUE)
[1] 15831.436304 37.801487 59.333288 121.330506 42.043098
[6] 11.651950 46.991655 60.007699 117.766712 57.497524
[11] 105.396625 40.349939 71.649695 50.667242 80.524962
[16] 40.226682 58.562806 5.694847 57.696821 81.057764
> colSd(tmp5,na.rm=TRUE)
[1] 125.823036 6.148291 7.702810 11.015013 6.484065 3.413495
[7] 6.855046 7.746464 10.852037 7.582712 10.266286 6.352160
[13] 8.464614 7.118093 8.973570 6.342451 7.652634 2.386388
[19] 7.595842 9.003209
> colMax(tmp5,na.rm=TRUE)
[1] 466.51152 76.48952 79.43393 86.46031 82.32837 82.55369 79.99301
[8] 82.57699 87.75122 79.26516 94.31463 79.90706 79.63290 82.84886
[15] 83.63603 79.95145 84.62832 76.68629 82.76951 82.89955
> colMin(tmp5,na.rm=TRUE)
[1] 54.42881 60.12839 55.77667 53.29497 64.16486 71.63969 58.11500 57.37290
[9] 55.00788 57.98628 55.40658 58.34224 53.60277 60.95623 57.23199 61.96344
[17] 61.25360 68.61313 58.42323 55.03333
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 86.73421 70.55359 69.42108 NaN 71.72442 69.57015 73.53940 70.50963
[9] 72.65773 71.57357
> rowSums(tmp5,na.rm=TRUE)
[1] 1734.684 1411.072 1388.422 0.000 1434.488 1391.403 1470.788 1410.193
[9] 1453.155 1431.471
> rowVars(tmp5,na.rm=TRUE)
[1] 8046.86839 63.25989 91.52616 NA 73.81251 46.95843
[7] 95.22455 35.75970 55.89994 27.66618
> rowSd(tmp5,na.rm=TRUE)
[1] 89.704339 7.953609 9.566931 NA 8.591421 6.852622 9.758307
[8] 5.979941 7.476626 5.259865
> rowMax(tmp5,na.rm=TRUE)
[1] 466.51152 79.92837 87.75122 NA 94.31463 79.90706 85.66349
[8] 79.49754 84.62832 81.17865
> rowMin(tmp5,na.rm=TRUE)
[1] 53.29497 54.42881 55.03333 NA 60.13616 57.97670 53.60277 59.32015
[9] 58.42323 61.62094
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 113.48913 68.16987 72.01847 72.08595 72.97192 76.06224 69.84767
[8] 67.23766 68.93635 68.30927 75.20355 70.14022 67.17600 71.48044
[15] 66.54364 71.53240 74.07253 NaN 72.16175 69.34535
> colSums(tmp5,na.rm=TRUE)
[1] 1021.4022 613.5289 648.1662 648.7735 656.7473 684.5601 628.6290
[8] 605.1390 620.4272 614.7834 676.8320 631.2620 604.5840 643.3240
[15] 598.8928 643.7916 666.6527 0.0000 649.4557 624.1081
> colVars(tmp5,na.rm=TRUE)
[1] 17618.08282 35.52606 37.07288 113.25180 38.19085 13.08076
[7] 42.99380 56.56089 131.51673 60.58965 117.97093 44.65924
[13] 80.59803 56.30981 57.72372 45.23191 59.52598 NA
[19] 64.90351 70.52189
> colSd(tmp5,na.rm=TRUE)
[1] 132.733126 5.960374 6.088750 10.641983 6.179875 3.616733
[7] 6.556966 7.520697 11.468074 7.783935 10.861442 6.682757
[13] 8.977641 7.503986 7.597613 6.725467 7.715308 NA
[19] 8.056271 8.397731
> colMax(tmp5,na.rm=TRUE)
[1] 466.51152 76.48952 79.43393 84.01778 82.32837 82.55369 79.99301
[8] 82.57699 87.75122 79.26516 94.31463 79.90706 79.63290 82.84886
[15] 77.16080 79.95145 84.62832 -Inf 82.76951 81.10027
> colMin(tmp5,na.rm=TRUE)
[1] 54.42881 60.12839 62.00886 53.29497 64.16486 71.63969 58.11500 59.54226
[9] 55.00788 57.98628 55.40658 58.34224 53.60277 60.95623 57.23199 61.96344
[17] 61.25360 Inf 58.42323 55.03333
>
>
>
>
> 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] 125.76997 203.31321 169.25568 404.48010 181.02685 290.46456 138.78192
[8] 306.11612 201.04124 95.05424
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 125.76997 203.31321 169.25568 404.48010 181.02685 290.46456 138.78192
[8] 306.11612 201.04124 95.05424
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 2.273737e-13 2.842171e-14 -2.842171e-14 2.273737e-13 2.842171e-14
[6] -1.421085e-14 -5.684342e-14 2.557954e-13 1.278977e-13 -2.842171e-14
[11] -2.984279e-13 5.684342e-14 5.115908e-13 -1.421085e-14 5.684342e-14
[16] -2.842171e-14 1.705303e-13 0.000000e+00 -1.421085e-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)
+ }
10 3
3 19
2 4
6 6
9 15
8 18
7 13
8 6
1 11
8 10
1 20
8 2
10 3
3 20
9 18
10 15
3 13
7 3
5 15
3 8
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] 2.700212
> Min(tmp)
[1] -2.419866
> mean(tmp)
[1] 0.143221
> Sum(tmp)
[1] 14.3221
> Var(tmp)
[1] 1.081938
>
> rowMeans(tmp)
[1] 0.143221
> rowSums(tmp)
[1] 14.3221
> rowVars(tmp)
[1] 1.081938
> rowSd(tmp)
[1] 1.040162
> rowMax(tmp)
[1] 2.700212
> rowMin(tmp)
[1] -2.419866
>
> colMeans(tmp)
[1] -0.85556083 -0.55538251 0.31556161 -0.37351147 0.11501822 1.50951741
[7] -0.70928633 1.09035891 1.71916338 -0.01284316 -0.93363161 0.36510399
[13] 0.55693555 0.47998905 -0.71536879 1.01263380 -0.10622140 0.36482408
[19] -1.36018795 -1.00384425 -0.88848523 -0.38350858 1.66850586 -1.12585319
[25] 1.49473218 0.32576627 -0.34563086 -0.69280834 -2.41986585 -0.07571651
[31] -0.32768696 1.42575701 0.48224776 0.21067309 0.30979396 1.71392291
[37] 0.17217039 0.13079414 2.40070320 1.75221037 0.02735658 1.27056685
[43] 1.09762579 0.24079350 0.51134501 -0.89544809 -0.46128639 -1.71631220
[49] 1.31144690 0.92899532 -0.73512147 0.45482553 0.11005897 -0.63451293
[55] 0.79513540 -0.51570204 1.09550972 1.26595773 0.02614560 -0.83328645
[61] 0.26329115 0.60479799 -0.53662296 -1.81604446 -2.09864664 -0.99446974
[67] 0.43798850 -2.26363220 1.45736369 -0.50449232 0.81616322 -0.44356455
[73] 1.36607987 0.53204016 1.09452610 2.70021179 0.87176331 1.54740480
[79] 0.03874004 -0.42270634 1.77362529 1.49065296 -1.60806550 0.28964705
[85] 0.20468142 0.57496488 -0.15551790 -1.44189903 -0.86304716 1.19705218
[91] -1.02454296 -0.67638530 -0.07446313 -1.36877309 0.23703365 1.08892980
[97] 0.08420625 0.16283119 0.24227418 1.46361667
> colSums(tmp)
[1] -0.85556083 -0.55538251 0.31556161 -0.37351147 0.11501822 1.50951741
[7] -0.70928633 1.09035891 1.71916338 -0.01284316 -0.93363161 0.36510399
[13] 0.55693555 0.47998905 -0.71536879 1.01263380 -0.10622140 0.36482408
[19] -1.36018795 -1.00384425 -0.88848523 -0.38350858 1.66850586 -1.12585319
[25] 1.49473218 0.32576627 -0.34563086 -0.69280834 -2.41986585 -0.07571651
[31] -0.32768696 1.42575701 0.48224776 0.21067309 0.30979396 1.71392291
[37] 0.17217039 0.13079414 2.40070320 1.75221037 0.02735658 1.27056685
[43] 1.09762579 0.24079350 0.51134501 -0.89544809 -0.46128639 -1.71631220
[49] 1.31144690 0.92899532 -0.73512147 0.45482553 0.11005897 -0.63451293
[55] 0.79513540 -0.51570204 1.09550972 1.26595773 0.02614560 -0.83328645
[61] 0.26329115 0.60479799 -0.53662296 -1.81604446 -2.09864664 -0.99446974
[67] 0.43798850 -2.26363220 1.45736369 -0.50449232 0.81616322 -0.44356455
[73] 1.36607987 0.53204016 1.09452610 2.70021179 0.87176331 1.54740480
[79] 0.03874004 -0.42270634 1.77362529 1.49065296 -1.60806550 0.28964705
[85] 0.20468142 0.57496488 -0.15551790 -1.44189903 -0.86304716 1.19705218
[91] -1.02454296 -0.67638530 -0.07446313 -1.36877309 0.23703365 1.08892980
[97] 0.08420625 0.16283119 0.24227418 1.46361667
> 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] -0.85556083 -0.55538251 0.31556161 -0.37351147 0.11501822 1.50951741
[7] -0.70928633 1.09035891 1.71916338 -0.01284316 -0.93363161 0.36510399
[13] 0.55693555 0.47998905 -0.71536879 1.01263380 -0.10622140 0.36482408
[19] -1.36018795 -1.00384425 -0.88848523 -0.38350858 1.66850586 -1.12585319
[25] 1.49473218 0.32576627 -0.34563086 -0.69280834 -2.41986585 -0.07571651
[31] -0.32768696 1.42575701 0.48224776 0.21067309 0.30979396 1.71392291
[37] 0.17217039 0.13079414 2.40070320 1.75221037 0.02735658 1.27056685
[43] 1.09762579 0.24079350 0.51134501 -0.89544809 -0.46128639 -1.71631220
[49] 1.31144690 0.92899532 -0.73512147 0.45482553 0.11005897 -0.63451293
[55] 0.79513540 -0.51570204 1.09550972 1.26595773 0.02614560 -0.83328645
[61] 0.26329115 0.60479799 -0.53662296 -1.81604446 -2.09864664 -0.99446974
[67] 0.43798850 -2.26363220 1.45736369 -0.50449232 0.81616322 -0.44356455
[73] 1.36607987 0.53204016 1.09452610 2.70021179 0.87176331 1.54740480
[79] 0.03874004 -0.42270634 1.77362529 1.49065296 -1.60806550 0.28964705
[85] 0.20468142 0.57496488 -0.15551790 -1.44189903 -0.86304716 1.19705218
[91] -1.02454296 -0.67638530 -0.07446313 -1.36877309 0.23703365 1.08892980
[97] 0.08420625 0.16283119 0.24227418 1.46361667
> colMin(tmp)
[1] -0.85556083 -0.55538251 0.31556161 -0.37351147 0.11501822 1.50951741
[7] -0.70928633 1.09035891 1.71916338 -0.01284316 -0.93363161 0.36510399
[13] 0.55693555 0.47998905 -0.71536879 1.01263380 -0.10622140 0.36482408
[19] -1.36018795 -1.00384425 -0.88848523 -0.38350858 1.66850586 -1.12585319
[25] 1.49473218 0.32576627 -0.34563086 -0.69280834 -2.41986585 -0.07571651
[31] -0.32768696 1.42575701 0.48224776 0.21067309 0.30979396 1.71392291
[37] 0.17217039 0.13079414 2.40070320 1.75221037 0.02735658 1.27056685
[43] 1.09762579 0.24079350 0.51134501 -0.89544809 -0.46128639 -1.71631220
[49] 1.31144690 0.92899532 -0.73512147 0.45482553 0.11005897 -0.63451293
[55] 0.79513540 -0.51570204 1.09550972 1.26595773 0.02614560 -0.83328645
[61] 0.26329115 0.60479799 -0.53662296 -1.81604446 -2.09864664 -0.99446974
[67] 0.43798850 -2.26363220 1.45736369 -0.50449232 0.81616322 -0.44356455
[73] 1.36607987 0.53204016 1.09452610 2.70021179 0.87176331 1.54740480
[79] 0.03874004 -0.42270634 1.77362529 1.49065296 -1.60806550 0.28964705
[85] 0.20468142 0.57496488 -0.15551790 -1.44189903 -0.86304716 1.19705218
[91] -1.02454296 -0.67638530 -0.07446313 -1.36877309 0.23703365 1.08892980
[97] 0.08420625 0.16283119 0.24227418 1.46361667
> colMedians(tmp)
[1] -0.85556083 -0.55538251 0.31556161 -0.37351147 0.11501822 1.50951741
[7] -0.70928633 1.09035891 1.71916338 -0.01284316 -0.93363161 0.36510399
[13] 0.55693555 0.47998905 -0.71536879 1.01263380 -0.10622140 0.36482408
[19] -1.36018795 -1.00384425 -0.88848523 -0.38350858 1.66850586 -1.12585319
[25] 1.49473218 0.32576627 -0.34563086 -0.69280834 -2.41986585 -0.07571651
[31] -0.32768696 1.42575701 0.48224776 0.21067309 0.30979396 1.71392291
[37] 0.17217039 0.13079414 2.40070320 1.75221037 0.02735658 1.27056685
[43] 1.09762579 0.24079350 0.51134501 -0.89544809 -0.46128639 -1.71631220
[49] 1.31144690 0.92899532 -0.73512147 0.45482553 0.11005897 -0.63451293
[55] 0.79513540 -0.51570204 1.09550972 1.26595773 0.02614560 -0.83328645
[61] 0.26329115 0.60479799 -0.53662296 -1.81604446 -2.09864664 -0.99446974
[67] 0.43798850 -2.26363220 1.45736369 -0.50449232 0.81616322 -0.44356455
[73] 1.36607987 0.53204016 1.09452610 2.70021179 0.87176331 1.54740480
[79] 0.03874004 -0.42270634 1.77362529 1.49065296 -1.60806550 0.28964705
[85] 0.20468142 0.57496488 -0.15551790 -1.44189903 -0.86304716 1.19705218
[91] -1.02454296 -0.67638530 -0.07446313 -1.36877309 0.23703365 1.08892980
[97] 0.08420625 0.16283119 0.24227418 1.46361667
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.8555608 -0.5553825 0.3155616 -0.3735115 0.1150182 1.509517 -0.7092863
[2,] -0.8555608 -0.5553825 0.3155616 -0.3735115 0.1150182 1.509517 -0.7092863
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1.090359 1.719163 -0.01284316 -0.9336316 0.365104 0.5569355 0.4799891
[2,] 1.090359 1.719163 -0.01284316 -0.9336316 0.365104 0.5569355 0.4799891
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.7153688 1.012634 -0.1062214 0.3648241 -1.360188 -1.003844 -0.8884852
[2,] -0.7153688 1.012634 -0.1062214 0.3648241 -1.360188 -1.003844 -0.8884852
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.3835086 1.668506 -1.125853 1.494732 0.3257663 -0.3456309 -0.6928083
[2,] -0.3835086 1.668506 -1.125853 1.494732 0.3257663 -0.3456309 -0.6928083
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -2.419866 -0.07571651 -0.327687 1.425757 0.4822478 0.2106731 0.309794
[2,] -2.419866 -0.07571651 -0.327687 1.425757 0.4822478 0.2106731 0.309794
[,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43]
[1,] 1.713923 0.1721704 0.1307941 2.400703 1.75221 0.02735658 1.270567 1.097626
[2,] 1.713923 0.1721704 0.1307941 2.400703 1.75221 0.02735658 1.270567 1.097626
[,44] [,45] [,46] [,47] [,48] [,49] [,50]
[1,] 0.2407935 0.511345 -0.8954481 -0.4612864 -1.716312 1.311447 0.9289953
[2,] 0.2407935 0.511345 -0.8954481 -0.4612864 -1.716312 1.311447 0.9289953
[,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] -0.7351215 0.4548255 0.110059 -0.6345129 0.7951354 -0.515702 1.09551
[2,] -0.7351215 0.4548255 0.110059 -0.6345129 0.7951354 -0.515702 1.09551
[,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] 1.265958 0.0261456 -0.8332864 0.2632911 0.604798 -0.536623 -1.816044
[2,] 1.265958 0.0261456 -0.8332864 0.2632911 0.604798 -0.536623 -1.816044
[,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] -2.098647 -0.9944697 0.4379885 -2.263632 1.457364 -0.5044923 0.8161632
[2,] -2.098647 -0.9944697 0.4379885 -2.263632 1.457364 -0.5044923 0.8161632
[,72] [,73] [,74] [,75] [,76] [,77] [,78]
[1,] -0.4435646 1.36608 0.5320402 1.094526 2.700212 0.8717633 1.547405
[2,] -0.4435646 1.36608 0.5320402 1.094526 2.700212 0.8717633 1.547405
[,79] [,80] [,81] [,82] [,83] [,84] [,85]
[1,] 0.03874004 -0.4227063 1.773625 1.490653 -1.608066 0.289647 0.2046814
[2,] 0.03874004 -0.4227063 1.773625 1.490653 -1.608066 0.289647 0.2046814
[,86] [,87] [,88] [,89] [,90] [,91] [,92]
[1,] 0.5749649 -0.1555179 -1.441899 -0.8630472 1.197052 -1.024543 -0.6763853
[2,] 0.5749649 -0.1555179 -1.441899 -0.8630472 1.197052 -1.024543 -0.6763853
[,93] [,94] [,95] [,96] [,97] [,98] [,99]
[1,] -0.07446313 -1.368773 0.2370336 1.08893 0.08420625 0.1628312 0.2422742
[2,] -0.07446313 -1.368773 0.2370336 1.08893 0.08420625 0.1628312 0.2422742
[,100]
[1,] 1.463617
[2,] 1.463617
>
>
> Max(tmp2)
[1] 2.110904
> Min(tmp2)
[1] -2.429587
> mean(tmp2)
[1] -0.05692503
> Sum(tmp2)
[1] -5.692503
> Var(tmp2)
[1] 0.7775179
>
> rowMeans(tmp2)
[1] 0.47787789 1.19771159 -0.09686490 -0.74423531 -1.40270286 -0.34077495
[7] 0.03319939 -0.41588675 1.36424511 0.09874971 -0.81825212 1.08681309
[13] 0.09536982 -0.24872474 1.88850459 -1.07059150 -1.35525122 -0.67951850
[19] -0.58741718 -0.63761871 -1.45289668 0.34497125 0.06351485 0.46547817
[25] -0.33285899 2.11090369 0.68664150 0.88970045 0.23052625 -0.40018797
[31] 0.81925503 -0.98162476 0.09712280 1.38784181 1.19144717 -0.07368061
[37] 0.35439992 -0.06709913 -2.42958663 0.62280975 0.59856200 -0.25320099
[43] -0.94756042 0.13376824 -2.11275679 0.42992664 -0.27534392 -0.48273778
[49] -0.12063515 0.60846553 0.20175076 -0.64728703 0.44007644 -0.16405106
[55] -0.31700601 -0.02731981 -0.16000359 -0.59831818 -1.50649843 -0.69021767
[61] 0.23458333 -0.01669753 0.36451809 -0.48117029 -0.07620102 1.01487296
[67] -1.51841327 0.32307773 -1.18830268 -0.33736037 -1.23528997 -1.16240477
[73] 0.35746367 0.96653405 0.40098487 -0.07305460 0.70958528 0.02188681
[79] -0.94962728 -0.15383640 -0.69913972 1.48562179 -0.35841640 0.01986986
[85] -1.53927479 -0.01820191 0.61885101 -1.32695100 -1.87927212 0.77109524
[91] 0.23597043 0.28838655 -0.19452244 0.52306577 -1.05905415 0.76878114
[97] 0.20761900 2.04043377 1.36187832 0.37868454
> rowSums(tmp2)
[1] 0.47787789 1.19771159 -0.09686490 -0.74423531 -1.40270286 -0.34077495
[7] 0.03319939 -0.41588675 1.36424511 0.09874971 -0.81825212 1.08681309
[13] 0.09536982 -0.24872474 1.88850459 -1.07059150 -1.35525122 -0.67951850
[19] -0.58741718 -0.63761871 -1.45289668 0.34497125 0.06351485 0.46547817
[25] -0.33285899 2.11090369 0.68664150 0.88970045 0.23052625 -0.40018797
[31] 0.81925503 -0.98162476 0.09712280 1.38784181 1.19144717 -0.07368061
[37] 0.35439992 -0.06709913 -2.42958663 0.62280975 0.59856200 -0.25320099
[43] -0.94756042 0.13376824 -2.11275679 0.42992664 -0.27534392 -0.48273778
[49] -0.12063515 0.60846553 0.20175076 -0.64728703 0.44007644 -0.16405106
[55] -0.31700601 -0.02731981 -0.16000359 -0.59831818 -1.50649843 -0.69021767
[61] 0.23458333 -0.01669753 0.36451809 -0.48117029 -0.07620102 1.01487296
[67] -1.51841327 0.32307773 -1.18830268 -0.33736037 -1.23528997 -1.16240477
[73] 0.35746367 0.96653405 0.40098487 -0.07305460 0.70958528 0.02188681
[79] -0.94962728 -0.15383640 -0.69913972 1.48562179 -0.35841640 0.01986986
[85] -1.53927479 -0.01820191 0.61885101 -1.32695100 -1.87927212 0.77109524
[91] 0.23597043 0.28838655 -0.19452244 0.52306577 -1.05905415 0.76878114
[97] 0.20761900 2.04043377 1.36187832 0.37868454
> 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] 0.47787789 1.19771159 -0.09686490 -0.74423531 -1.40270286 -0.34077495
[7] 0.03319939 -0.41588675 1.36424511 0.09874971 -0.81825212 1.08681309
[13] 0.09536982 -0.24872474 1.88850459 -1.07059150 -1.35525122 -0.67951850
[19] -0.58741718 -0.63761871 -1.45289668 0.34497125 0.06351485 0.46547817
[25] -0.33285899 2.11090369 0.68664150 0.88970045 0.23052625 -0.40018797
[31] 0.81925503 -0.98162476 0.09712280 1.38784181 1.19144717 -0.07368061
[37] 0.35439992 -0.06709913 -2.42958663 0.62280975 0.59856200 -0.25320099
[43] -0.94756042 0.13376824 -2.11275679 0.42992664 -0.27534392 -0.48273778
[49] -0.12063515 0.60846553 0.20175076 -0.64728703 0.44007644 -0.16405106
[55] -0.31700601 -0.02731981 -0.16000359 -0.59831818 -1.50649843 -0.69021767
[61] 0.23458333 -0.01669753 0.36451809 -0.48117029 -0.07620102 1.01487296
[67] -1.51841327 0.32307773 -1.18830268 -0.33736037 -1.23528997 -1.16240477
[73] 0.35746367 0.96653405 0.40098487 -0.07305460 0.70958528 0.02188681
[79] -0.94962728 -0.15383640 -0.69913972 1.48562179 -0.35841640 0.01986986
[85] -1.53927479 -0.01820191 0.61885101 -1.32695100 -1.87927212 0.77109524
[91] 0.23597043 0.28838655 -0.19452244 0.52306577 -1.05905415 0.76878114
[97] 0.20761900 2.04043377 1.36187832 0.37868454
> rowMin(tmp2)
[1] 0.47787789 1.19771159 -0.09686490 -0.74423531 -1.40270286 -0.34077495
[7] 0.03319939 -0.41588675 1.36424511 0.09874971 -0.81825212 1.08681309
[13] 0.09536982 -0.24872474 1.88850459 -1.07059150 -1.35525122 -0.67951850
[19] -0.58741718 -0.63761871 -1.45289668 0.34497125 0.06351485 0.46547817
[25] -0.33285899 2.11090369 0.68664150 0.88970045 0.23052625 -0.40018797
[31] 0.81925503 -0.98162476 0.09712280 1.38784181 1.19144717 -0.07368061
[37] 0.35439992 -0.06709913 -2.42958663 0.62280975 0.59856200 -0.25320099
[43] -0.94756042 0.13376824 -2.11275679 0.42992664 -0.27534392 -0.48273778
[49] -0.12063515 0.60846553 0.20175076 -0.64728703 0.44007644 -0.16405106
[55] -0.31700601 -0.02731981 -0.16000359 -0.59831818 -1.50649843 -0.69021767
[61] 0.23458333 -0.01669753 0.36451809 -0.48117029 -0.07620102 1.01487296
[67] -1.51841327 0.32307773 -1.18830268 -0.33736037 -1.23528997 -1.16240477
[73] 0.35746367 0.96653405 0.40098487 -0.07305460 0.70958528 0.02188681
[79] -0.94962728 -0.15383640 -0.69913972 1.48562179 -0.35841640 0.01986986
[85] -1.53927479 -0.01820191 0.61885101 -1.32695100 -1.87927212 0.77109524
[91] 0.23597043 0.28838655 -0.19452244 0.52306577 -1.05905415 0.76878114
[97] 0.20761900 2.04043377 1.36187832 0.37868454
>
> colMeans(tmp2)
[1] -0.05692503
> colSums(tmp2)
[1] -5.692503
> colVars(tmp2)
[1] 0.7775179
> colSd(tmp2)
[1] 0.8817698
> colMax(tmp2)
[1] 2.110904
> colMin(tmp2)
[1] -2.429587
> colMedians(tmp2)
[1] -0.02276086
> colRanges(tmp2)
[,1]
[1,] -2.429587
[2,] 2.110904
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.2164982 -4.5249469 -3.5319182 4.2377240 -1.3717349 4.7401688
[7] 6.3225137 1.0911217 1.9666315 5.9318299
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.72564326
[2,] -0.41664208
[3,] 0.05017492
[4,] 0.47023324
[5,] 0.61660498
>
> rowApply(tmp,sum)
[1] -1.8801918 -1.1540391 -0.5917600 2.9096708 -0.2796122 0.3417871
[7] 2.3364104 4.3503659 3.5775413 5.4677152
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 4 3 4 3 7 7 5 6 6 5
[2,] 6 1 5 2 2 3 4 5 7 2
[3,] 5 2 3 5 6 6 10 2 1 6
[4,] 7 9 8 4 1 8 8 7 8 1
[5,] 1 6 6 7 3 5 1 8 5 9
[6,] 9 5 7 8 8 9 3 1 10 4
[7,] 10 4 9 6 9 1 7 10 4 7
[8,] 3 10 1 1 4 4 9 4 9 3
[9,] 8 7 2 9 5 10 2 3 2 8
[10,] 2 8 10 10 10 2 6 9 3 10
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 5.21521937 -1.76097070 5.50805903 2.83003972 5.94367221 1.50322543
[7] -3.16539547 -1.47768463 -4.42012123 -0.14547134 -4.18505855 0.14676228
[13] 0.33309496 0.04433698 1.12330595 2.76827997 0.76031363 3.65871760
[19] 1.34234133 1.18990795
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.1881699
[2,] 0.1320955
[3,] 1.0687305
[4,] 1.5253360
[5,] 2.6772272
>
> rowApply(tmp,sum)
[1] 3.396034 6.889411 7.300141 -4.299735 3.926724
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 7 18 15 20 10
[2,] 8 12 2 7 7
[3,] 13 20 12 16 20
[4,] 18 19 13 14 4
[5,] 19 5 17 19 19
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.1881699 -0.1424370 0.2326865 1.2817618 1.5613890 2.53903128
[2,] 1.5253360 0.6570494 1.8115655 1.5992623 -0.6050691 -1.18484053
[3,] 1.0687305 -1.0205016 0.5299896 0.6153759 1.5400022 -0.24693105
[4,] 2.6772272 -0.9981666 0.8358420 0.1097681 1.8904792 -0.09213055
[5,] 0.1320955 -0.2569149 2.0979753 -0.7761283 1.5568709 0.48809628
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.3182121 0.04382091 -0.76110688 0.2209047 -0.9761827 0.1099178
[2,] -0.7020436 0.50985886 -0.40050213 -1.1918297 -0.3493285 1.0219695
[3,] 0.2564870 -1.13183809 -0.78242690 1.9767192 -0.9197738 0.4563642
[4,] -0.1687831 -1.14432824 -2.56216014 -0.4090196 -1.0687436 -2.0395615
[5,] -2.2328436 0.24480194 0.08607482 -0.7422458 -0.8710300 0.5980723
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 1.1728197 -1.02436489 -0.03825263 -0.2677595 0.7620057 0.66452641
[2,] -0.6512967 0.88884483 1.42389344 1.0684075 -0.5132574 0.48157261
[3,] -0.8171388 0.38683313 1.80286121 1.0594608 1.1085097 -0.01372924
[4,] 1.7522116 0.07133448 -1.94312286 0.4313154 -1.9868588 1.20306195
[5,] -1.1235008 -0.27831056 -0.12207321 0.4768558 1.3899144 1.32328588
[,19] [,20]
[1,] -1.7540174 0.2776729
[2,] 0.4154859 1.0843335
[3,] 1.5746565 -0.1435097
[4,] -0.2034359 -0.6546644
[5,] 1.3096522 0.6260757
>
>
> 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 : 654 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 -1.081643 -3.371951 -1.424617 -0.7319935 -0.8023512 -1.657783 0.4066202
col8 col9 col10 col11 col12 col13 col14
row1 -1.730136 1.541008 -0.291941 -2.031996 -1.569549 0.7105461 -1.127821
col15 col16 col17 col18 col19 col20
row1 -0.8100486 -0.6939074 -0.1751673 0.3600653 0.1604633 -0.005905167
> tmp[,"col10"]
col10
row1 -0.29194099
row2 0.03384845
row3 1.04184937
row4 -1.23777920
row5 0.30775552
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -1.0816431 -3.3719514 -1.424617 -0.7319935 -0.8023512 -1.6577830
row5 0.7136422 0.6072285 1.812962 -0.4340849 0.2204864 -0.7253097
col7 col8 col9 col10 col11 col12
row1 0.4066202 -1.7301358 1.5410078 -0.2919410 -2.0319960 -1.5695486
row5 -0.5073899 -0.3193704 -0.1641842 0.3077555 -0.5739378 -0.3103419
col13 col14 col15 col16 col17 col18
row1 0.7105461 -1.1278215 -0.8100486 -0.6939074 -0.1751673 0.3600653
row5 -0.4830081 0.1275819 1.8969061 -0.9162223 -0.6629977 -0.3658834
col19 col20
row1 0.1604633 -0.005905167
row5 -1.1793413 -0.096435848
> tmp[,c("col6","col20")]
col6 col20
row1 -1.6577830074 -0.005905167
row2 0.5288028888 1.518494064
row3 -0.0763199793 -0.592326589
row4 0.0008385636 1.101722118
row5 -0.7253096606 -0.096435848
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.6577830 -0.005905167
row5 -0.7253097 -0.096435848
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.03353 49.37513 47.847 50.5488 49.74248 104.0878 49.4387 49.91143
col9 col10 col11 col12 col13 col14 col15 col16
row1 47.72785 50.25267 48.19657 49.32862 51.90244 49.02985 50.39974 50.46421
col17 col18 col19 col20
row1 49.85924 48.65041 49.64717 104.7869
> tmp[,"col10"]
col10
row1 50.25267
row2 31.18578
row3 30.96903
row4 30.52643
row5 50.13717
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.03353 49.37513 47.84700 50.54880 49.74248 104.0878 49.43870 49.91143
row5 50.46263 50.09935 49.26583 50.70383 50.32786 106.3051 50.32262 50.29794
col9 col10 col11 col12 col13 col14 col15 col16
row1 47.72785 50.25267 48.19657 49.32862 51.90244 49.02985 50.39974 50.46421
row5 50.48163 50.13717 50.80587 51.62410 51.20759 51.72149 50.37789 47.53124
col17 col18 col19 col20
row1 49.85924 48.65041 49.64717 104.7869
row5 49.28853 49.61602 49.26163 103.0051
> tmp[,c("col6","col20")]
col6 col20
row1 104.08784 104.78687
row2 75.14315 74.61602
row3 74.94135 76.01758
row4 74.18077 77.03899
row5 106.30507 103.00513
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.0878 104.7869
row5 106.3051 103.0051
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.0878 104.7869
row5 106.3051 103.0051
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.92824947
[2,] 0.37022439
[3,] -0.40333010
[4,] -0.02470226
[5,] 0.74877741
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.6933786 0.1089321
[2,] -0.2963341 -0.9429138
[3,] 1.4193730 0.2238436
[4,] -1.0713666 0.5872540
[5,] 0.5512176 -1.5502332
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.3567662 1.7177391
[2,] -0.1678385 0.6196940
[3,] 0.6208752 -0.6571554
[4,] -2.0565386 -0.9022938
[5,] -0.1915889 -0.2771544
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.3567662
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.3567662
[2,] -0.1678385
>
>
>
> 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 1.99528744 -1.350161 0.7290678 -0.01811664 -1.034553 -0.8236920 1.498659
row1 0.06542641 -0.816270 1.3508293 1.04219707 1.284945 -0.9835039 1.018942
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.5396676 0.7219186 0.2932345 0.6274699 -2.1086001 -1.2815300
row1 -1.6157885 -1.1946532 -1.7928825 0.2992685 0.2534027 -0.6652745
[,14] [,15] [,16] [,17] [,18] [,19]
row3 -0.8622574 0.07003131 -0.8140957 -0.4801200 0.9637271 -0.37141851
row1 -1.2084120 -0.58432239 -1.4068181 0.5085009 0.8792414 -0.01419661
[,20]
row3 0.21699878
row1 -0.01124617
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.476735 -0.1550821 -0.5827744 -0.1544353 0.6828301 -0.9532816 -0.7876988
[,8] [,9] [,10]
row2 1.061061 -0.8906903 0.5824382
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.88182 0.07135382 -1.316982 -0.1421417 1.62771 1.231425 -1.729071
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -1.201718 0.5964317 0.2029275 -0.9529545 -0.2517866 -1.393942 -1.763071
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.4151443 -0.829887 -1.248219 0.3737392 0.6094729 -2.220885
>
>
> 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: 0x631b6feace40>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d843dbcd5"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d84f734b19"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d8f852298"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d85ce0d0df"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d86279d48"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d86bea89ae"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d853355a40"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d8c34af09"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d86e865e30"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d83faae92c"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d87504875a"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d83b12a945"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d82d983912"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d850275c61"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM2858d87cc10a26"
>
>
> ### 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: 0x631b6f85dd30>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x631b6f85dd30>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x631b6f85dd30>
> rowMedians(tmp)
[1] 0.338187727 0.233875273 -0.372368701 0.000370937 0.158355296
[6] 0.581330299 0.089086603 0.097974409 -0.285532386 0.387534589
[11] 0.210849660 0.244826484 0.003311016 0.090857634 0.078401698
[16] -0.048728803 -0.210856969 -0.525540952 0.304873362 -0.056230203
[21] 0.030053158 0.179223412 -0.305745229 -0.067466998 -0.473647328
[26] -0.001153693 0.173125280 -0.074992504 0.253865296 -0.429403793
[31] 0.357394109 -0.706570369 -0.603002766 0.363850217 0.089589988
[36] -0.158030879 -0.091631377 -0.119088970 -0.110695129 0.623528456
[41] -0.325249883 0.118802752 0.187311893 0.490110009 -0.223270241
[46] 0.053372924 0.026183380 -0.193707451 0.056170942 0.033932562
[51] -0.065695759 -0.056292000 0.355416908 -0.045520223 0.013069902
[56] 0.143650658 -0.199218037 -0.444125024 -0.474673126 -0.152974184
[61] 0.088151519 0.231991755 -0.192173496 0.302598535 -0.009861880
[66] 0.011242884 0.308434434 -0.599545702 -0.283375891 0.329975725
[71] -0.470704543 -0.236754816 -0.401376621 -0.366146011 -0.238870661
[76] -0.411819019 -0.122981728 -0.090865215 -0.297639980 -0.065647688
[81] 0.720525263 -0.583481036 0.279162664 -0.221155787 -0.102637556
[86] -0.073612207 -0.039470295 -0.293957204 0.286216469 0.598129821
[91] 0.063570833 -0.235859665 0.075631312 0.144248662 0.644494985
[96] -0.373973475 -0.443301415 0.928792728 -0.611002587 -0.181474176
[101] -0.414263939 -0.143745265 -0.400212050 0.114535607 0.738349285
[106] 0.236512758 0.195532077 0.409119427 0.022198973 0.213444832
[111] -0.368428176 0.196163979 0.106724514 0.724087271 -0.399326776
[116] -0.147082608 -0.158397981 -0.352720560 0.042627399 -0.340264353
[121] -0.027136185 0.338482023 0.063545503 0.023362210 -0.336507060
[126] 0.298763445 0.227896682 0.291220208 0.050511845 -0.037054753
[131] 0.086345199 -0.564822736 -0.038279140 0.056753005 -0.462716032
[136] -0.275194519 -0.117038835 0.170641060 0.116863271 0.037037788
[141] -0.015037780 0.584954225 0.070949152 -0.020628152 -0.272385143
[146] -0.605583718 0.372068699 -0.137119292 0.767089944 -0.176311692
[151] 0.303876705 0.189818696 0.575915911 -0.371579958 -0.460975335
[156] -0.223373693 -0.022015658 -0.119765872 0.384324243 0.217157612
[161] 0.115457407 -0.116487192 -0.138256231 -0.358342294 0.403370092
[166] -0.155436352 -0.537293846 0.040031846 0.090290867 -0.081105247
[171] 0.546733667 0.138935538 0.502321611 -0.185281706 0.556381274
[176] 0.048486338 -0.203373844 -0.047633597 -0.247686466 0.384268061
[181] 0.534870416 0.044754986 0.364270646 -0.407507210 -0.091965310
[186] 0.001928658 -0.367830527 0.063725419 0.324617829 0.500582304
[191] -0.158049606 -0.270048790 0.586871072 -0.315212364 -0.276115967
[196] 0.100772707 0.498307372 -0.268305109 -0.797642005 0.077167480
[201] -0.040997315 -0.051060501 -0.031071000 -0.411966426 0.349951305
[206] 0.042294059 -0.401981243 0.163054965 -0.573107328 -0.244053663
[211] -0.128697397 0.032629572 0.230095530 -0.546793627 0.097537351
[216] 0.202027209 -0.220355246 0.471432315 0.294241354 -0.214188418
[221] -0.203563342 0.195176059 -0.010253152 -0.151563352 0.358333161
[226] 0.314631876 -0.285417439 -0.008235007 -0.002269653 -0.430879922
>
> proc.time()
user system elapsed
1.297 1.484 2.770
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 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: 0x5bc2d3ed55f0>
> .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: 0x5bc2d3ed55f0>
> .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: 0x5bc2d3ed55f0>
> .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: 0x5bc2d3ed55f0>
> 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: 0x5bc2d47532b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bc2d47532b0>
> .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: 0x5bc2d47532b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bc2d47532b0>
> .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: 0x5bc2d47532b0>
> 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: 0x5bc2d3e36a20>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bc2d3e36a20>
> .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: 0x5bc2d3e36a20>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5bc2d3e36a20>
> .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: 0x5bc2d3e36a20>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5bc2d3e36a20>
> .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: 0x5bc2d3e36a20>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5bc2d3e36a20>
> .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: 0x5bc2d3e36a20>
> 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: 0x5bc2d4613e00>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5bc2d4613e00>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bc2d4613e00>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bc2d4613e00>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile28596e1fd955a4" "BufferedMatrixFile28596e52b921cd"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile28596e1fd955a4" "BufferedMatrixFile28596e52b921cd"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bc2d451b4c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bc2d451b4c0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5bc2d451b4c0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5bc2d451b4c0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5bc2d451b4c0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5bc2d451b4c0>
> .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: 0x5bc2d48c47e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bc2d48c47e0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5bc2d48c47e0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5bc2d48c47e0>
> 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: 0x5bc2d599d520>
> .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: 0x5bc2d599d520>
> rm(P)
>
> proc.time()
user system elapsed
0.260 0.047 0.296
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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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
0.247 0.040 0.275